Starting phenix.real_space_refine
on Wed Feb  4 02:11:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u9v_63971/02_2026/9u9v_63971.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.036
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      55      5.16       5
     C    5254      2.51       5
     N    1436      2.21       5
     O    1530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8275
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1947
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2603
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 442
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2299
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'B40': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.56, per 1000 atoms: 0.19
  Number of scatterers: 8275
  At special positions: 0
  Unit cell: (76.59, 103.822, 136.16, 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      55     16.00
     O    1530      8.00
     N    1436      7.00
     C    5254      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 287.1 milliseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  B40 R 401 "
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      43.0% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.866A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.519A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.520A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.844A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.568A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.965A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 36
      removed outlier: 3.902A  pdb=" N   GLN B  20 " --> pdb=" O   ASP B  16 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 45
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 3.924A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.579A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.830A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.571A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE R  55 " --> pdb=" O   ASN R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 86
      removed outlier: 3.649A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.509A  pdb=" N   THR R 110 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 3.835A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.673A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 201 through 208
    Processing helix  chain 'R' and resid 208 through 238
      removed outlier: 3.551A  pdb=" N   GLN R 229 " --> pdb=" O   GLU R 225 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS R 235 " --> pdb=" O   GLN R 231 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.771A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR R 283 " --> pdb=" O   MET R 279 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LEU R 284 " --> pdb=" O   GLY R 280 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.556A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 315
      removed outlier: 3.632A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 321
    Processing helix  chain 'R' and resid 322 through 327
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.535A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 3.924A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 62
      removed outlier: 6.334A  pdb=" N   THR B  58 " --> pdb=" O   ASN B 351 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ASN B 351 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   CYS B 328 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74
      removed outlier: 6.829A  pdb=" N   ALA B  84 " --> pdb=" O   TYR B  70 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   MET B  72 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL B  82 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP B  74 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   LEU B  80 " --> pdb=" O   TRP B  74 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ASP B  94 " --> pdb=" O   LYS B 100 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   LYS B 100 " --> pdb=" O   ASP B  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 116
      removed outlier: 7.078A  pdb=" N   GLY B 126 " --> pdb=" O   MET B 112 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 114 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ALA B 124 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 122 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   TYR B 122 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   CYS B 132 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU B 149 " --> pdb=" O   CYS B 132 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE B 134 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN B 136 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ARG B 145 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 163
      removed outlier: 6.672A  pdb=" N   SER B 171 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   CYS B 160 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   VAL B 169 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   PHE B 162 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   GLN B 167 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   THR B 176 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   ASP B 181 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   GLN B 187 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203
      removed outlier: 6.999A  pdb=" N   GLY B 213 " --> pdb=" O   MET B 199 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU B 201 " --> pdb=" O   VAL B 211 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B 211 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   LEU B 209 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA B 219 " --> pdb=" O   THR B 232 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   THR B 232 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LEU B 221 " --> pdb=" O   ARG B 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245
      removed outlier: 6.613A  pdb=" N   CYS B 261 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   THR B 274 " --> pdb=" O   CYS B 261 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU B 263 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 270 " --> pdb=" O   ASP B 265 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289
      removed outlier: 3.592A  pdb=" N   SER B 286 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   CYS B 305 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL B 318 " --> pdb=" O   CYS B 305 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 307 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.079A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1128 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.86

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1688
        1.33 -     1.45: 2055
        1.45 -     1.57: 4624
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 8445
  Sorted by residual:
  bond pdb=" C   SER B 256 "
       pdb=" O   SER B 256 "
    ideal  model  delta    sigma   weight residual
    1.235  1.207  0.028 1.28e-02 6.10e+03 4.72e+00
  bond pdb=" C   ASP B 257 "
       pdb=" O   ASP B 257 "
    ideal  model  delta    sigma   weight residual
    1.236  1.210  0.026 1.29e-02 6.01e+03 3.95e+00
  bond pdb=" CA  SER B 256 "
       pdb=" CB  SER B 256 "
    ideal  model  delta    sigma   weight residual
    1.534  1.505  0.029 1.57e-02 4.06e+03 3.37e+00
  bond pdb=" CB  ASP B 258 "
       pdb=" CG  ASP B 258 "
    ideal  model  delta    sigma   weight residual
    1.516  1.472  0.044 2.50e-02 1.60e+03 3.16e+00
  bond pdb=" CA  ASP B 257 "
       pdb=" CB  ASP B 257 "
    ideal  model  delta    sigma   weight residual
    1.529  1.500  0.029 1.74e-02 3.30e+03 2.80e+00
  ... (remaining 8440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11335
        2.17 -     4.33: 83
        4.33 -     6.50: 14
        6.50 -     8.67: 1
        8.67 -    10.84: 1
  Bond angle restraints: 11434
  Sorted by residual:
  angle pdb=" N   SER B 256 "
        pdb=" CA  SER B 256 "
        pdb=" C   SER B 256 "
      ideal   model   delta    sigma   weight residual
     108.86  119.70  -10.84 1.41e+00 5.03e-01 5.91e+01
  angle pdb=" C   SER B 256 "
        pdb=" CA  SER B 256 "
        pdb=" CB  SER B 256 "
      ideal   model   delta    sigma   weight residual
     111.65  104.47    7.18 2.40e+00 1.74e-01 8.94e+00
  angle pdb=" C   ASP B 258 "
        pdb=" N   ALA B 259 "
        pdb=" CA  ALA B 259 "
      ideal   model   delta    sigma   weight residual
     121.54  126.80   -5.26 1.91e+00 2.74e-01 7.58e+00
  angle pdb=" C   GLN A 262 "
        pdb=" N   THR A 263 "
        pdb=" CA  THR A 263 "
      ideal   model   delta    sigma   weight residual
     121.54  126.46   -4.92 1.91e+00 2.74e-01 6.65e+00
  angle pdb=" N   GLY R 320 "
        pdb=" CA  GLY R 320 "
        pdb=" C   GLY R 320 "
      ideal   model   delta    sigma   weight residual
     115.66  111.95    3.71 1.56e+00 4.11e-01 5.64e+00
  ... (remaining 11429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 4550
       16.80 -    33.59: 368
       33.59 -    50.39: 78
       50.39 -    67.19: 11
       67.19 -    83.98: 16
  Dihedral angle restraints: 5023
    sinusoidal: 1986
      harmonic: 3037
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.78   79.78     1      1.00e+01 1.00e-02 7.90e+01
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.88  -43.88     1      1.00e+01 1.00e-02 2.68e+01
  dihedral pdb=" CA  LYS B  89 "
           pdb=" C   LYS B  89 "
           pdb=" N   LEU B  90 "
           pdb=" CA  LEU B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.60   20.40     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 861
       0.038 -    0.075: 312
       0.075 -    0.113: 83
       0.113 -    0.150: 24
       0.150 -    0.188: 3
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" CA  B40 R 401 "
            pdb=" N   B40 R 401 "
            pdb=" C   B40 R 401 "
            pdb=" CB  B40 R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.61    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CA  GLU A  21 "
            pdb=" N   GLU A  21 "
            pdb=" C   GLU A  21 "
            pdb=" CB  GLU A  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  chirality pdb=" CA  VAL N  37 "
            pdb=" N   VAL N  37 "
            pdb=" C   VAL N  37 "
            pdb=" CB  VAL N  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.81e-01
  ... (remaining 1280 not shown)

  Planarity restraints: 1457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA N  40 "    0.046 5.00e-02 4.00e+02   6.97e-02 7.78e+00
        pdb=" N   PRO N  41 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO N  41 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO N  41 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 246 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO B 247 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 255 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.81e+00
        pdb=" C   GLY B 255 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLY B 255 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER B 256 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1454 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1886
        2.79 -     3.32: 7379
        3.32 -     3.84: 13143
        3.84 -     4.37: 15916
        4.37 -     4.90: 28141
  Nonbonded interactions: 66465
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 204 "
            pdb=" OD1 ASN R 293 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 197 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OE2 GLU R 225 "
            pdb=" NH2 ARG R 228 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER B 292 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.322 3.040
  ... (remaining 66460 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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      :  0.003   0.044   8448  Z= 0.128
  Angle     :  0.533  10.836  11440  Z= 0.298
  Chirality :  0.043   0.188   1283
  Planarity :  0.004   0.070   1457
  Dihedral  : 13.614  83.984   3048
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.45 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.26), residues: 1028
  helix:  1.69 (0.27), residues: 391
  sheet:  0.86 (0.34), residues: 224
  loop : -0.71 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 140 
 TYR   0.036   0.001   TYR B  70 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.024   0.001   TRP B  93 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8445)
  covalent geometry    : angle       0.53269 (11434)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       0.90593 (    6)
  hydrogen bonds       : bond        0.16666 (  396)
  hydrogen bonds       : angle       6.39132 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.325 
Fit side-chains
REVERT: R  284 LEU cc_start: 0.8194 (tp) cc_final: 0.7947 (tp)
  outliers start: 1
  outliers final: 2
  residues processed: 132
  average time/residue: 0.6143
  time to fit residues: 85.4025
Evaluate side-chains
  100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain R residue  309 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 294 GLN
A 384 GLN
N 120 GLN
R 197 GLN
R 293 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.161724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.119218 restraints weight = 8714.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.88
r_work: 0.3065 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8448  Z= 0.171
  Angle     :  0.570   7.012  11440  Z= 0.307
  Chirality :  0.044   0.149   1283
  Planarity :  0.005   0.057   1457
  Dihedral  :  4.866  38.360   1143
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.39 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1028
  helix:  1.84 (0.26), residues: 404
  sheet:  1.02 (0.36), residues: 215
  loop : -0.82 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 107 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.025   0.002   TRP B  93 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8445)
  covalent geometry    : angle       0.56957 (11434)
  SS BOND              : bond        0.00599 (    3)
  SS BOND              : angle       1.23854 (    6)
  hydrogen bonds       : bond        0.05367 (  396)
  hydrogen bonds       : angle       4.65931 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.7594 (ttmm) cc_final: 0.7340 (ttmt)
REVERT: B   57 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8153 (mtm180)
REVERT: B  129 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6940 (p0)
REVERT: B  145 ARG cc_start: 0.7064 (ttp-170) cc_final: 0.6807 (ttm170)
REVERT: B  146 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (p)
REVERT: R  234 ASP cc_start: 0.7816 (m-30) cc_final: 0.7586 (t0)
REVERT: R  284 LEU cc_start: 0.8001 (tp) cc_final: 0.7662 (tp)
  outliers start: 16
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6189
  time to fit residues: 69.9822
Evaluate side-chains
  111 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0040
   chunk 38 optimal weight:    0.1980
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 94 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.164956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.121880 restraints weight = 8667.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.87
r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8448  Z= 0.103
  Angle     :  0.471   4.938  11440  Z= 0.258
  Chirality :  0.041   0.136   1283
  Planarity :  0.004   0.059   1457
  Dihedral  :  4.325  23.173   1139
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.96 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1028
  helix:  2.28 (0.27), residues: 399
  sheet:  0.90 (0.35), residues: 224
  loop : -0.76 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 107 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.025   0.001   TRP B  93 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8445)
  covalent geometry    : angle       0.47068 (11434)
  SS BOND              : bond        0.00466 (    3)
  SS BOND              : angle       0.86742 (    6)
  hydrogen bonds       : bond        0.04120 (  396)
  hydrogen bonds       : angle       4.25774 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8108 (mtm180)
REVERT: B  129 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6895 (p0)
REVERT: B  146 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8344 (p)
REVERT: R  172 HIS cc_start: 0.8583 (m-70) cc_final: 0.8298 (m-70)
REVERT: R  228 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7577 (ttp80)
REVERT: R  284 LEU cc_start: 0.8011 (tp) cc_final: 0.7735 (tp)
  outliers start: 18
  outliers final: 4
  residues processed: 114
  average time/residue: 0.5787
  time to fit residues: 69.7467
Evaluate side-chains
  109 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 186 GLN
N   1 GLN
R 197 GLN
R 296 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.160364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.117757 restraints weight = 8866.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.88
r_work: 0.3046 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8448  Z= 0.188
  Angle     :  0.586   7.892  11440  Z= 0.313
  Chirality :  0.045   0.151   1283
  Planarity :  0.004   0.056   1457
  Dihedral  :  4.657  26.896   1139
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.74 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.26), residues: 1028
  helix:  2.04 (0.26), residues: 400
  sheet:  0.93 (0.34), residues: 220
  loop : -0.82 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 107 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.017   0.002   PHE A 212 
 TRP   0.022   0.002   TRP B  93 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 8445)
  covalent geometry    : angle       0.58569 (11434)
  SS BOND              : bond        0.00665 (    3)
  SS BOND              : angle       1.04344 (    6)
  hydrogen bonds       : bond        0.05267 (  396)
  hydrogen bonds       : angle       4.41893 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (mtm180)
REVERT: B  129 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7086 (p0)
REVERT: B  146 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (p)
REVERT: B  225 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8019 (mpt-90)
REVERT: B  228 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7449 (pp-130)
REVERT: R  228 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7199 (ttm-80)
REVERT: R  284 LEU cc_start: 0.8005 (tp) cc_final: 0.7712 (tp)
  outliers start: 25
  outliers final: 10
  residues processed: 112
  average time/residue: 0.6492
  time to fit residues: 76.5856
Evaluate side-chains
  114 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
R 197 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.159229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.116732 restraints weight = 8758.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.87
r_work: 0.3034 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   8448  Z= 0.231
  Angle     :  0.621   8.092  11440  Z= 0.332
  Chirality :  0.046   0.150   1283
  Planarity :  0.005   0.057   1457
  Dihedral  :  4.806  27.391   1139
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.30 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 1028
  helix:  1.88 (0.26), residues: 399
  sheet:  0.86 (0.34), residues: 220
  loop : -0.88 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R  63 
 TYR   0.012   0.002   TYR A 339 
 PHE   0.016   0.002   PHE A 222 
 TRP   0.024   0.002   TRP B  93 
 HIS   0.010   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 8445)
  covalent geometry    : angle       0.62118 (11434)
  SS BOND              : bond        0.00795 (    3)
  SS BOND              : angle       1.04855 (    6)
  hydrogen bonds       : bond        0.05604 (  396)
  hydrogen bonds       : angle       4.48890 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  344 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8244 (mm-30)
REVERT: B   57 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (mtm180)
REVERT: B  107 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8148 (ttm-80)
REVERT: B  129 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7110 (p0)
REVERT: B  146 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8283 (p)
REVERT: B  225 ARG cc_start: 0.8215 (mpp80) cc_final: 0.7922 (mpt-90)
REVERT: B  228 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7480 (pp-130)
REVERT: R  175 ARG cc_start: 0.8361 (mmt180) cc_final: 0.7517 (mmt180)
REVERT: R  228 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7213 (ttm-80)
REVERT: R  284 LEU cc_start: 0.8001 (tp) cc_final: 0.7695 (tp)
  outliers start: 23
  outliers final: 12
  residues processed: 113
  average time/residue: 0.5966
  time to fit residues: 71.3062
Evaluate side-chains
  117 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0060
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
R 296 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.163098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.120987 restraints weight = 8758.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.89
r_work: 0.3094 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8448  Z= 0.110
  Angle     :  0.491   5.713  11440  Z= 0.266
  Chirality :  0.041   0.134   1283
  Planarity :  0.004   0.059   1457
  Dihedral  :  4.387  24.145   1139
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 12.63 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.26), residues: 1028
  helix:  2.22 (0.26), residues: 400
  sheet:  0.94 (0.34), residues: 222
  loop : -0.84 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R  63 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.025   0.002   TRP B  93 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8445)
  covalent geometry    : angle       0.49035 (11434)
  SS BOND              : bond        0.00507 (    3)
  SS BOND              : angle       0.84743 (    6)
  hydrogen bonds       : bond        0.04129 (  396)
  hydrogen bonds       : angle       4.15575 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.275 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8163 (mtm180)
REVERT: B  107 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8147 (ttm-80)
REVERT: B  129 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6890 (p0)
REVERT: B  146 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (p)
REVERT: B  225 ARG cc_start: 0.8248 (mpp80) cc_final: 0.7950 (mpt-90)
REVERT: B  228 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7420 (pp-130)
REVERT: R  172 HIS cc_start: 0.8646 (m-70) cc_final: 0.8339 (m-70)
REVERT: R  228 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7168 (ttm-80)
REVERT: R  239 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7015 (mtm-85)
REVERT: R  284 LEU cc_start: 0.7952 (tp) cc_final: 0.7685 (tp)
  outliers start: 29
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5250
  time to fit residues: 68.4592
Evaluate side-chains
  117 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.163318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.121248 restraints weight = 8791.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.87
r_work: 0.3166 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8448  Z= 0.113
  Angle     :  0.494   6.026  11440  Z= 0.267
  Chirality :  0.041   0.135   1283
  Planarity :  0.004   0.058   1457
  Dihedral  :  4.322  24.245   1139
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.41 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.26), residues: 1028
  helix:  2.31 (0.26), residues: 400
  sheet:  0.98 (0.34), residues: 222
  loop : -0.81 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R  63 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 222 
 TRP   0.023   0.001   TRP B  93 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8445)
  covalent geometry    : angle       0.49389 (11434)
  SS BOND              : bond        0.00489 (    3)
  SS BOND              : angle       0.80841 (    6)
  hydrogen bonds       : bond        0.04125 (  396)
  hydrogen bonds       : angle       4.11269 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   32 LYS cc_start: 0.7587 (ttmm) cc_final: 0.7370 (ttmt)
REVERT: A   60 MET cc_start: 0.5311 (mmp) cc_final: 0.3854 (mpm)
REVERT: B   57 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8111 (mtm180)
REVERT: B  129 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.6882 (p0)
REVERT: B  225 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7910 (mpt-90)
REVERT: B  228 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7429 (pp-130)
REVERT: R  172 HIS cc_start: 0.8671 (m-70) cc_final: 0.8377 (m-70)
REVERT: R  228 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7193 (ttm-80)
REVERT: R  239 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.7125 (mtm-85)
REVERT: R  284 LEU cc_start: 0.7996 (tp) cc_final: 0.7733 (tp)
  outliers start: 27
  outliers final: 14
  residues processed: 120
  average time/residue: 0.5281
  time to fit residues: 67.0654
Evaluate side-chains
  120 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue   70 TYR
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  225 ARG
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 6 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0970
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.161405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.119099 restraints weight = 8767.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.87
r_work: 0.3066 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8448  Z= 0.151
  Angle     :  0.537   6.797  11440  Z= 0.289
  Chirality :  0.043   0.145   1283
  Planarity :  0.004   0.057   1457
  Dihedral  :  4.495  25.419   1139
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.63 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.26), residues: 1028
  helix:  2.24 (0.26), residues: 400
  sheet:  1.02 (0.34), residues: 220
  loop : -0.80 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 107 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.016   0.001   PHE A 222 
 TRP   0.023   0.002   TRP B  93 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8445)
  covalent geometry    : angle       0.53710 (11434)
  SS BOND              : bond        0.00592 (    3)
  SS BOND              : angle       0.86684 (    6)
  hydrogen bonds       : bond        0.04664 (  396)
  hydrogen bonds       : angle       4.21628 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7017 (mp0)
REVERT: A   32 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7362 (ttmt)
REVERT: A   60 MET cc_start: 0.5242 (mmp) cc_final: 0.3814 (mpm)
REVERT: B   57 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8176 (mtm180)
REVERT: B  129 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6959 (p0)
REVERT: B  228 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7435 (pp-130)
REVERT: R  172 HIS cc_start: 0.8655 (m-70) cc_final: 0.8353 (m-70)
REVERT: R  228 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7190 (ttm-80)
REVERT: R  239 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7119 (mtm-85)
REVERT: R  284 LEU cc_start: 0.7998 (tp) cc_final: 0.7729 (tp)
  outliers start: 30
  outliers final: 15
  residues processed: 118
  average time/residue: 0.5475
  time to fit residues: 68.3630
Evaluate side-chains
  118 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.161532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.119174 restraints weight = 8753.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.88
r_work: 0.3067 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8448  Z= 0.147
  Angle     :  0.534   6.959  11440  Z= 0.287
  Chirality :  0.043   0.144   1283
  Planarity :  0.004   0.057   1457
  Dihedral  :  4.482  24.791   1139
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.86 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.26), residues: 1028
  helix:  2.24 (0.26), residues: 400
  sheet:  1.13 (0.34), residues: 218
  loop : -0.83 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 107 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 222 
 TRP   0.023   0.002   TRP B  93 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8445)
  covalent geometry    : angle       0.53378 (11434)
  SS BOND              : bond        0.00581 (    3)
  SS BOND              : angle       0.86199 (    6)
  hydrogen bonds       : bond        0.04603 (  396)
  hydrogen bonds       : angle       4.21959 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7107 (mp0)
REVERT: A   60 MET cc_start: 0.5201 (mmp) cc_final: 0.3761 (mpm)
REVERT: B   57 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8177 (mtm180)
REVERT: B  107 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8117 (ttm-80)
REVERT: B  129 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.6991 (p0)
REVERT: B  225 ARG cc_start: 0.8214 (mpp80) cc_final: 0.7829 (mpt-90)
REVERT: B  228 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7446 (pp-130)
REVERT: R  228 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7166 (ttm-80)
REVERT: R  239 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7132 (mtm-85)
REVERT: R  284 LEU cc_start: 0.8004 (tp) cc_final: 0.7722 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 113
  average time/residue: 0.6234
  time to fit residues: 74.5049
Evaluate side-chains
  115 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 304 ASN
R 197 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.164401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.123599 restraints weight = 8719.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.79
r_work: 0.3117 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8448  Z= 0.108
  Angle     :  0.492   6.852  11440  Z= 0.266
  Chirality :  0.041   0.137   1283
  Planarity :  0.004   0.058   1457
  Dihedral  :  4.267  22.060   1139
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.64 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.26), residues: 1028
  helix:  2.40 (0.26), residues: 400
  sheet:  1.03 (0.34), residues: 222
  loop : -0.80 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 107 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.023   0.001   TRP B  93 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8445)
  covalent geometry    : angle       0.49138 (11434)
  SS BOND              : bond        0.00473 (    3)
  SS BOND              : angle       0.76197 (    6)
  hydrogen bonds       : bond        0.03987 (  396)
  hydrogen bonds       : angle       4.07029 ( 1128)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   21 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7132 (mp0)
REVERT: A   32 LYS cc_start: 0.7611 (ttmm) cc_final: 0.7329 (ttmt)
REVERT: A   60 MET cc_start: 0.5176 (mmp) cc_final: 0.3720 (mpm)
REVERT: B   57 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8166 (mtm180)
REVERT: B  107 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8097 (ttm-80)
REVERT: B  129 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6873 (p0)
REVERT: B  225 ARG cc_start: 0.8194 (mpp80) cc_final: 0.7936 (mpt-90)
REVERT: B  228 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7423 (pp-130)
REVERT: R  228 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7192 (ttm-80)
REVERT: R  239 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7178 (mtm-85)
REVERT: R  284 LEU cc_start: 0.8010 (tp) cc_final: 0.7750 (tp)
  outliers start: 24
  outliers final: 14
  residues processed: 119
  average time/residue: 0.5379
  time to fit residues: 67.9537
Evaluate side-chains
  120 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   57 ARG
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  254 THR
Chi-restraints excluded: chain B residue  281 ILE
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  112 ILE
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  294 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0020
   chunk 96 optimal weight:    0.6980
   chunk 23 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
R 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.162230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.120035 restraints weight = 8737.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.88
r_work: 0.3078 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8448  Z= 0.131
  Angle     :  0.518   6.273  11440  Z= 0.278
  Chirality :  0.042   0.139   1283
  Planarity :  0.004   0.057   1457
  Dihedral  :  4.355  23.090   1139
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.64 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1028
  helix:  2.32 (0.26), residues: 399
  sheet:  1.11 (0.34), residues: 218
  loop : -0.82 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 107 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 222 
 TRP   0.023   0.002   TRP B  93 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8445)
  covalent geometry    : angle       0.51782 (11434)
  SS BOND              : bond        0.00528 (    3)
  SS BOND              : angle       0.80540 (    6)
  hydrogen bonds       : bond        0.04356 (  396)
  hydrogen bonds       : angle       4.13414 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2944.88 seconds
wall clock time: 50 minutes 47.45 seconds (3047.45 seconds total)