Starting phenix.real_space_refine
on Tue Mar  3 20:31:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6whc_21671/03_2026/6whc_21671.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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    5528      2.51       5
     N    1528      2.21       5
     O    1598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8709
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1823
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 6, 'TRANS': 212}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2547
          Classifications: {'peptide': 332}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
    Chain: "C"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 363
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 4, 'TRANS': 42}
    Chain: "E"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 238
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    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: 2765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2765
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 355}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 276
          Unresolved non-hydrogen angles: 361
          Unresolved non-hydrogen dihedrals: 244
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'TRP:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 6}
          Unresolved non-hydrogen planarities: 186
  Time building chain proxies: 2.03, per 1000 atoms: 0.23
  Number of scatterers: 8709
  At special positions: 0
  Unit cell: (92.13, 101.26, 161.85, 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    1598      8.00
     N    1528      7.00
     C    5528      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " 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: 0.72
  Conformation dependent library (CDL) restraints added in 324.7 milliseconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 11 sheets defined
      37.0% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 3.596A  pdb=" N   ASN A  14 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.812A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.913A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 304
      removed outlier: 3.654A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.591A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 333 through 350
      removed outlier: 3.536A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.703A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 25
      removed outlier: 3.792A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.551A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 29
      removed outlier: 3.551A  pdb=" N   GLU E  16 " --> pdb=" O   LYS E  12 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA E  18 " --> pdb=" O   LEU E  14 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA E  19 " --> pdb=" O   ASP E  15 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LYS E  20 " --> pdb=" O   GLU E  16 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU E  21 " --> pdb=" O   GLN E  17 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TRP E  25 " --> pdb=" O   GLU E  21 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU E  26 " --> pdb=" O   PHE E  22 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.928A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 28 through 39
      removed outlier: 3.985A  pdb=" N   GLU R  34 " --> pdb=" O   ASP R  30 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS R  37 " --> pdb=" O   PHE R  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 40 through 50
      removed outlier: 3.560A  pdb=" N   HIS R  44 " --> pdb=" O   GLY R  40 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU R  47 " --> pdb=" O   CYS R  43 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER R  48 " --> pdb=" O   HIS R  44 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU R  49 " --> pdb=" O   HIS R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 163
      removed outlier: 3.781A  pdb=" N   MET R 144 " --> pdb=" O   SER R 140 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR R 146 " --> pdb=" O   GLN R 142 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL R 147 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA R 155 " --> pdb=" O   LEU R 151 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LEU R 158 " --> pdb=" O   GLY R 154 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA R 161 " --> pdb=" O   LEU R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 202
      removed outlier: 3.822A  pdb=" N   LYS R 187 " --> pdb=" O   SER R 183 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   SER R 190 " --> pdb=" O   LEU R 186 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG R 201 " --> pdb=" O   LEU R 197 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR R 202 " --> pdb=" O   LEU R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 255
      removed outlier: 3.632A  pdb=" N   VAL R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA R 222 " --> pdb=" O   ASP R 218 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY R 223 " --> pdb=" O   GLY R 219 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE R 230 " --> pdb=" O   VAL R 226 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TRP R 241 " --> pdb=" O   ALA R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 277
      removed outlier: 4.020A  pdb=" N   ALA R 274 " --> pdb=" O   ILE R 270 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 278 through 289
      removed outlier: 3.563A  pdb=" N   VAL R 285 " --> pdb=" O   PRO R 281 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU R 288 " --> pdb=" O   VAL R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 330
      Proline residue:  R 310  - end of helix
      removed outlier: 3.515A  pdb=" N   ILE R 315 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASN R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 344 through 348
    Processing helix  chain 'R' and resid 361 through 365
      removed outlier: 3.632A  pdb=" N   VAL R 364 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 400
      removed outlier: 3.977A  pdb=" N   LEU R 388 " --> pdb=" O   PHE R 384 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL R 396 " --> pdb=" O   GLN R 392 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA R 397 " --> pdb=" O   GLY R 393 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 418
      removed outlier: 3.880A  pdb=" N   GLU R 410 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG R 417 " --> pdb=" O   ARG R 413 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213
      removed outlier: 3.627A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 9.375A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.365A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50
      removed outlier: 3.551A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.565A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.308A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.673A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.277A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.525A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.539A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.602A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.709A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 77 through 80
      removed outlier: 4.194A  pdb=" N   VAL R  96 " --> pdb=" O   ILE R  79 " (cutoff:3.500A)

    344 hydrogen bonds defined for protein.
    984 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: 1.34

  Time building geometry restraints manager: 0.97 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: 1779
        1.33 -     1.45: 2177
        1.45 -     1.57: 4865
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8897
  Sorted by residual:
  bond pdb=" N   ALA N 101 "
       pdb=" CA  ALA N 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.029 8.30e-03 1.45e+04 1.26e+01
  bond pdb=" CA  ALA N 101 "
       pdb=" CB  ALA N 101 "
    ideal  model  delta    sigma   weight residual
    1.536  1.501  0.035 1.23e-02 6.61e+03 8.30e+00
  bond pdb=" N   ASP N 109 "
       pdb=" CA  ASP N 109 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.22e-02 6.72e+03 7.78e+00
  bond pdb=" N   CYS N 107 "
       pdb=" CA  CYS N 107 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.23e-02 6.61e+03 7.50e+00
  bond pdb=" N   ARG R 378 "
       pdb=" CA  ARG R 378 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.31e+00
  ... (remaining 8892 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 11546
        1.73 -     3.45: 446
        3.45 -     5.18: 46
        5.18 -     6.90: 16
        6.90 -     8.63: 8
  Bond angle restraints: 12062
  Sorted by residual:
  angle pdb=" C   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" CB  ASP N 109 "
      ideal   model   delta    sigma   weight residual
     111.18  104.50    6.68 1.56e+00 4.11e-01 1.83e+01
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     123.05  128.74   -5.69 1.57e+00 4.06e-01 1.31e+01
  angle pdb=" N   LYS R 349 "
        pdb=" CA  LYS R 349 "
        pdb=" C   LYS R 349 "
      ideal   model   delta    sigma   weight residual
     114.56  110.01    4.55 1.27e+00 6.20e-01 1.28e+01
  angle pdb=" C   THR A 369 "
        pdb=" N   GLU A 370 "
        pdb=" CA  GLU A 370 "
      ideal   model   delta    sigma   weight residual
     121.54  128.18   -6.64 1.91e+00 2.74e-01 1.21e+01
  angle pdb=" N   GLU E  21 "
        pdb=" CA  GLU E  21 "
        pdb=" C   GLU E  21 "
      ideal   model   delta    sigma   weight residual
     111.07  107.53    3.54 1.07e+00 8.73e-01 1.09e+01
  ... (remaining 12057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4698
       17.79 -    35.58: 480
       35.58 -    53.38: 66
       53.38 -    71.17: 15
       71.17 -    88.96: 11
  Dihedral angle restraints: 5270
    sinusoidal: 2007
      harmonic: 3263
  Sorted by residual:
  dihedral pdb=" CB  CYS R  58 "
           pdb=" SG  CYS R  58 "
           pdb=" SG  CYS R 100 "
           pdb=" CB  CYS R 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.52   79.52     1      1.00e+01 1.00e-02 7.85e+01
  dihedral pdb=" CA  ILE R 355 "
           pdb=" C   ILE R 355 "
           pdb=" N   PRO R 356 "
           pdb=" CA  PRO R 356 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.59  -24.41     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" SG  CYS R 294 "
           pdb=" CB  CYS R 294 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.20  -40.20     1      1.00e+01 1.00e-02 2.27e+01
  ... (remaining 5267 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1074
       0.058 -    0.116: 218
       0.116 -    0.174: 42
       0.174 -    0.232: 9
       0.232 -    0.290: 2
  Chirality restraints: 1345
  Sorted by residual:
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  GLU B 130 "
            pdb=" N   GLU B 130 "
            pdb=" C   GLU B 130 "
            pdb=" CB  GLU B 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  ASP N 109 "
            pdb=" N   ASP N 109 "
            pdb=" C   ASP N 109 "
            pdb=" CB  ASP N 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1342 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.044 5.00e-02 4.00e+02   6.72e-02 7.24e+00
        pdb=" N   PRO B 236 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 274 "   -0.041 5.00e-02 4.00e+02   6.18e-02 6.11e+00
        pdb=" N   PRO R 275 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO R 275 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 275 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  54 "    0.040 5.00e-02 4.00e+02   6.00e-02 5.76e+00
        pdb=" N   PRO C  55 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1679
        2.77 -     3.30: 7669
        3.30 -     3.84: 14504
        3.84 -     4.37: 16487
        4.37 -     4.90: 28357
  Nonbonded interactions: 68696
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 130 "
            pdb=" OE1 GLU B 130 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.302 3.040
  ... (remaining 68691 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=0.00 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:             1.180
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.320
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8902  Z= 0.236
  Angle     :  0.789   8.629  12072  Z= 0.471
  Chirality :  0.051   0.290   1345
  Planarity :  0.006   0.067   1548
  Dihedral  : 14.512  88.960   3143
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  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: -4.67 (0.20), residues: 1104
  helix: -4.41 (0.10), residues: 392
  sheet: -2.10 (0.35), residues: 197
  loop : -2.25 (0.24), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 336 
 TYR   0.010   0.001   TYR N  32 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8897)
  covalent geometry    : angle       0.78772 (12062)
  SS BOND              : bond        0.00477 (    5)
  SS BOND              : angle       1.54125 (   10)
  hydrogen bonds       : bond        0.28397 (  344)
  hydrogen bonds       : angle      10.59389 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8439 (pt0) cc_final: 0.8002 (mt0)
REVERT: C   29 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8501 (mtpp)
REVERT: E    9 ASP cc_start: 0.9154 (t0) cc_final: 0.8911 (t70)
REVERT: E   10 TYR cc_start: 0.8823 (t80) cc_final: 0.8564 (t80)
REVERT: E   14 LEU cc_start: 0.9072 (mt) cc_final: 0.8866 (mt)
REVERT: N   43 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7761 (mtpp)
REVERT: N   86 LEU cc_start: 0.9079 (mm) cc_final: 0.8492 (tt)
REVERT: R  231 MET cc_start: 0.8932 (tmm) cc_final: 0.8181 (tmm)
REVERT: R  238 ASN cc_start: 0.8061 (t0) cc_final: 0.7799 (t0)
REVERT: R  290 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7711 (mm-30)
REVERT: R  298 ASN cc_start: 0.7889 (t0) cc_final: 0.6980 (t0)
REVERT: R  301 MET cc_start: 0.7712 (mmm) cc_final: 0.6959 (mmp)
REVERT: R  362 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7067 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.1011
  time to fit residues: 27.1036
Evaluate side-chains
  145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  23 ASN
A 267 GLN
B  62 HIS
B 119 ASN
B 293 ASN
B 295 ASN
C  18 GLN
E   3 GLN
E  28 ASN
N  31 ASN
R  46 ASN
R 392 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.121392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.084693 restraints weight = 17227.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.33
r_work: 0.3169 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8902  Z= 0.229
  Angle     :  0.662   8.979  12072  Z= 0.348
  Chirality :  0.044   0.203   1345
  Planarity :  0.005   0.049   1548
  Dihedral  :  4.917  27.754   1216
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.00 %
    Favored  : 82.22 %
  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: -2.91 (0.23), residues: 1104
  helix: -2.16 (0.20), residues: 395
  sheet: -1.84 (0.34), residues: 209
  loop : -1.59 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  96 
 TYR   0.032   0.002   TYR R 145 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 8897)
  covalent geometry    : angle       0.65979 (12062)
  SS BOND              : bond        0.00250 (    5)
  SS BOND              : angle       2.05404 (   10)
  hydrogen bonds       : bond        0.05197 (  344)
  hydrogen bonds       : angle       5.71361 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   21 MET cc_start: 0.5625 (ptt) cc_final: 0.5084 (ppp)
REVERT: C   29 LYS cc_start: 0.8985 (mtmm) cc_final: 0.8530 (mtpp)
REVERT: N   43 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7887 (mmmt)
REVERT: R  231 MET cc_start: 0.9011 (tmm) cc_final: 0.8528 (tmm)
REVERT: R  290 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: R  298 ASN cc_start: 0.7992 (t0) cc_final: 0.7008 (t0)
REVERT: R  301 MET cc_start: 0.7639 (mmm) cc_final: 0.7058 (mmp)
REVERT: R  362 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7272 (tm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 158
  average time/residue: 0.0997
  time to fit residues: 21.3875
Evaluate side-chains
  138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue    7 THR
Chi-restraints excluded: chain E residue   12 LYS
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain R residue  244 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 76 optimal weight:   50.0000
   chunk 50 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0970
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 259 GLN
B 295 ASN
B 340 ASN
C  59 ASN
R 238 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.121985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.084491 restraints weight = 17199.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.37
r_work: 0.3197 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8902  Z= 0.157
  Angle     :  0.580   7.838  12072  Z= 0.303
  Chirality :  0.042   0.192   1345
  Planarity :  0.004   0.045   1548
  Dihedral  :  4.649  31.277   1216
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.78 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -1.87 (0.24), residues: 1104
  helix: -0.77 (0.25), residues: 395
  sheet: -1.71 (0.34), residues: 211
  loop : -1.25 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  72 
 TYR   0.023   0.001   TYR R 145 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8897)
  covalent geometry    : angle       0.57856 (12062)
  SS BOND              : bond        0.00120 (    5)
  SS BOND              : angle       1.39356 (   10)
  hydrogen bonds       : bond        0.04016 (  344)
  hydrogen bonds       : angle       4.95743 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8606 (tpt170) cc_final: 0.8111 (mmm160)
REVERT: A   35 GLN cc_start: 0.8851 (pt0) cc_final: 0.8325 (mt0)
REVERT: C   59 ASN cc_start: 0.8531 (t0) cc_final: 0.8293 (t0)
REVERT: N   89 GLU cc_start: 0.8876 (pm20) cc_final: 0.8556 (pm20)
REVERT: R  231 MET cc_start: 0.8978 (tmm) cc_final: 0.8666 (tmm)
REVERT: R  241 TRP cc_start: 0.8627 (t-100) cc_final: 0.7723 (m-90)
REVERT: R  245 GLU cc_start: 0.9173 (tp30) cc_final: 0.8500 (tp30)
REVERT: R  290 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8082 (mm-30)
REVERT: R  298 ASN cc_start: 0.7935 (t0) cc_final: 0.7292 (t0)
REVERT: R  301 MET cc_start: 0.7643 (mmm) cc_final: 0.7168 (mmp)
REVERT: R  362 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7216 (tm-30)
  outliers start: 23
  outliers final: 12
  residues processed: 157
  average time/residue: 0.0919
  time to fit residues: 20.2442
Evaluate side-chains
  147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 89 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0870
   chunk 92 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.124357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.086953 restraints weight = 17341.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 3.38
r_work: 0.3241 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8902  Z= 0.106
  Angle     :  0.540   8.061  12072  Z= 0.280
  Chirality :  0.042   0.184   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.348  30.951   1216
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.89 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -1.36 (0.25), residues: 1104
  helix: -0.14 (0.26), residues: 396
  sheet: -1.65 (0.34), residues: 209
  loop : -1.05 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.009   0.001   TYR B 111 
 PHE   0.014   0.001   PHE E  22 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8897)
  covalent geometry    : angle       0.53872 (12062)
  SS BOND              : bond        0.00116 (    5)
  SS BOND              : angle       1.26640 (   10)
  hydrogen bonds       : bond        0.03418 (  344)
  hydrogen bonds       : angle       4.52640 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8597 (tpt170) cc_final: 0.8114 (mmm160)
REVERT: A   35 GLN cc_start: 0.8827 (pt0) cc_final: 0.8288 (mt0)
REVERT: B  264 TYR cc_start: 0.8747 (m-80) cc_final: 0.8501 (m-80)
REVERT: C   59 ASN cc_start: 0.8452 (t0) cc_final: 0.7937 (t0)
REVERT: R  241 TRP cc_start: 0.8501 (t-100) cc_final: 0.7746 (m-90)
REVERT: R  290 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8098 (mm-30)
REVERT: R  298 ASN cc_start: 0.7903 (t0) cc_final: 0.7254 (t0)
REVERT: R  301 MET cc_start: 0.7666 (mmm) cc_final: 0.7187 (mmp)
REVERT: R  362 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7149 (tm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 166
  average time/residue: 0.0857
  time to fit residues: 20.1949
Evaluate side-chains
  152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 17 optimal weight:    0.4980
   chunk 79 optimal weight:   50.0000
   chunk 92 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.124727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.087358 restraints weight = 17225.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 3.37
r_work: 0.3253 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8902  Z= 0.107
  Angle     :  0.545   9.496  12072  Z= 0.279
  Chirality :  0.042   0.169   1345
  Planarity :  0.003   0.047   1548
  Dihedral  :  4.207  30.207   1216
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 22.00 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -1.08 (0.26), residues: 1104
  helix:  0.20 (0.27), residues: 394
  sheet: -1.52 (0.35), residues: 207
  loop : -0.99 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  67 
 TYR   0.016   0.001   TYR B 111 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8897)
  covalent geometry    : angle       0.54434 (12062)
  SS BOND              : bond        0.00123 (    5)
  SS BOND              : angle       1.26142 (   10)
  hydrogen bonds       : bond        0.03192 (  344)
  hydrogen bonds       : angle       4.35897 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8587 (tpt170) cc_final: 0.8101 (mmm160)
REVERT: A   35 GLN cc_start: 0.8801 (pt0) cc_final: 0.8305 (mt0)
REVERT: B  220 GLN cc_start: 0.8177 (mt0) cc_final: 0.7973 (mt0)
REVERT: B  264 TYR cc_start: 0.8760 (m-80) cc_final: 0.8529 (m-80)
REVERT: C   59 ASN cc_start: 0.8372 (t0) cc_final: 0.7774 (t0)
REVERT: R   29 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7210 (mmt)
REVERT: R  241 TRP cc_start: 0.8548 (t-100) cc_final: 0.7758 (m-90)
REVERT: R  290 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: R  298 ASN cc_start: 0.7896 (t0) cc_final: 0.7274 (t0)
REVERT: R  301 MET cc_start: 0.7687 (mmm) cc_final: 0.7241 (mmp)
  outliers start: 23
  outliers final: 16
  residues processed: 170
  average time/residue: 0.0911
  time to fit residues: 21.6371
Evaluate side-chains
  156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   29 MET
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0570
   chunk 95 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 21 optimal weight:   30.0000
   overall best weight:    0.9900

-------------------------------------------------------------------------------
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
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.124181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.086926 restraints weight = 17209.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.35
r_work: 0.3232 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8902  Z= 0.123
  Angle     :  0.572  10.288  12072  Z= 0.292
  Chirality :  0.042   0.202   1345
  Planarity :  0.003   0.047   1548
  Dihedral  :  4.293  42.344   1216
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 22.44 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.86 (0.26), residues: 1104
  helix:  0.44 (0.27), residues: 397
  sheet: -1.44 (0.35), residues: 206
  loop : -0.90 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.009   0.001   TYR B 111 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8897)
  covalent geometry    : angle       0.56332 (12062)
  SS BOND              : bond        0.00159 (    5)
  SS BOND              : angle       3.45954 (   10)
  hydrogen bonds       : bond        0.03123 (  344)
  hydrogen bonds       : angle       4.30926 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A   15 GLU cc_start: 0.8941 (pt0) cc_final: 0.8611 (pm20)
REVERT: A   20 ARG cc_start: 0.8629 (tpt170) cc_final: 0.8110 (mmm160)
REVERT: A   35 GLN cc_start: 0.8789 (pt0) cc_final: 0.8330 (mt0)
REVERT: B  130 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8168 (mp0)
REVERT: B  260 GLU cc_start: 0.8752 (tt0) cc_final: 0.8370 (tp30)
REVERT: B  264 TYR cc_start: 0.8775 (m-80) cc_final: 0.8553 (m-80)
REVERT: C   29 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8157 (tppt)
REVERT: C   59 ASN cc_start: 0.8383 (t0) cc_final: 0.7974 (t0)
REVERT: R   29 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7277 (mmt)
REVERT: R  241 TRP cc_start: 0.8617 (t-100) cc_final: 0.7826 (m-90)
REVERT: R  290 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8121 (mm-30)
REVERT: R  298 ASN cc_start: 0.7915 (t0) cc_final: 0.7292 (t0)
REVERT: R  301 MET cc_start: 0.7710 (mmm) cc_final: 0.7271 (mmp)
REVERT: R  338 MET cc_start: 0.6642 (mpp) cc_final: 0.5145 (ptp)
  outliers start: 25
  outliers final: 15
  residues processed: 159
  average time/residue: 0.0915
  time to fit residues: 20.3942
Evaluate side-chains
  156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue   29 LYS
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   29 MET
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 99 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0870
   chunk 77 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 104 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0020
   overall best weight:    0.4366

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B 220 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.125540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.088265 restraints weight = 17296.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 3.38
r_work: 0.3279 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8902  Z= 0.100
  Angle     :  0.558   9.662  12072  Z= 0.284
  Chirality :  0.041   0.170   1345
  Planarity :  0.003   0.049   1548
  Dihedral  :  4.099  38.022   1216
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 23.78 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.75 (0.26), residues: 1104
  helix:  0.63 (0.27), residues: 393
  sheet: -1.30 (0.33), residues: 221
  loop : -0.94 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  96 
 TYR   0.026   0.001   TYR E  10 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.000   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8897)
  covalent geometry    : angle       0.55429 (12062)
  SS BOND              : bond        0.00221 (    5)
  SS BOND              : angle       2.15836 (   10)
  hydrogen bonds       : bond        0.02941 (  344)
  hydrogen bonds       : angle       4.18789 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8605 (tpt170) cc_final: 0.8107 (mmm160)
REVERT: A   35 GLN cc_start: 0.8786 (pt0) cc_final: 0.8345 (mt0)
REVERT: B  220 GLN cc_start: 0.8201 (mt0) cc_final: 0.7896 (mt0)
REVERT: B  264 TYR cc_start: 0.8752 (m-80) cc_final: 0.8506 (m-80)
REVERT: C   59 ASN cc_start: 0.8300 (t0) cc_final: 0.7875 (t0)
REVERT: R  241 TRP cc_start: 0.8516 (t-100) cc_final: 0.7754 (m-90)
REVERT: R  290 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8148 (mm-30)
REVERT: R  295 TRP cc_start: 0.8659 (m-10) cc_final: 0.7997 (m-10)
REVERT: R  298 ASN cc_start: 0.7872 (t0) cc_final: 0.7243 (t0)
REVERT: R  301 MET cc_start: 0.7712 (mmm) cc_final: 0.7277 (mmp)
REVERT: R  338 MET cc_start: 0.6290 (mpp) cc_final: 0.5121 (ptp)
  outliers start: 16
  outliers final: 7
  residues processed: 157
  average time/residue: 0.0926
  time to fit residues: 20.3096
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  200 THR
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0670
   chunk 8 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0970
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.125669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.088501 restraints weight = 17083.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 3.37
r_work: 0.3285 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8902  Z= 0.101
  Angle     :  0.567  10.711  12072  Z= 0.283
  Chirality :  0.042   0.166   1345
  Planarity :  0.003   0.048   1548
  Dihedral  :  4.032  36.350   1216
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.67 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.67 (0.26), residues: 1104
  helix:  0.76 (0.27), residues: 392
  sheet: -1.33 (0.33), residues: 218
  loop : -0.91 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.024   0.001   TYR E  10 
 PHE   0.011   0.001   PHE N 108 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.000   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8897)
  covalent geometry    : angle       0.56487 (12062)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       1.86719 (   10)
  hydrogen bonds       : bond        0.02849 (  344)
  hydrogen bonds       : angle       4.14550 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8087 (mmm160)
REVERT: A   35 GLN cc_start: 0.8776 (pt0) cc_final: 0.8345 (mt0)
REVERT: B  220 GLN cc_start: 0.8245 (mt0) cc_final: 0.7953 (mt0)
REVERT: B  262 MET cc_start: 0.8127 (ttm) cc_final: 0.7862 (ttm)
REVERT: C   59 ASN cc_start: 0.8291 (t0) cc_final: 0.7951 (t0)
REVERT: R  241 TRP cc_start: 0.8543 (t-100) cc_final: 0.7719 (m-90)
REVERT: R  290 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8144 (mm-30)
REVERT: R  295 TRP cc_start: 0.8649 (m-10) cc_final: 0.7997 (m-10)
REVERT: R  298 ASN cc_start: 0.7882 (t0) cc_final: 0.7255 (t0)
REVERT: R  301 MET cc_start: 0.7715 (mmm) cc_final: 0.7289 (mmp)
REVERT: R  338 MET cc_start: 0.6331 (mpp) cc_final: 0.5177 (ptt)
  outliers start: 9
  outliers final: 6
  residues processed: 148
  average time/residue: 0.0884
  time to fit residues: 18.5718
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 134
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 28 optimal weight:    0.8980
   chunk 104 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0050
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    2.3800

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.121193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.083639 restraints weight = 17278.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.34
r_work: 0.3180 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8902  Z= 0.214
  Angle     :  0.652   9.952  12072  Z= 0.329
  Chirality :  0.044   0.224   1345
  Planarity :  0.004   0.046   1548
  Dihedral  :  4.421  38.875   1216
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 24.89 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.74 (0.26), residues: 1104
  helix:  0.75 (0.27), residues: 395
  sheet: -1.55 (0.32), residues: 231
  loop : -0.87 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 219 
 TYR   0.026   0.002   TYR E  10 
 PHE   0.029   0.002   PHE N 108 
 TRP   0.013   0.001   TRP R 241 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8897)
  covalent geometry    : angle       0.64763 (12062)
  SS BOND              : bond        0.00241 (    5)
  SS BOND              : angle       2.57617 (   10)
  hydrogen bonds       : bond        0.03264 (  344)
  hydrogen bonds       : angle       4.45221 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 GLU cc_start: 0.8918 (pt0) cc_final: 0.8558 (pm20)
REVERT: A   20 ARG cc_start: 0.8633 (tpt170) cc_final: 0.8136 (mmm160)
REVERT: A   35 GLN cc_start: 0.8770 (pt0) cc_final: 0.8318 (mt0)
REVERT: B  105 TYR cc_start: 0.8875 (t80) cc_final: 0.8666 (t80)
REVERT: B  217 MET cc_start: 0.8119 (pmm) cc_final: 0.7905 (pmm)
REVERT: B  220 GLN cc_start: 0.8215 (mt0) cc_final: 0.7965 (mt0)
REVERT: B  264 TYR cc_start: 0.8859 (m-80) cc_final: 0.8656 (m-80)
REVERT: C   59 ASN cc_start: 0.8385 (t0) cc_final: 0.8041 (t0)
REVERT: R  241 TRP cc_start: 0.8707 (t-100) cc_final: 0.7942 (m-90)
REVERT: R  290 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8133 (mm-30)
REVERT: R  298 ASN cc_start: 0.7957 (t0) cc_final: 0.7327 (t0)
REVERT: R  301 MET cc_start: 0.7746 (mmm) cc_final: 0.7299 (mmp)
  outliers start: 14
  outliers final: 11
  residues processed: 143
  average time/residue: 0.0853
  time to fit residues: 17.5060
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   chunk 21 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 77 optimal weight:   40.0000
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 392 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.123837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.086399 restraints weight = 17153.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 3.38
r_work: 0.3231 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8902  Z= 0.113
  Angle     :  0.603  10.800  12072  Z= 0.301
  Chirality :  0.042   0.221   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.217  37.308   1216
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 25.11 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.58 (0.26), residues: 1104
  helix:  0.85 (0.27), residues: 395
  sheet: -1.40 (0.33), residues: 216
  loop : -0.83 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.022   0.001   TYR E  10 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8897)
  covalent geometry    : angle       0.60100 (12062)
  SS BOND              : bond        0.00156 (    5)
  SS BOND              : angle       1.96420 (   10)
  hydrogen bonds       : bond        0.03077 (  344)
  hydrogen bonds       : angle       4.34717 (  984)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8143 (p0)
REVERT: A   15 GLU cc_start: 0.8888 (pt0) cc_final: 0.8415 (pm20)
REVERT: A   35 GLN cc_start: 0.8758 (pt0) cc_final: 0.8310 (mt0)
REVERT: B  220 GLN cc_start: 0.8217 (mt0) cc_final: 0.7900 (mt0)
REVERT: C   59 ASN cc_start: 0.8385 (t0) cc_final: 0.7926 (t0)
REVERT: N   73 ASP cc_start: 0.9090 (t0) cc_final: 0.8880 (t70)
REVERT: R  241 TRP cc_start: 0.8558 (t-100) cc_final: 0.7676 (m-90)
REVERT: R  290 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: R  298 ASN cc_start: 0.7908 (t0) cc_final: 0.7259 (t0)
REVERT: R  301 MET cc_start: 0.7775 (mmm) cc_final: 0.7340 (mmp)
REVERT: R  338 MET cc_start: 0.6520 (mpp) cc_final: 0.5037 (ptt)
  outliers start: 14
  outliers final: 10
  residues processed: 148
  average time/residue: 0.0796
  time to fit residues: 17.1561
Evaluate side-chains
  142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  200 THR
Chi-restraints excluded: chain R residue  357 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.124381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.086953 restraints weight = 17003.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.37
r_work: 0.3244 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8902  Z= 0.114
  Angle     :  0.592  10.505  12072  Z= 0.296
  Chirality :  0.042   0.216   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.127  35.857   1216
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 25.33 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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: -0.49 (0.26), residues: 1104
  helix:  0.94 (0.28), residues: 394
  sheet: -1.42 (0.33), residues: 218
  loop : -0.75 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.021   0.001   TYR E  10 
 PHE   0.016   0.001   PHE N 108 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS E   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8897)
  covalent geometry    : angle       0.58928 (12062)
  SS BOND              : bond        0.00148 (    5)
  SS BOND              : angle       1.90060 (   10)
  hydrogen bonds       : bond        0.03014 (  344)
  hydrogen bonds       : angle       4.29011 (  984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2311.77 seconds
wall clock time: 40 minutes 19.72 seconds (2419.72 seconds total)