Starting phenix.real_space_refine
on Tue Apr 29 14:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yh5_39281/04_2025/8yh5_39281.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   1.084
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      66      5.16       5
     C    5564      2.51       5
     N    1462      2.21       5
     O    1603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8695
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1700
          Classifications: {'peptide': 211}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 208}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 2198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2198
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'ZIR%rna3p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 5.17, per 1000 atoms: 0.59
  Number of scatterers: 8695
  At special positions: 0
  Unit cell: (89.91, 122.1, 124.32, 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      66     16.00
     O    1603      8.00
     N    1462      7.00
     C    5564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 103 " - pdb=" SG  CYS B 114 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  83 " - pdb=" SG  CYS R 165 " 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: 2.21
  Conformation dependent library (CDL) restraints added in 967.5 milliseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      37.8% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.863A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 33 through 44
      removed outlier: 3.506A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.706A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.576A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.501A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.541A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 275 through 281
      removed outlier: 3.665A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.682A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.544A  pdb=" N   GLY A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 10 through 40
      removed outlier: 3.659A  pdb=" N   LYS R  38 " --> pdb=" O   ILE R  34 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 45 through 64
      removed outlier: 3.637A  pdb=" N   PHE R  50 " --> pdb=" O   THR R  46 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA R  60 " --> pdb=" O   LEU R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 75
    Processing helix  chain 'R' and resid 79 through 115
      removed outlier: 3.613A  pdb=" N   PHE R  93 " --> pdb=" O   LEU R  89 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR R  94 " --> pdb=" O   MET R  90 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR R 115 " --> pdb=" O   ARG R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 122
    Processing helix  chain 'R' and resid 123 through 144
    Processing helix  chain 'R' and resid 145 through 148
      removed outlier: 3.786A  pdb=" N   GLY R 148 " --> pdb=" O   PRO R 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 145 through 148'
    Processing helix  chain 'R' and resid 150 through 154
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.684A  pdb=" N   MET R 171 " --> pdb=" O   PHE R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 4.020A  pdb=" N   MET R 176 " --> pdb=" O   ARG R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 185
    Processing helix  chain 'R' and resid 185 through 207
    Processing helix  chain 'R' and resid 225 through 254
      removed outlier: 3.591A  pdb=" N   CYS R 241 " --> pdb=" O   LEU R 237 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP R 242 " --> pdb=" O   PHE R 238 " (cutoff:3.500A)
      Proline residue:  R 244  - end of helix
      removed outlier: 3.561A  pdb=" N   TYR R 253 " --> pdb=" O   ASN R 249 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE R 254 " --> pdb=" O   CYS R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 282
      removed outlier: 3.517A  pdb=" N   ILE R 267 " --> pdb=" O   LEU R 263 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER R 274 " --> pdb=" O   SER R 270 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   MET R 275 " --> pdb=" O   HIS R 271 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 285 through 295
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.728A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.840A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.974A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.512A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.568A  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=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.541A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.303A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.458A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.780A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.123A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 129 through 130
      removed outlier: 3.591A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.049A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   TYR S 216 " --> pdb=" O   PHE S 165 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE S 165 " --> pdb=" O   TYR S 216 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.500A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1107 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: 2.40

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2733
        1.34 -     1.46: 1661
        1.46 -     1.58: 4386
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 8878
  Sorted by residual:
  bond pdb=" N   ILE R 248 "
       pdb=" CA  ILE R 248 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.16e+00
  bond pdb=" N   ARG S  18 "
       pdb=" CA  ARG S  18 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.16e-02 7.43e+03 8.96e+00
  bond pdb=" N   LYS S  19 "
       pdb=" CA  LYS S  19 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.25e-02 6.40e+03 8.42e+00
  bond pdb=" N   GLN B 259 "
       pdb=" CA  GLN B 259 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.23e-02 6.61e+03 8.39e+00
  bond pdb=" N   ARG S  98 "
       pdb=" CA  ARG S  98 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.15e-02 7.56e+03 7.68e+00
  ... (remaining 8873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 11314
        1.37 -     2.73: 551
        2.73 -     4.10: 130
        4.10 -     5.47: 23
        5.47 -     6.84: 5
  Bond angle restraints: 12023
  Sorted by residual:
  angle pdb=" N   ASN R 249 "
        pdb=" CA  ASN R 249 "
        pdb=" C   ASN R 249 "
      ideal   model   delta    sigma   weight residual
     113.28  107.60    5.68 1.22e+00 6.72e-01 2.17e+01
  angle pdb=" CA  ILE S 100 "
        pdb=" C   ILE S 100 "
        pdb=" O   ILE S 100 "
      ideal   model   delta    sigma   weight residual
     120.36  115.52    4.84 1.06e+00 8.90e-01 2.08e+01
  angle pdb=" N   ILE R 185 "
        pdb=" CA  ILE R 185 "
        pdb=" C   ILE R 185 "
      ideal   model   delta    sigma   weight residual
     112.12  108.39    3.73 8.40e-01 1.42e+00 1.97e+01
  angle pdb=" N   GLU G  22 "
        pdb=" CA  GLU G  22 "
        pdb=" C   GLU G  22 "
      ideal   model   delta    sigma   weight residual
     112.54  107.53    5.01 1.22e+00 6.72e-01 1.69e+01
  angle pdb=" CA  ARG S  18 "
        pdb=" C   ARG S  18 "
        pdb=" O   ARG S  18 "
      ideal   model   delta    sigma   weight residual
     121.89  116.71    5.18 1.27e+00 6.20e-01 1.67e+01
  ... (remaining 12018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.20: 5044
       25.20 -    50.40: 213
       50.40 -    75.60: 17
       75.60 -   100.80: 1
      100.80 -   126.00: 1
  Dihedral angle restraints: 5276
    sinusoidal: 2074
      harmonic: 3202
  Sorted by residual:
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.18  -43.18     1      1.00e+01 1.00e-02 2.60e+01
  dihedral pdb=" CD  ARG S  18 "
           pdb=" NE  ARG S  18 "
           pdb=" CZ  ARG S  18 "
           pdb=" NH1 ARG S  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -41.92   41.92     1      1.00e+01 1.00e-02 2.46e+01
  dihedral pdb=" CA  PHE B 292 "
           pdb=" C   PHE B 292 "
           pdb=" N   ASN B 293 "
           pdb=" CA  ASN B 293 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 5273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1004
       0.040 -    0.080: 258
       0.080 -    0.121: 82
       0.121 -    0.161: 24
       0.161 -    0.201: 8
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" C3' ZIR R 801 "
            pdb=" C2' ZIR R 801 "
            pdb=" C4' ZIR R 801 "
            pdb=" O3' ZIR R 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  ILE R 248 "
            pdb=" N   ILE R 248 "
            pdb=" C   ILE R 248 "
            pdb=" CB  ILE R 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.57e-01
  chirality pdb=" CA  ILE S 100 "
            pdb=" N   ILE S 100 "
            pdb=" C   ILE S 100 "
            pdb=" CB  ILE S 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.13e-01
  ... (remaining 1373 not shown)

  Planarity restraints: 1499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG S  18 "    0.713 9.50e-02 1.11e+02   3.20e-01 6.24e+01
        pdb=" NE  ARG S  18 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  ARG S  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG S  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG S  18 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "   -0.671 9.50e-02 1.11e+02   3.01e-01 5.51e+01
        pdb=" NE  ARG B 219 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  52 "   -0.586 9.50e-02 1.11e+02   2.63e-01 4.23e+01
        pdb=" NE  ARG B  52 "    0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  52 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  52 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  52 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1496 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 191
        2.66 -     3.22: 8904
        3.22 -     3.78: 13512
        3.78 -     4.34: 18835
        4.34 -     4.90: 30019
  Nonbonded interactions: 71461
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OG  SER B 160 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OE1 GLN R 260 "
            pdb=" OH  TYR R 264 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.150 3.040
  ... (remaining 71456 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     22.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6122
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      :  0.004   0.051   8882  Z= 0.263
  Angle     :  0.719   6.835  12031  Z= 0.454
  Chirality :  0.045   0.201   1376
  Planarity :  0.017   0.320   1499
  Dihedral  : 13.334 125.995   3198
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.42 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.26), residues: 1085
  helix:  0.28 (0.27), residues: 375
  sheet: -1.68 (0.30), residues: 290
  loop : -1.51 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.021   0.001   PHE A 267 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.008   0.001   ARG R 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23728 (  392)
  hydrogen bonds       : angle       8.63096 ( 1107)
  SS BOND              : bond        0.00548 (    4)
  SS BOND              : angle       2.79689 (    8)
  covalent geometry    : bond        0.00425 ( 8878)
  covalent geometry    : angle       0.71549 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.8491 (mp0) cc_final: 0.8262 (mp0)
REVERT: B  260 GLU cc_start: 0.5471 (tt0) cc_final: 0.4674 (tm-30)
REVERT: G   58 GLU cc_start: 0.8754 (mp0) cc_final: 0.8537 (mp0)
REVERT: S   46 GLU cc_start: 0.6451 (tp30) cc_final: 0.6006 (tt0)
REVERT: S   93 MET cc_start: 0.6921 (tpt) cc_final: 0.6669 (tpt)
REVERT: S  190 ARG cc_start: 0.4456 (mtp-110) cc_final: 0.4223 (mtp180)
REVERT: S  219 GLN cc_start: 0.3092 (pp30) cc_final: 0.2329 (pp30)
REVERT: A  276 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7803 (mp0)
REVERT: A  322 HIS cc_start: 0.6592 (t70) cc_final: 0.6254 (t-90)
REVERT: A  333 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8132 (mm-40)
REVERT: A  345 LYS cc_start: 0.7926 (mptt) cc_final: 0.7539 (tptp)
REVERT: R  173 MET cc_start: 0.8499 (mmt) cc_final: 0.8139 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2441
  time to fit residues: 75.1874
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 110 ASN
B 230 ASN
S  82 GLN
S 219 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
A 306 GLN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  30 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.161349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.132782 restraints weight = 19719.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.136307 restraints weight = 11079.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.138955 restraints weight = 7740.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6464
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8882  Z= 0.192
  Angle     :  0.733  10.190  12031  Z= 0.382
  Chirality :  0.047   0.198   1376
  Planarity :  0.004   0.036   1499
  Dihedral  :  6.398 118.415   1216
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.79 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.17 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.26), residues: 1085
  helix:  0.42 (0.26), residues: 386
  sheet: -1.32 (0.31), residues: 279
  loop : -1.48 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R  35 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.022   0.002   PHE R 288 
 TYR   0.024   0.002   TYR S 178 
 ARG   0.005   0.001   ARG R 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  392)
  hydrogen bonds       : angle       5.69310 ( 1107)
  SS BOND              : bond        0.00514 (    4)
  SS BOND              : angle       2.52664 (    8)
  covalent geometry    : bond        0.00443 ( 8878)
  covalent geometry    : angle       0.73000 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.8492 (mp0) cc_final: 0.8185 (mp0)
REVERT: B  300 LEU cc_start: 0.9169 (mp) cc_final: 0.8922 (mp)
REVERT: G   58 GLU cc_start: 0.8897 (mp0) cc_final: 0.8612 (mp0)
REVERT: S  210 GLU cc_start: 0.6917 (mp0) cc_final: 0.6359 (mp0)
REVERT: A   34 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7008 (t)
REVERT: A  216 GLU cc_start: 0.8157 (tt0) cc_final: 0.7797 (mt-10)
REVERT: A  269 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.5962 (m-40)
REVERT: A  289 GLU cc_start: 0.8829 (tp30) cc_final: 0.7989 (mp0)
REVERT: A  313 ARG cc_start: 0.6647 (mtt180) cc_final: 0.6069 (mmt90)
REVERT: A  345 LYS cc_start: 0.7868 (mptt) cc_final: 0.7509 (tptp)
  outliers start: 28
  outliers final: 13
  residues processed: 201
  average time/residue: 0.2158
  time to fit residues: 59.3780
Evaluate side-chains
  172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  189 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 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 = 0.4323 r_free = 0.4323 target = 0.163151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.133928 restraints weight = 19887.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.137680 restraints weight = 11194.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.140401 restraints weight = 7786.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8882  Z= 0.133
  Angle     :  0.659   9.255  12031  Z= 0.339
  Chirality :  0.044   0.210   1376
  Planarity :  0.004   0.036   1499
  Dihedral  :  6.045 114.549   1216
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.05 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.26), residues: 1085
  helix:  0.68 (0.26), residues: 386
  sheet: -1.31 (0.30), residues: 282
  loop : -1.15 (0.33), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S 155 
 PHE   0.017   0.002   PHE A 267 
 TYR   0.019   0.002   TYR S 178 
 ARG   0.009   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03990 (  392)
  hydrogen bonds       : angle       5.21968 ( 1107)
  SS BOND              : bond        0.00987 (    4)
  SS BOND              : angle       2.38162 (    8)
  covalent geometry    : bond        0.00299 ( 8878)
  covalent geometry    : angle       0.65685 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 0.952 
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: B  130 GLU cc_start: 0.8490 (mp0) cc_final: 0.8165 (mp0)
REVERT: G   22 GLU cc_start: 0.3493 (tp30) cc_final: 0.2983 (tp30)
REVERT: A  186 GLU cc_start: 0.7399 (mp0) cc_final: 0.6948 (mp0)
REVERT: A  216 GLU cc_start: 0.8027 (tt0) cc_final: 0.7796 (mt-10)
REVERT: A  289 GLU cc_start: 0.8858 (tp30) cc_final: 0.8200 (mp0)
REVERT: A  313 ARG cc_start: 0.6446 (mtt180) cc_final: 0.6217 (mmt90)
REVERT: R  140 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7671 (tp)
REVERT: R  171 MET cc_start: 0.8840 (tpp) cc_final: 0.8428 (tpp)
REVERT: R  173 MET cc_start: 0.7784 (mmt) cc_final: 0.7583 (mmt)
  outliers start: 33
  outliers final: 18
  residues processed: 200
  average time/residue: 0.2146
  time to fit residues: 58.5364
Evaluate side-chains
  186 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   52 VAL
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  114 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
S 171 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 ASN
R 273 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.160868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.131884 restraints weight = 20013.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.135441 restraints weight = 11522.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.138173 restraints weight = 8138.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8882  Z= 0.143
  Angle     :  0.653   8.618  12031  Z= 0.334
  Chirality :  0.043   0.220   1376
  Planarity :  0.004   0.039   1499
  Dihedral  :  5.952 112.145   1216
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.42 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.26), residues: 1085
  helix:  0.84 (0.26), residues: 387
  sheet: -1.06 (0.31), residues: 272
  loop : -1.14 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S 220 
 PHE   0.027   0.002   PHE R  93 
 TYR   0.019   0.002   TYR S 178 
 ARG   0.007   0.001   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  392)
  hydrogen bonds       : angle       4.95681 ( 1107)
  SS BOND              : bond        0.00710 (    4)
  SS BOND              : angle       2.74097 (    8)
  covalent geometry    : bond        0.00326 ( 8878)
  covalent geometry    : angle       0.64895 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.7616 (mpp) cc_final: 0.7386 (mpp)
REVERT: B  130 GLU cc_start: 0.8621 (mp0) cc_final: 0.8250 (mp0)
REVERT: G   21 MET cc_start: 0.7610 (ppp) cc_final: 0.7055 (ppp)
REVERT: G   22 GLU cc_start: 0.3598 (tp30) cc_final: 0.2967 (tp30)
REVERT: S  168 ARG cc_start: 0.8552 (tpt170) cc_final: 0.8258 (tpt170)
REVERT: S  171 GLN cc_start: 0.8360 (mp10) cc_final: 0.7644 (mp10)
REVERT: A  186 GLU cc_start: 0.7575 (mp0) cc_final: 0.6866 (mp0)
REVERT: A  216 GLU cc_start: 0.8065 (tt0) cc_final: 0.7733 (mt-10)
REVERT: A  275 GLU cc_start: 0.8082 (pp20) cc_final: 0.7636 (pm20)
REVERT: A  287 TYR cc_start: 0.7347 (m-80) cc_final: 0.7058 (m-80)
REVERT: A  289 GLU cc_start: 0.9020 (tp30) cc_final: 0.8317 (mp0)
REVERT: A  313 ARG cc_start: 0.6635 (mtt180) cc_final: 0.6244 (mmt90)
REVERT: A  315 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7991 (p0)
REVERT: R  117 ARG cc_start: 0.5486 (mtm-85) cc_final: 0.5109 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7636 (tp)
REVERT: R  171 MET cc_start: 0.8819 (tpp) cc_final: 0.8536 (tpp)
REVERT: R  176 MET cc_start: 0.8187 (tpp) cc_final: 0.7917 (mtp)
REVERT: R  268 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6231 (tp)
  outliers start: 32
  outliers final: 20
  residues processed: 196
  average time/residue: 0.2107
  time to fit residues: 56.5668
Evaluate side-chains
  189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0270
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 92 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 108 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.168176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.141127 restraints weight = 21792.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.144341 restraints weight = 13406.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.146405 restraints weight = 9856.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8882  Z= 0.119
  Angle     :  0.651  10.620  12031  Z= 0.329
  Chirality :  0.043   0.230   1376
  Planarity :  0.004   0.036   1499
  Dihedral  :  5.760 112.986   1216
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.41 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.26), residues: 1085
  helix:  1.02 (0.26), residues: 386
  sheet: -0.82 (0.31), residues: 272
  loop : -1.11 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.018   0.001   PHE R 238 
 TYR   0.020   0.001   TYR S 178 
 ARG   0.006   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  392)
  hydrogen bonds       : angle       4.85976 ( 1107)
  SS BOND              : bond        0.00483 (    4)
  SS BOND              : angle       2.60111 (    8)
  covalent geometry    : bond        0.00267 ( 8878)
  covalent geometry    : angle       0.64748 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 180
  time to evaluate  : 0.932 
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: B  101 MET cc_start: 0.7483 (mpp) cc_final: 0.7180 (mpp)
REVERT: B  130 GLU cc_start: 0.8607 (mp0) cc_final: 0.8239 (mp0)
REVERT: G   21 MET cc_start: 0.7775 (ppp) cc_final: 0.7231 (ppp)
REVERT: G   22 GLU cc_start: 0.3810 (tp30) cc_final: 0.2984 (tp30)
REVERT: S  168 ARG cc_start: 0.8570 (tpt170) cc_final: 0.8182 (tpt170)
REVERT: S  171 GLN cc_start: 0.8463 (mp10) cc_final: 0.7870 (mp10)
REVERT: S  206 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8382 (mpp80)
REVERT: A   20 ASP cc_start: 0.6075 (m-30) cc_final: 0.5736 (m-30)
REVERT: A   34 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.6955 (t)
REVERT: A  186 GLU cc_start: 0.7424 (mp0) cc_final: 0.6789 (mp0)
REVERT: A  216 GLU cc_start: 0.7978 (tt0) cc_final: 0.7635 (mt-10)
REVERT: A  275 GLU cc_start: 0.8072 (pp20) cc_final: 0.7619 (pm20)
REVERT: A  289 GLU cc_start: 0.9099 (tp30) cc_final: 0.8396 (mp0)
REVERT: A  313 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6212 (mmt90)
REVERT: A  315 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7946 (p0)
REVERT: R  117 ARG cc_start: 0.5462 (mtm-85) cc_final: 0.5087 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7595 (tp)
REVERT: R  173 MET cc_start: 0.7785 (mmt) cc_final: 0.7524 (mmt)
REVERT: R  181 PHE cc_start: 0.5616 (t80) cc_final: 0.5354 (t80)
  outliers start: 34
  outliers final: 20
  residues processed: 202
  average time/residue: 0.2154
  time to fit residues: 58.6902
Evaluate side-chains
  193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    0.7980
   chunk 57 optimal weight:    8.9990
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  44 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.162463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.131960 restraints weight = 19681.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.135481 restraints weight = 11748.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.138052 restraints weight = 8473.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6521
moved from start:          0.5493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8882  Z= 0.130
  Angle     :  0.691  12.515  12031  Z= 0.349
  Chirality :  0.044   0.240   1376
  Planarity :  0.004   0.035   1499
  Dihedral  :  5.798 111.292   1216
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.20 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.26), residues: 1085
  helix:  1.11 (0.26), residues: 380
  sheet: -0.76 (0.32), residues: 266
  loop : -0.99 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.016   0.001   PHE S 200 
 TYR   0.018   0.001   TYR S 178 
 ARG   0.004   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  392)
  hydrogen bonds       : angle       4.85728 ( 1107)
  SS BOND              : bond        0.00785 (    4)
  SS BOND              : angle       4.71817 (    8)
  covalent geometry    : bond        0.00299 ( 8878)
  covalent geometry    : angle       0.68031 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.7380 (mpp) cc_final: 0.7165 (mpp)
REVERT: B  130 GLU cc_start: 0.8694 (mp0) cc_final: 0.8242 (mp0)
REVERT: B  234 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6290 (m-80)
REVERT: G   21 MET cc_start: 0.7845 (ppp) cc_final: 0.7341 (ppp)
REVERT: G   22 GLU cc_start: 0.3987 (tp30) cc_final: 0.3241 (tp30)
REVERT: S  128 MET cc_start: 0.6314 (mmt) cc_final: 0.6001 (mmp)
REVERT: S  168 ARG cc_start: 0.8589 (tpt170) cc_final: 0.8354 (tpt170)
REVERT: S  206 ARG cc_start: 0.8831 (mpp80) cc_final: 0.8340 (mpp80)
REVERT: A  249 LEU cc_start: 0.7912 (tp) cc_final: 0.7703 (tp)
REVERT: A  275 GLU cc_start: 0.8085 (pp20) cc_final: 0.7622 (pm20)
REVERT: A  289 GLU cc_start: 0.9144 (tp30) cc_final: 0.8477 (mp0)
REVERT: A  315 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7990 (p0)
REVERT: R  117 ARG cc_start: 0.5495 (mtm-85) cc_final: 0.5063 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7836 (tt) cc_final: 0.7555 (tp)
REVERT: R  152 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7461 (mmtm)
REVERT: R  171 MET cc_start: 0.8636 (tpp) cc_final: 0.8250 (tpp)
REVERT: R  181 PHE cc_start: 0.5594 (t80) cc_final: 0.5375 (t80)
  outliers start: 40
  outliers final: 27
  residues processed: 199
  average time/residue: 0.2117
  time to fit residues: 57.9406
Evaluate side-chains
  193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 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 = 0.4314 r_free = 0.4314 target = 0.162790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.134062 restraints weight = 19978.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.137648 restraints weight = 11456.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.140369 restraints weight = 8039.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.5760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8882  Z= 0.126
  Angle     :  0.680  10.377  12031  Z= 0.342
  Chirality :  0.044   0.256   1376
  Planarity :  0.004   0.034   1499
  Dihedral  :  5.798 111.166   1216
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.24 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.83 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.26), residues: 1085
  helix:  1.10 (0.26), residues: 386
  sheet: -0.74 (0.32), residues: 271
  loop : -0.87 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.015   0.001   PHE R  48 
 TYR   0.018   0.001   TYR S 178 
 ARG   0.012   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  392)
  hydrogen bonds       : angle       4.83363 ( 1107)
  SS BOND              : bond        0.00338 (    4)
  SS BOND              : angle       3.98299 (    8)
  covalent geometry    : bond        0.00286 ( 8878)
  covalent geometry    : angle       0.67222 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.8627 (mp0) cc_final: 0.8196 (mp0)
REVERT: B  234 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.6304 (m-80)
REVERT: G   21 MET cc_start: 0.7804 (ppp) cc_final: 0.7338 (ppp)
REVERT: G   22 GLU cc_start: 0.3853 (tp30) cc_final: 0.3118 (tp30)
REVERT: S  148 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7671 (mmm-85)
REVERT: S  206 ARG cc_start: 0.8863 (mpp80) cc_final: 0.8599 (mpp80)
REVERT: A  186 GLU cc_start: 0.7315 (mp0) cc_final: 0.6813 (mp0)
REVERT: A  275 GLU cc_start: 0.8144 (pp20) cc_final: 0.7653 (pm20)
REVERT: A  289 GLU cc_start: 0.9093 (tp30) cc_final: 0.8493 (mp0)
REVERT: A  313 ARG cc_start: 0.6218 (mmt90) cc_final: 0.5989 (mmp80)
REVERT: A  315 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8062 (p0)
REVERT: R  117 ARG cc_start: 0.5540 (mtm-85) cc_final: 0.5193 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7677 (tp)
REVERT: R  152 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7625 (mmtm)
REVERT: R  171 MET cc_start: 0.8577 (tpp) cc_final: 0.8185 (tpp)
REVERT: R  173 MET cc_start: 0.7795 (mmt) cc_final: 0.7537 (mmt)
REVERT: R  181 PHE cc_start: 0.5644 (t80) cc_final: 0.5419 (t80)
  outliers start: 36
  outliers final: 28
  residues processed: 193
  average time/residue: 0.2569
  time to fit residues: 67.6306
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 52 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 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 = 0.4287 r_free = 0.4287 target = 0.160419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.130925 restraints weight = 20299.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.134504 restraints weight = 11881.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.137158 restraints weight = 8442.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8882  Z= 0.147
  Angle     :  0.735  14.306  12031  Z= 0.367
  Chirality :  0.045   0.273   1376
  Planarity :  0.004   0.038   1499
  Dihedral  :  5.931 110.093   1216
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 22.77 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.26), residues: 1085
  helix:  1.15 (0.26), residues: 381
  sheet: -0.75 (0.31), residues: 271
  loop : -0.87 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.019   0.002   PHE A 189 
 TYR   0.019   0.001   TYR A 302 
 ARG   0.011   0.001   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03833 (  392)
  hydrogen bonds       : angle       4.81964 ( 1107)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       3.67160 (    8)
  covalent geometry    : bond        0.00339 ( 8878)
  covalent geometry    : angle       0.72938 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7385 (t0) cc_final: 0.6871 (t0)
REVERT: B  130 GLU cc_start: 0.8725 (mp0) cc_final: 0.8244 (mp0)
REVERT: B  234 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.6695 (m-80)
REVERT: G   21 MET cc_start: 0.7828 (ppp) cc_final: 0.7395 (ppp)
REVERT: G   22 GLU cc_start: 0.4027 (tp30) cc_final: 0.3258 (tp30)
REVERT: S  148 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7766 (mmm-85)
REVERT: A   20 ASP cc_start: 0.6185 (m-30) cc_final: 0.5845 (m-30)
REVERT: A  216 GLU cc_start: 0.8003 (tt0) cc_final: 0.7755 (mt-10)
REVERT: A  289 GLU cc_start: 0.9079 (tp30) cc_final: 0.8519 (mp0)
REVERT: A  313 ARG cc_start: 0.6215 (mmt90) cc_final: 0.5975 (mmp80)
REVERT: R  117 ARG cc_start: 0.5642 (mtm-85) cc_final: 0.5238 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7716 (tp)
REVERT: R  152 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7946 (mmtm)
REVERT: R  171 MET cc_start: 0.8509 (tpp) cc_final: 0.8236 (tpp)
  outliers start: 35
  outliers final: 26
  residues processed: 197
  average time/residue: 0.2704
  time to fit residues: 73.9950
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  111 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 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 = 0.4299 r_free = 0.4299 target = 0.161871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.132209 restraints weight = 19957.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.135792 restraints weight = 11652.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.138489 restraints weight = 8310.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.6230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8882  Z= 0.136
  Angle     :  0.770  12.944  12031  Z= 0.382
  Chirality :  0.046   0.287   1376
  Planarity :  0.004   0.075   1499
  Dihedral  :  5.991 110.309   1216
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.15 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.40 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1085
  helix:  1.18 (0.26), residues: 380
  sheet: -0.72 (0.31), residues: 274
  loop : -0.82 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.020   0.001   PHE S 200 
 TYR   0.018   0.001   TYR S 178 
 ARG   0.008   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  392)
  hydrogen bonds       : angle       4.80419 ( 1107)
  SS BOND              : bond        0.00190 (    4)
  SS BOND              : angle       3.37404 (    8)
  covalent geometry    : bond        0.00309 ( 8878)
  covalent geometry    : angle       0.76507 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 170
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7331 (t0) cc_final: 0.6838 (t0)
REVERT: B  101 MET cc_start: 0.6571 (mpp) cc_final: 0.6144 (mpp)
REVERT: B  130 GLU cc_start: 0.8737 (mp0) cc_final: 0.8403 (mp0)
REVERT: B  234 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.6571 (m-80)
REVERT: B  266 HIS cc_start: 0.6917 (t-90) cc_final: 0.6581 (t-90)
REVERT: G   21 MET cc_start: 0.7791 (ppp) cc_final: 0.7378 (ppp)
REVERT: G   22 GLU cc_start: 0.4061 (tp30) cc_final: 0.3307 (tp30)
REVERT: G   48 ASP cc_start: 0.6674 (m-30) cc_final: 0.6425 (m-30)
REVERT: S  128 MET cc_start: 0.6016 (mmp) cc_final: 0.5701 (mmm)
REVERT: S  148 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7656 (mmm-85)
REVERT: A  244 HIS cc_start: 0.8811 (m170) cc_final: 0.8584 (m90)
REVERT: R  117 ARG cc_start: 0.5620 (mtm-85) cc_final: 0.5183 (mtm-85)
REVERT: R  140 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7702 (tp)
REVERT: R  152 LYS cc_start: 0.8250 (mmtp) cc_final: 0.8012 (mmtm)
REVERT: R  171 MET cc_start: 0.8518 (tpp) cc_final: 0.8263 (tpp)
REVERT: R  181 PHE cc_start: 0.5828 (t80) cc_final: 0.5429 (t80)
  outliers start: 29
  outliers final: 25
  residues processed: 189
  average time/residue: 0.2422
  time to fit residues: 63.7751
Evaluate side-chains
  198 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0000
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
S 174 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** 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 = 0.4319 r_free = 0.4319 target = 0.163362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.134072 restraints weight = 19746.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.137690 restraints weight = 11413.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.140378 restraints weight = 8070.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.6413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8882  Z= 0.133
  Angle     :  0.796  12.539  12031  Z= 0.389
  Chirality :  0.047   0.328   1376
  Planarity :  0.004   0.076   1499
  Dihedral  :  6.089 110.050   1216
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.42 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.67 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.27), residues: 1085
  helix:  1.21 (0.26), residues: 380
  sheet: -0.72 (0.32), residues: 268
  loop : -0.78 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.018   0.001   PHE S 200 
 TYR   0.018   0.001   TYR S 178 
 ARG   0.004   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  392)
  hydrogen bonds       : angle       4.75907 ( 1107)
  SS BOND              : bond        0.00217 (    4)
  SS BOND              : angle       3.17779 (    8)
  covalent geometry    : bond        0.00302 ( 8878)
  covalent geometry    : angle       0.79177 (12023)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 2.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7367 (t0) cc_final: 0.6864 (t0)
REVERT: B  130 GLU cc_start: 0.8720 (mp0) cc_final: 0.8101 (mp0)
REVERT: B  234 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6474 (m-80)
REVERT: G   21 MET cc_start: 0.7806 (ppp) cc_final: 0.7446 (ppp)
REVERT: G   22 GLU cc_start: 0.4038 (tp30) cc_final: 0.3354 (tp30)
REVERT: G   48 ASP cc_start: 0.6559 (m-30) cc_final: 0.6327 (m-30)
REVERT: S  128 MET cc_start: 0.5915 (mmp) cc_final: 0.5665 (mmm)
REVERT: S  148 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7588 (mmm-85)
REVERT: S  190 ARG cc_start: 0.5568 (mtp180) cc_final: 0.5233 (mtp180)
REVERT: S  210 GLU cc_start: 0.5941 (tm-30) cc_final: 0.5617 (tm-30)
REVERT: A  184 ILE cc_start: 0.6826 (pt) cc_final: 0.6619 (mp)
REVERT: A  186 GLU cc_start: 0.7217 (mp0) cc_final: 0.6998 (mp0)
REVERT: A  216 GLU cc_start: 0.7944 (tt0) cc_final: 0.7711 (mt-10)
REVERT: A  276 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8542 (mm-30)
REVERT: A  289 GLU cc_start: 0.9014 (tp30) cc_final: 0.8589 (mp0)
REVERT: R  117 ARG cc_start: 0.5492 (mtm-85) cc_final: 0.5056 (mtm-85)
REVERT: R  140 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7765 (tp)
REVERT: R  152 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8045 (mmtm)
REVERT: R  171 MET cc_start: 0.8512 (tpp) cc_final: 0.8270 (tpp)
REVERT: R  181 PHE cc_start: 0.6058 (t80) cc_final: 0.5625 (t80)
  outliers start: 28
  outliers final: 21
  residues processed: 198
  average time/residue: 0.2708
  time to fit residues: 73.6720
Evaluate side-chains
  197 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain R residue   94 THR
Chi-restraints excluded: chain R residue   99 MET
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  107 ASP
Chi-restraints excluded: chain R residue  112 VAL
Chi-restraints excluded: chain R residue  140 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  191 VAL
Chi-restraints excluded: chain R residue  251 ILE
Chi-restraints excluded: chain R residue  265 LEU
Chi-restraints excluded: chain R residue  268 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
A 331 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.161795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.132630 restraints weight = 20173.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.136294 restraints weight = 11675.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.138643 restraints weight = 8228.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8882  Z= 0.144
  Angle     :  0.806  14.058  12031  Z= 0.389
  Chirality :  0.047   0.327   1376
  Planarity :  0.004   0.079   1499
  Dihedral  :  5.991 111.057   1216
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 23.50 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.26), residues: 1085
  helix:  1.19 (0.26), residues: 381
  sheet: -0.80 (0.32), residues: 262
  loop : -0.72 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 322 
 PHE   0.017   0.001   PHE S 200 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.006   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  392)
  hydrogen bonds       : angle       4.76440 ( 1107)
  SS BOND              : bond        0.00146 (    4)
  SS BOND              : angle       3.25949 (    8)
  covalent geometry    : bond        0.00331 ( 8878)
  covalent geometry    : angle       0.80163 (12023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3808.17 seconds
wall clock time: 68 minutes 36.31 seconds (4116.31 seconds total)