Starting phenix.real_space_refine
on Sat Jun  7 12:27:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yh5_39281/06_2025/8yh5_39281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yh5_39281/06_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_39281/06_2025/8yh5_39281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yh5_39281/06_2025/8yh5_39281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yh5_39281/06_2025/8yh5_39281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yh5_39281/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.10, 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 964.0 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: 0.93
  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: 2.45

  Time building geometry restraints manager: 2.54 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: 11313
        1.37 -     2.73: 552
        2.73 -     4.10: 131
        4.10 -     5.47: 22
        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 -    25.22: 5045
       25.22 -    50.44: 211
       50.44 -    75.67: 17
       75.67 -   100.89: 1
      100.89 -   126.11: 2
  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 -    0.039: 979
       0.039 -    0.078: 276
       0.078 -    0.117: 80
       0.117 -    0.157: 33
       0.157 -    0.196: 8
  Chirality restraints: 1376
  Sorted by residual:
  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
  chirality pdb=" CA  LEU B 168 "
            pdb=" N   LEU B 168 "
            pdb=" C   LEU B 168 "
            pdb=" CB  LEU B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.60e-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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.080
  Find NCS groups from input model:        0.100
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.150
-------------------------------------------------------------------------------
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= 0.453
  Chirality :  0.044   0.196   1376
  Planarity :  0.017   0.320   1499
  Dihedral  : 13.520 126.109   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        0.00426 ( 8878)
  covalent geometry    : angle       0.71553 (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  : 1.033 
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: 0.2271
  time to fit residues: 70.1227
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  : 1.067 
-------------------------------------------------------------------------------
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:    6.9990
   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 = 0.161343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.132395 restraints weight = 19812.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.135978 restraints weight = 11327.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.138261 restraints weight = 7994.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.3518

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= 0.204
  Angle     :  0.729  10.148  12031  Z= 0.381
  Chirality :  0.047   0.198   1376
  Planarity :  0.004   0.041   1499
  Dihedral  :  6.156  71.803   1216
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.75 %
    Favored  : 85.20 %
  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: -1.21 (0.26), residues: 1085
  helix:  0.44 (0.26), residues: 386
  sheet: -1.32 (0.31), residues: 279
  loop : -1.49 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R  35 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.020   0.002   PHE R 288 
 TYR   0.022   0.002   TYR S 178 
 ARG   0.008   0.001   ARG R 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04671 (  392)
  hydrogen bonds       : angle       5.69552 ( 1107)
  SS BOND              : bond        0.00534 (    4)
  SS BOND              : angle       2.54931 (    8)
  covalent geometry    : bond        0.00448 ( 8878)
  covalent geometry    : angle       0.72625 (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
  218 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  130 GLU cc_start: 0.8468 (mp0) cc_final: 0.8172 (mp0)
REVERT: B  256 ARG cc_start: 0.7456 (mmp-170) cc_final: 0.7231 (mmp-170)
REVERT: G   58 GLU cc_start: 0.8882 (mp0) cc_final: 0.8626 (mp0)
REVERT: S  210 GLU cc_start: 0.6937 (mp0) cc_final: 0.6377 (mp0)
REVERT: A  216 GLU cc_start: 0.8124 (tt0) cc_final: 0.7791 (mt-10)
REVERT: A  269 ASN cc_start: 0.6498 (OUTLIER) cc_final: 0.5996 (m-40)
REVERT: A  289 GLU cc_start: 0.8826 (tp30) cc_final: 0.7992 (mp0)
REVERT: A  313 ARG cc_start: 0.6656 (mtt180) cc_final: 0.6079 (mmt90)
REVERT: A  345 LYS cc_start: 0.7893 (mptt) cc_final: 0.7539 (tptp)
  outliers start: 29
  outliers final: 13
  residues processed: 204
  average time/residue: 0.2091
  time to fit residues: 58.7780
Evaluate side-chains
  174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 HIS
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:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 18 optimal weight:    0.1980
   chunk 74 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4328 r_free = 0.4328 target = 0.163603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.134118 restraints weight = 19922.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.137810 restraints weight = 11317.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.140537 restraints weight = 7916.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.4201

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= 0.134
  Angle     :  0.651   7.831  12031  Z= 0.337
  Chirality :  0.044   0.212   1376
  Planarity :  0.004   0.036   1499
  Dihedral  :  5.408  48.337   1216
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.05 %
    Favored  : 81.01 %
  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: -0.88 (0.26), residues: 1085
  helix:  0.66 (0.26), residues: 386
  sheet: -1.27 (0.31), residues: 281
  loop : -1.12 (0.33), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 244 
 PHE   0.020   0.002   PHE A 267 
 TYR   0.020   0.002   TYR S 178 
 ARG   0.007   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  392)
  hydrogen bonds       : angle       5.26398 ( 1107)
  SS BOND              : bond        0.00370 (    4)
  SS BOND              : angle       2.42389 (    8)
  covalent geometry    : bond        0.00308 ( 8878)
  covalent geometry    : angle       0.64839 (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
  211 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.7762 (m100) cc_final: 0.7559 (m100)
REVERT: B  101 MET cc_start: 0.7552 (mpp) cc_final: 0.7020 (mpp)
REVERT: B  130 GLU cc_start: 0.8485 (mp0) cc_final: 0.8159 (mp0)
REVERT: G   22 GLU cc_start: 0.3038 (tp30) cc_final: 0.2565 (tp30)
REVERT: A  186 GLU cc_start: 0.7340 (mp0) cc_final: 0.6976 (mp0)
REVERT: A  216 GLU cc_start: 0.7997 (tt0) cc_final: 0.7777 (mt-10)
REVERT: A  289 GLU cc_start: 0.8880 (tp30) cc_final: 0.8220 (mp0)
REVERT: A  313 ARG cc_start: 0.6434 (mtt180) cc_final: 0.6210 (mmt90)
REVERT: R  173 MET cc_start: 0.7791 (mmt) cc_final: 0.7584 (mmt)
  outliers start: 28
  outliers final: 15
  residues processed: 196
  average time/residue: 0.2078
  time to fit residues: 55.4704
Evaluate side-chains
  179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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 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  163 LEU
Chi-restraints excluded: chain R residue  251 ILE
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:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 95 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.4269 r_free = 0.4269 target = 0.159341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.130181 restraints weight = 20044.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.133694 restraints weight = 11592.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.136300 restraints weight = 8246.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.4913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8882  Z= 0.163
  Angle     :  0.681  10.493  12031  Z= 0.351
  Chirality :  0.044   0.217   1376
  Planarity :  0.004   0.038   1499
  Dihedral  :  5.337  49.940   1216
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.16 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.36 %
    Favored  : 78.59 %
  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: -0.72 (0.26), residues: 1085
  helix:  0.79 (0.26), residues: 387
  sheet: -1.10 (0.32), residues: 270
  loop : -1.12 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 184 
 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   0.005   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  392)
  hydrogen bonds       : angle       5.02490 ( 1107)
  SS BOND              : bond        0.00883 (    4)
  SS BOND              : angle       3.00036 (    8)
  covalent geometry    : bond        0.00376 ( 8878)
  covalent geometry    : angle       0.67689 (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
  204 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.7650 (mpp) cc_final: 0.7316 (mpp)
REVERT: B  130 GLU cc_start: 0.8672 (mp0) cc_final: 0.8276 (mp0)
REVERT: B  256 ARG cc_start: 0.7378 (mmp-170) cc_final: 0.6459 (mmp80)
REVERT: G   21 MET cc_start: 0.7616 (ppp) cc_final: 0.7058 (ppp)
REVERT: G   22 GLU cc_start: 0.3625 (tp30) cc_final: 0.2981 (tp30)
REVERT: G   48 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6644 (m-30)
REVERT: S  171 GLN cc_start: 0.8395 (mp10) cc_final: 0.8133 (mp10)
REVERT: S  206 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8410 (mpp80)
REVERT: A  216 GLU cc_start: 0.8123 (tt0) cc_final: 0.7767 (mt-10)
REVERT: A  275 GLU cc_start: 0.8084 (pp20) cc_final: 0.7627 (pm20)
REVERT: A  287 TYR cc_start: 0.7357 (m-80) cc_final: 0.7143 (m-80)
REVERT: A  289 GLU cc_start: 0.9041 (tp30) cc_final: 0.8330 (mp0)
REVERT: A  313 ARG cc_start: 0.6676 (mtt180) cc_final: 0.6254 (mmt90)
REVERT: A  315 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (p0)
REVERT: R  117 ARG cc_start: 0.5601 (mtm-85) cc_final: 0.5224 (mtm-85)
REVERT: R  171 MET cc_start: 0.8612 (tpp) cc_final: 0.8309 (tpp)
  outliers start: 29
  outliers final: 19
  residues processed: 193
  average time/residue: 0.2166
  time to fit residues: 56.8663
Evaluate side-chains
  184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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  331 SER
Chi-restraints excluded: chain G residue   48 ASP
Chi-restraints excluded: chain S residue  220 HIS
Chi-restraints excluded: chain A residue  195 HIS
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  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:    5.9990
   chunk 51 optimal weight:   20.0000
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0570
   chunk 92 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 88 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.6300

-------------------------------------------------------------------------------
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 = 0.4310 r_free = 0.4310 target = 0.162682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.133832 restraints weight = 19753.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.137427 restraints weight = 11440.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.140052 restraints weight = 8029.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.5257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8882  Z= 0.122
  Angle     :  0.653  10.843  12031  Z= 0.331
  Chirality :  0.043   0.233   1376
  Planarity :  0.004   0.036   1499
  Dihedral  :  5.001  46.061   1216
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.33 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.57 %
    Favored  : 76.39 %
  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: -0.48 (0.26), residues: 1085
  helix:  0.96 (0.26), residues: 386
  sheet: -0.83 (0.32), residues: 266
  loop : -1.05 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.017   0.001   PHE R 238 
 TYR   0.021   0.001   TYR S 178 
 ARG   0.004   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03521 (  392)
  hydrogen bonds       : angle       4.87772 ( 1107)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       2.60046 (    8)
  covalent geometry    : bond        0.00276 ( 8878)
  covalent geometry    : angle       0.64989 (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
  208 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.7904 (m100) cc_final: 0.7682 (m100)
REVERT: B  101 MET cc_start: 0.7413 (mpp) cc_final: 0.7003 (mpp)
REVERT: B  130 GLU cc_start: 0.8623 (mp0) cc_final: 0.8210 (mp0)
REVERT: B  256 ARG cc_start: 0.7477 (mmp-170) cc_final: 0.6981 (mmp80)
REVERT: G   21 MET cc_start: 0.7697 (ppp) cc_final: 0.7141 (ppp)
REVERT: G   22 GLU cc_start: 0.3847 (tp30) cc_final: 0.2964 (tp30)
REVERT: S  171 GLN cc_start: 0.8487 (mp10) cc_final: 0.7785 (mp10)
REVERT: S  206 ARG cc_start: 0.8809 (mpp80) cc_final: 0.8331 (mpp80)
REVERT: A  186 GLU cc_start: 0.7505 (mp0) cc_final: 0.6839 (mp0)
REVERT: A  216 GLU cc_start: 0.8086 (tt0) cc_final: 0.7709 (mt-10)
REVERT: A  275 GLU cc_start: 0.8117 (pp20) cc_final: 0.7675 (pm20)
REVERT: A  289 GLU cc_start: 0.9115 (tp30) cc_final: 0.8462 (mp0)
REVERT: A  313 ARG cc_start: 0.6547 (mtt180) cc_final: 0.6231 (mmt90)
REVERT: A  315 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7971 (p0)
REVERT: R  117 ARG cc_start: 0.5440 (mtm-85) cc_final: 0.5044 (mtm-85)
REVERT: R  152 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7514 (mmtm)
REVERT: R  173 MET cc_start: 0.7748 (mmt) cc_final: 0.7499 (mmt)
  outliers start: 29
  outliers final: 20
  residues processed: 196
  average time/residue: 0.2275
  time to fit residues: 60.4699
Evaluate side-chains
  187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
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 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  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  112 VAL
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  165 CYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 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 = 0.4270 r_free = 0.4270 target = 0.159150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.129883 restraints weight = 20110.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.133275 restraints weight = 11856.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.135845 restraints weight = 8524.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.5577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8882  Z= 0.161
  Angle     :  0.709  12.978  12031  Z= 0.359
  Chirality :  0.045   0.241   1376
  Planarity :  0.004   0.038   1499
  Dihedral  :  5.200  44.994   1216
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.57 %
    Favored  : 74.82 %
  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: -0.48 (0.26), residues: 1085
  helix:  1.01 (0.26), residues: 385
  sheet: -0.91 (0.32), residues: 271
  loop : -1.05 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 220 
 PHE   0.017   0.002   PHE S 200 
 TYR   0.017   0.002   TYR S 178 
 ARG   0.008   0.001   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03859 (  392)
  hydrogen bonds       : angle       4.89769 ( 1107)
  SS BOND              : bond        0.00705 (    4)
  SS BOND              : angle       4.72539 (    8)
  covalent geometry    : bond        0.00375 ( 8878)
  covalent geometry    : angle       0.69902 (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
  212 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 168
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.7446 (mpp) cc_final: 0.7160 (mpp)
REVERT: B  130 GLU cc_start: 0.8733 (mp0) cc_final: 0.8220 (mp0)
REVERT: B  234 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.6667 (m-80)
REVERT: B  256 ARG cc_start: 0.7437 (mmp-170) cc_final: 0.6884 (mmp80)
REVERT: G   21 MET cc_start: 0.7746 (ppp) cc_final: 0.7252 (ppp)
REVERT: G   22 GLU cc_start: 0.4057 (tp30) cc_final: 0.3266 (tp30)
REVERT: A  249 LEU cc_start: 0.8025 (tp) cc_final: 0.7823 (tp)
REVERT: A  289 GLU cc_start: 0.9172 (tp30) cc_final: 0.8521 (mp0)
REVERT: A  313 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6188 (mmt90)
REVERT: A  315 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (p0)
REVERT: R  117 ARG cc_start: 0.5563 (mtm-85) cc_final: 0.5117 (mtm-85)
REVERT: R  152 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7580 (mmtm)
  outliers start: 44
  outliers final: 26
  residues processed: 195
  average time/residue: 0.2129
  time to fit residues: 56.5692
Evaluate side-chains
  187 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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   13 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  221 ILE
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  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  136 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 ** 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 = 0.4287 r_free = 0.4287 target = 0.160655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.131453 restraints weight = 20170.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.134821 restraints weight = 11754.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.137381 restraints weight = 8389.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.5879

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= 0.143
  Angle     :  0.716  11.025  12031  Z= 0.364
  Chirality :  0.045   0.261   1376
  Planarity :  0.004   0.045   1499
  Dihedral  :  5.143  39.059   1216
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.93 %
    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: -0.35 (0.26), residues: 1085
  helix:  1.09 (0.27), residues: 386
  sheet: -0.80 (0.32), residues: 271
  loop : -0.98 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  35 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.013   0.001   PHE R  48 
 TYR   0.018   0.001   TYR S 178 
 ARG   0.010   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  392)
  hydrogen bonds       : angle       4.86316 ( 1107)
  SS BOND              : bond        0.00303 (    4)
  SS BOND              : angle       3.99795 (    8)
  covalent geometry    : bond        0.00331 ( 8878)
  covalent geometry    : angle       0.70899 (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
  204 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.7251 (mpp) cc_final: 0.7046 (mpp)
REVERT: B  130 GLU cc_start: 0.8731 (mp0) cc_final: 0.8225 (mp0)
REVERT: B  234 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6749 (m-80)
REVERT: B  256 ARG cc_start: 0.7384 (mmp-170) cc_final: 0.6629 (mmp80)
REVERT: G   21 MET cc_start: 0.7845 (ppp) cc_final: 0.7392 (ppp)
REVERT: G   22 GLU cc_start: 0.4030 (tp30) cc_final: 0.3277 (tp30)
REVERT: A   20 ASP cc_start: 0.6274 (m-30) cc_final: 0.5933 (m-30)
REVERT: A  289 GLU cc_start: 0.9136 (tp30) cc_final: 0.8541 (mp0)
REVERT: A  315 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (p0)
REVERT: R  117 ARG cc_start: 0.5534 (mtm-85) cc_final: 0.5044 (mtm-85)
REVERT: R  152 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7735 (mmtm)
REVERT: R  173 MET cc_start: 0.7850 (mmt) cc_final: 0.7584 (mmt)
REVERT: R  181 PHE cc_start: 0.5894 (t80) cc_final: 0.5614 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 192
  average time/residue: 0.2460
  time to fit residues: 64.0328
Evaluate side-chains
  189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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   13 VAL
Chi-restraints excluded: chain A residue   18 MET
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  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  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:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0070
   chunk 106 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 52 optimal weight:   20.0000
   chunk 77 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.7002

-------------------------------------------------------------------------------
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 ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.161488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.131939 restraints weight = 20091.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.135445 restraints weight = 11707.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.137988 restraints weight = 8331.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8882  Z= 0.129
  Angle     :  0.723  10.266  12031  Z= 0.361
  Chirality :  0.045   0.290   1376
  Planarity :  0.004   0.041   1499
  Dihedral  :  5.096  39.172   1216
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.79 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.98 %
    Favored  : 74.08 %
  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:  1.09 (0.26), residues: 385
  sheet: -0.67 (0.32), residues: 272
  loop : -0.88 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  99 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.019   0.001   PHE A 189 
 TYR   0.019   0.001   TYR S 178 
 ARG   0.006   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  392)
  hydrogen bonds       : angle       4.86219 ( 1107)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       3.53585 (    8)
  covalent geometry    : bond        0.00292 ( 8878)
  covalent geometry    : angle       0.71718 (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
  203 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   43 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7239 (mp)
REVERT: B   76 ASP cc_start: 0.7393 (t0) cc_final: 0.6907 (t0)
REVERT: B   82 TRP cc_start: 0.8097 (m100) cc_final: 0.7753 (m100)
REVERT: B  101 MET cc_start: 0.7100 (mpp) cc_final: 0.6893 (mpp)
REVERT: B  130 GLU cc_start: 0.8713 (mp0) cc_final: 0.8213 (mp0)
REVERT: B  234 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.6661 (m-80)
REVERT: B  256 ARG cc_start: 0.7313 (mmp-170) cc_final: 0.6569 (mmp80)
REVERT: G   21 MET cc_start: 0.7822 (ppp) cc_final: 0.7389 (ppp)
REVERT: G   22 GLU cc_start: 0.4043 (tp30) cc_final: 0.3354 (tp30)
REVERT: S  206 ARG cc_start: 0.8851 (mpp80) cc_final: 0.8645 (mpp80)
REVERT: S  210 GLU cc_start: 0.5912 (tm-30) cc_final: 0.5482 (tm-30)
REVERT: A  186 GLU cc_start: 0.7404 (mp0) cc_final: 0.6898 (mp0)
REVERT: A  276 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8617 (mm-30)
REVERT: A  313 ARG cc_start: 0.6233 (mmt90) cc_final: 0.6020 (mmp80)
REVERT: R  117 ARG cc_start: 0.5641 (mtm-85) cc_final: 0.5217 (mtm-85)
REVERT: R  152 LYS cc_start: 0.8306 (mmtp) cc_final: 0.8092 (mptt)
REVERT: R  173 MET cc_start: 0.7745 (mmt) cc_final: 0.7529 (mmt)
REVERT: R  181 PHE cc_start: 0.5757 (t80) cc_final: 0.5452 (t80)
  outliers start: 28
  outliers final: 23
  residues processed: 196
  average time/residue: 0.2478
  time to fit residues: 66.6481
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   43 ILE
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 B residue  296 VAL
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 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 37 optimal weight:    0.2980
   chunk 52 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 68 optimal weight:    0.2980
   chunk 65 optimal weight:    7.9990
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 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 = 0.4304 r_free = 0.4304 target = 0.161814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.132351 restraints weight = 20073.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.135810 restraints weight = 11817.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.138472 restraints weight = 8454.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8882  Z= 0.133
  Angle     :  0.739  11.529  12031  Z= 0.367
  Chirality :  0.046   0.278   1376
  Planarity :  0.004   0.043   1499
  Dihedral  :  5.061  41.126   1216
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.52 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.40 %
    Favored  : 73.87 %
  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: -0.16 (0.26), residues: 1085
  helix:  1.14 (0.26), residues: 383
  sheet: -0.59 (0.32), residues: 266
  loop : -0.82 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   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   0.007   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  392)
  hydrogen bonds       : angle       4.82207 ( 1107)
  SS BOND              : bond        0.00220 (    4)
  SS BOND              : angle       3.46858 (    8)
  covalent geometry    : bond        0.00303 ( 8878)
  covalent geometry    : angle       0.73414 (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: 26
    poor density    : 173
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 ASP cc_start: 0.7420 (t0) cc_final: 0.6958 (t0)
REVERT: B   82 TRP cc_start: 0.8085 (m100) cc_final: 0.7758 (m100)
REVERT: B  130 GLU cc_start: 0.8701 (mp0) cc_final: 0.8378 (mp0)
REVERT: B  234 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6728 (m-80)
REVERT: B  256 ARG cc_start: 0.7304 (mmp-170) cc_final: 0.6549 (mmp80)
REVERT: B  266 HIS cc_start: 0.6929 (t-90) cc_final: 0.6663 (t-90)
REVERT: G   21 MET cc_start: 0.7828 (ppp) cc_final: 0.7430 (ppp)
REVERT: G   22 GLU cc_start: 0.4095 (tp30) cc_final: 0.3412 (tp30)
REVERT: S  190 ARG cc_start: 0.5582 (mtp180) cc_final: 0.5357 (mtp180)
REVERT: A  289 GLU cc_start: 0.9018 (tp30) cc_final: 0.8576 (mp0)
REVERT: R  117 ARG cc_start: 0.5710 (mtm-85) cc_final: 0.5236 (mtm-85)
REVERT: R  152 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7895 (mmmt)
REVERT: R  173 MET cc_start: 0.7708 (mmt) cc_final: 0.7447 (mmt)
REVERT: R  181 PHE cc_start: 0.5936 (t80) cc_final: 0.5635 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 191
  average time/residue: 0.2335
  time to fit residues: 60.2972
Evaluate side-chains
  185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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 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  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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0470
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0470
   chunk 104 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0060
   overall best weight:    0.2392

-------------------------------------------------------------------------------
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**
S 174 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4353 r_free = 0.4353 target = 0.165765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.137407 restraints weight = 19734.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.140813 restraints weight = 11353.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.143211 restraints weight = 7937.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6455
moved from start:          0.6466

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= 0.125
  Angle     :  0.751  12.613  12031  Z= 0.370
  Chirality :  0.046   0.333   1376
  Planarity :  0.004   0.040   1499
  Dihedral  :  4.993  44.763   1216
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.33 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.61 %
    Favored  : 73.87 %
  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: -0.05 (0.27), residues: 1085
  helix:  1.19 (0.27), residues: 383
  sheet: -0.52 (0.32), residues: 265
  loop : -0.71 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S 155 
 PHE   0.018   0.001   PHE S 200 
 TYR   0.019   0.001   TYR S 178 
 ARG   0.005   0.000   ARG S 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  392)
  hydrogen bonds       : angle       4.76837 ( 1107)
  SS BOND              : bond        0.00252 (    4)
  SS BOND              : angle       3.19058 (    8)
  covalent geometry    : bond        0.00277 ( 8878)
  covalent geometry    : angle       0.74712 (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
  202 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 TRP cc_start: 0.7979 (m100) cc_final: 0.7669 (m100)
REVERT: B  130 GLU cc_start: 0.8643 (mp0) cc_final: 0.8047 (mp0)
REVERT: B  234 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.6519 (m-80)
REVERT: B  266 HIS cc_start: 0.6697 (t-90) cc_final: 0.6402 (t-90)
REVERT: G   21 MET cc_start: 0.7839 (ppp) cc_final: 0.7474 (ppp)
REVERT: G   22 GLU cc_start: 0.4038 (tp30) cc_final: 0.3359 (tp30)
REVERT: S  190 ARG cc_start: 0.5840 (mtp180) cc_final: 0.5538 (mtp180)
REVERT: A  186 GLU cc_start: 0.7206 (mp0) cc_final: 0.6962 (mp0)
REVERT: A  276 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8337 (mm-30)
REVERT: A  289 GLU cc_start: 0.9019 (tp30) cc_final: 0.8587 (mp0)
REVERT: R   99 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6732 (mmm)
REVERT: R  117 ARG cc_start: 0.5471 (mtm-85) cc_final: 0.5050 (mtm-85)
REVERT: R  173 MET cc_start: 0.7614 (mmt) cc_final: 0.7311 (mmt)
REVERT: R  181 PHE cc_start: 0.5656 (t80) cc_final: 0.5345 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 194
  average time/residue: 0.2141
  time to fit residues: 56.5579
Evaluate side-chains
  189 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 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 B residue  296 VAL
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  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  141 VAL
Chi-restraints excluded: chain R residue  143 LEU
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 90 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0870
   chunk 102 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.3760

-------------------------------------------------------------------------------
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
R  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.160741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.131944 restraints weight = 19985.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.135385 restraints weight = 11653.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.137932 restraints weight = 8222.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
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      :  0.004   0.041   8882  Z= 0.152
  Angle     :  0.780  12.708  12031  Z= 0.383
  Chirality :  0.047   0.332   1376
  Planarity :  0.004   0.052   1499
  Dihedral  :  5.041  37.478   1216
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.53 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.19 %
    Favored  : 73.77 %
  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: -0.11 (0.26), residues: 1085
  helix:  1.16 (0.26), residues: 384
  sheet: -0.54 (0.33), residues: 258
  loop : -0.79 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.017   0.001   PHE S 200 
 TYR   0.018   0.001   TYR S 102 
 ARG   0.009   0.001   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  392)
  hydrogen bonds       : angle       4.79910 ( 1107)
  SS BOND              : bond        0.00143 (    4)
  SS BOND              : angle       3.31677 (    8)
  covalent geometry    : bond        0.00351 ( 8878)
  covalent geometry    : angle       0.77550 (12023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3741.77 seconds
wall clock time: 67 minutes 36.91 seconds (4056.91 seconds total)