Starting phenix.real_space_refine
on Sat Apr  6 17:43:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_21671.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_21671.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_21671.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_21671.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/04_2024/6whc_21671.pdb"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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
    Residue "A GLU  299": "OE1" <-> "OE2"
    Residue "A GLU  322": "OE1" <-> "OE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B GLU   12": "OE1" <-> "OE2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "C GLU   17": "OE1" <-> "OE2"
    Residue "C ARG   62": "NH1" <-> "NH2"
    Residue "N TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R GLU   34": "OE1" <-> "OE2"
    Residue "R TYR  239": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  260": "OE1" <-> "OE2"
    Residue "R ARG  378": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 186
  Time building chain proxies: 5.17, per 1000 atoms: 0.59
  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  - 3.50
        Amino acid           : False - 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: 3.17
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 0.78
  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: 2.15

  Time building geometry restraints manager: 3.48 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:
      100.21 -   106.98: 222
      106.98 -   113.75: 4847
      113.75 -   120.52: 3531
      120.52 -   127.28: 3365
      127.28 -   134.05: 97
  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 2.520
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.287 2.440
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.301 2.440
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.302 2.440
  ... (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
========== 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:             6.740
  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:             0.000
  Extract box with map and model:          3.550
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     26.050
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.520
-------------------------------------------------------------------------------
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   8897  Z= 0.255
  Angle     :  0.788   8.629  12062  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 : 6.38
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.010   0.001   TYR N  32 
 ARG   0.002   0.000   ARG A 336 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.041 
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: 0.2313
  time to fit residues: 61.3790
Evaluate side-chains
  145 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 82 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 44 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    0.3980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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
A 371 ASN
B  62 HIS
B 119 ASN
B 293 ASN
B 295 ASN
B 340 ASN
C  18 GLN
C  59 ASN
E  28 ASN
N  31 ASN
R 392 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8897  Z= 0.195
  Angle     :  0.581   7.343  12062  Z= 0.302
  Chirality :  0.042   0.205   1345
  Planarity :  0.005   0.050   1548
  Dihedral  :  4.673  26.720   1216
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.33 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.23), residues: 1104
  helix: -2.14 (0.20), residues: 395
  sheet: -1.71 (0.35), residues: 205
  loop : -1.61 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 272 
 HIS   0.004   0.001   HIS R 339 
 PHE   0.019   0.001   PHE E  22 
 TYR   0.034   0.001   TYR R 145 
 ARG   0.007   0.000   ARG B  96 

*********************** 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
  167 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8496 (pt0) cc_final: 0.8050 (mt0)
REVERT: C   21 MET cc_start: 0.5025 (ptt) cc_final: 0.4503 (ppp)
REVERT: C   29 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8685 (mtpp)
REVERT: N   43 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7713 (mtpp)
REVERT: R  231 MET cc_start: 0.8901 (tmm) cc_final: 0.8267 (tmm)
REVERT: R  290 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7806 (mm-30)
REVERT: R  298 ASN cc_start: 0.7925 (t0) cc_final: 0.7044 (t0)
REVERT: R  301 MET cc_start: 0.7405 (mmm) cc_final: 0.7012 (mmp)
REVERT: R  362 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6908 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2101
  time to fit residues: 47.0734
Evaluate side-chains
  145 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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  186 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain E residue    7 THR
Chi-restraints excluded: chain E residue   12 LYS
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  214 THR
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 55 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 99 optimal weight:    6.9990
   chunk 107 optimal weight:    0.0770
   chunk 88 optimal weight:    4.9990
   chunk 98 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 79 optimal weight:   30.0000
   overall best weight:    2.4142

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 259 GLN
B 295 ASN
E   3 GLN
R 238 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8897  Z= 0.320
  Angle     :  0.594   8.772  12062  Z= 0.310
  Chirality :  0.043   0.174   1345
  Planarity :  0.004   0.044   1548
  Dihedral  :  4.751  30.595   1216
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.44 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.86 (0.24), residues: 1104
  helix: -0.80 (0.25), residues: 390
  sheet: -1.69 (0.34), residues: 216
  loop : -1.22 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.022   0.001   PHE N 108 
 TYR   0.022   0.002   TYR R 145 
 ARG   0.003   0.000   ARG B  96 

*********************** 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
  163 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8482 (pt0) cc_final: 0.8073 (mt0)
REVERT: B  172 GLU cc_start: 0.8122 (pm20) cc_final: 0.7909 (pm20)
REVERT: N   86 LEU cc_start: 0.9141 (mm) cc_final: 0.8482 (tt)
REVERT: R  145 TYR cc_start: 0.7520 (p90) cc_final: 0.7319 (p90)
REVERT: R  231 MET cc_start: 0.8870 (tmm) cc_final: 0.8349 (tmm)
REVERT: R  290 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7919 (mm-30)
REVERT: R  298 ASN cc_start: 0.7982 (t0) cc_final: 0.7576 (t0)
REVERT: R  301 MET cc_start: 0.7456 (mmm) cc_final: 0.7131 (mmp)
REVERT: R  362 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6989 (tm-30)
  outliers start: 30
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2014
  time to fit residues: 43.0409
Evaluate side-chains
  143 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   32 GLN
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  186 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  268 ASN
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  214 THR
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 97 optimal weight:   10.0000
   chunk 74 optimal weight:   50.0000
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8897  Z= 0.232
  Angle     :  0.544   8.324  12062  Z= 0.285
  Chirality :  0.042   0.176   1345
  Planarity :  0.004   0.044   1548
  Dihedral  :  4.566  31.730   1216
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.78 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.25), residues: 1104
  helix: -0.35 (0.26), residues: 398
  sheet: -1.65 (0.34), residues: 210
  loop : -1.10 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 339 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.018   0.001   TYR R 145 
 ARG   0.003   0.000   ARG A  20 

*********************** 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
  162 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8460 (pt0) cc_final: 0.8041 (mt0)
REVERT: N   86 LEU cc_start: 0.9129 (mm) cc_final: 0.8473 (tt)
REVERT: N   87 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7905 (mtmt)
REVERT: R  231 MET cc_start: 0.8827 (tmm) cc_final: 0.8416 (tmm)
REVERT: R  241 TRP cc_start: 0.8168 (t-100) cc_final: 0.7540 (m-90)
REVERT: R  290 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7907 (mm-30)
REVERT: R  298 ASN cc_start: 0.7978 (t0) cc_final: 0.7548 (t0)
REVERT: R  301 MET cc_start: 0.7472 (mmm) cc_final: 0.7135 (mmp)
REVERT: R  362 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7012 (tm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 151
  average time/residue: 0.2017
  time to fit residues: 42.3982
Evaluate side-chains
  141 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   32 GLN
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  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 89 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8897  Z= 0.147
  Angle     :  0.517   9.248  12062  Z= 0.267
  Chirality :  0.041   0.177   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.317  30.295   1216
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 22.78 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 1104
  helix:  0.02 (0.26), residues: 398
  sheet: -1.49 (0.34), residues: 210
  loop : -0.94 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 339 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.002   0.000   ARG A 333 

*********************** 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
  158 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8462 (pt0) cc_final: 0.8069 (mt0)
REVERT: B   61 MET cc_start: 0.8243 (ppp) cc_final: 0.8041 (ppp)
REVERT: N   86 LEU cc_start: 0.9058 (mm) cc_final: 0.8442 (tt)
REVERT: N   87 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7925 (mtmt)
REVERT: R   29 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7258 (mmt)
REVERT: R  231 MET cc_start: 0.8738 (tmm) cc_final: 0.8402 (tmm)
REVERT: R  241 TRP cc_start: 0.8062 (t-100) cc_final: 0.7573 (m-90)
REVERT: R  290 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: R  298 ASN cc_start: 0.7954 (t0) cc_final: 0.7550 (t0)
REVERT: R  301 MET cc_start: 0.7423 (mmm) cc_final: 0.7110 (mmp)
  outliers start: 20
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1904
  time to fit residues: 40.8119
Evaluate side-chains
  143 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
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  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   19 LEU
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   37 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   29 MET
Chi-restraints excluded: chain R residue  214 THR
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 94 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
E  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8897  Z= 0.153
  Angle     :  0.519   9.945  12062  Z= 0.267
  Chirality :  0.041   0.156   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.212  29.700   1216
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.11 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.26), residues: 1104
  helix:  0.31 (0.27), residues: 398
  sheet: -1.39 (0.34), residues: 210
  loop : -0.89 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 361 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.016   0.001   TYR B 111 
 ARG   0.012   0.000   ARG B  96 

*********************** 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
  156 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8457 (pt0) cc_final: 0.8096 (mt0)
REVERT: B  119 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7759 (m-40)
REVERT: N   83 MET cc_start: 0.7663 (mtt) cc_final: 0.7463 (mtt)
REVERT: N   86 LEU cc_start: 0.9024 (mm) cc_final: 0.8385 (tt)
REVERT: N   87 LYS cc_start: 0.8283 (mtpp) cc_final: 0.8046 (mtmm)
REVERT: R  231 MET cc_start: 0.8681 (tmm) cc_final: 0.8384 (tmm)
REVERT: R  241 TRP cc_start: 0.8119 (t-100) cc_final: 0.7661 (m-90)
REVERT: R  290 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7898 (mm-30)
REVERT: R  298 ASN cc_start: 0.8008 (t0) cc_final: 0.7635 (t0)
REVERT: R  301 MET cc_start: 0.7437 (mmm) cc_final: 0.7119 (mmp)
  outliers start: 24
  outliers final: 17
  residues processed: 148
  average time/residue: 0.1980
  time to fit residues: 41.5025
Evaluate side-chains
  143 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain E residue   12 LYS
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  214 THR
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 11 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 105 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.2186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8897  Z= 0.195
  Angle     :  0.539  10.817  12062  Z= 0.278
  Chirality :  0.041   0.156   1345
  Planarity :  0.003   0.045   1548
  Dihedral  :  4.228  30.006   1216
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1104
  helix:  0.46 (0.27), residues: 395
  sheet: -1.44 (0.35), residues: 207
  loop : -0.87 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS E   1 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.016   0.001   TYR R 145 
 ARG   0.002   0.000   ARG B  96 

*********************** 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
  155 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7640 (p0)
REVERT: A   35 GLN cc_start: 0.8460 (pt0) cc_final: 0.8121 (mt0)
REVERT: N   86 LEU cc_start: 0.9040 (mm) cc_final: 0.8427 (tt)
REVERT: R  231 MET cc_start: 0.8683 (tmm) cc_final: 0.8390 (tmm)
REVERT: R  241 TRP cc_start: 0.8207 (t-100) cc_final: 0.7704 (m-90)
REVERT: R  290 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7896 (mm-30)
REVERT: R  298 ASN cc_start: 0.8022 (t0) cc_final: 0.7671 (t0)
REVERT: R  301 MET cc_start: 0.7462 (mmm) cc_final: 0.7152 (mmp)
  outliers start: 24
  outliers final: 20
  residues processed: 147
  average time/residue: 0.2001
  time to fit residues: 41.3537
Evaluate side-chains
  148 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
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  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain C residue   37 LEU
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  214 THR
Chi-restraints excluded: chain R residue  244 VAL
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 62 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8897  Z= 0.161
  Angle     :  0.537   9.008  12062  Z= 0.276
  Chirality :  0.041   0.160   1345
  Planarity :  0.003   0.054   1548
  Dihedral  :  4.143  29.274   1216
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 24.67 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.26), residues: 1104
  helix:  0.65 (0.27), residues: 395
  sheet: -1.35 (0.34), residues: 210
  loop : -0.81 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.003   0.000   HIS E   1 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.028   0.001   TYR E  10 
 ARG   0.013   0.000   ARG B  96 

*********************** 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
  152 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A   14 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7502 (p0)
REVERT: A   35 GLN cc_start: 0.8449 (pt0) cc_final: 0.8119 (mt0)
REVERT: N   86 LEU cc_start: 0.8979 (mm) cc_final: 0.8402 (tt)
REVERT: N   87 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8126 (mtmt)
REVERT: N   90 ASP cc_start: 0.8354 (m-30) cc_final: 0.8142 (m-30)
REVERT: R  231 MET cc_start: 0.8646 (tmm) cc_final: 0.8445 (ttp)
REVERT: R  241 TRP cc_start: 0.8169 (t-100) cc_final: 0.7636 (m-90)
REVERT: R  290 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: R  298 ASN cc_start: 0.8077 (t0) cc_final: 0.7685 (t0)
REVERT: R  301 MET cc_start: 0.7455 (mmm) cc_final: 0.7127 (mmp)
  outliers start: 22
  outliers final: 17
  residues processed: 147
  average time/residue: 0.1828
  time to fit residues: 38.5468
Evaluate side-chains
  142 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
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  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  317 CYS
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  214 THR
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 97 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 76 optimal weight:   40.0000
   chunk 30 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
R 179 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8897  Z= 0.167
  Angle     :  0.547  10.964  12062  Z= 0.280
  Chirality :  0.041   0.223   1345
  Planarity :  0.003   0.048   1548
  Dihedral  :  4.097  28.935   1216
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 24.67 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1104
  helix:  0.80 (0.28), residues: 394
  sheet: -1.31 (0.35), residues: 205
  loop : -0.81 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.003   0.001   HIS E   1 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.019   0.001   TYR E  10 
 ARG   0.012   0.000   ARG B  96 

*********************** 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
  154 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8452 (pt0) cc_final: 0.8109 (mt0)
REVERT: B  220 GLN cc_start: 0.7838 (mt0) cc_final: 0.7616 (mt0)
REVERT: N   86 LEU cc_start: 0.8996 (mm) cc_final: 0.8428 (tt)
REVERT: N   87 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8210 (mttm)
REVERT: R  231 MET cc_start: 0.8662 (tmm) cc_final: 0.8379 (tmm)
REVERT: R  241 TRP cc_start: 0.8214 (t-100) cc_final: 0.7704 (m-90)
REVERT: R  290 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7893 (mm-30)
REVERT: R  298 ASN cc_start: 0.8013 (t0) cc_final: 0.7638 (t0)
REVERT: R  301 MET cc_start: 0.7462 (mmm) cc_final: 0.7147 (mmp)
  outliers start: 19
  outliers final: 16
  residues processed: 150
  average time/residue: 0.1944
  time to fit residues: 41.2770
Evaluate side-chains
  146 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
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  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   36 ASP
Chi-restraints excluded: chain E residue   23 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  214 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 49 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8897  Z= 0.277
  Angle     :  0.592   8.561  12062  Z= 0.303
  Chirality :  0.043   0.278   1345
  Planarity :  0.004   0.047   1548
  Dihedral  :  4.293  29.897   1216
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 24.78 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1104
  helix:  0.75 (0.28), residues: 396
  sheet: -1.40 (0.35), residues: 205
  loop : -0.78 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.019   0.001   PHE N 108 
 TYR   0.024   0.001   TYR E  10 
 ARG   0.011   0.000   ARG B  96 

********************** 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
  153 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A   14 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7448 (p0)
REVERT: A   35 GLN cc_start: 0.8449 (pt0) cc_final: 0.8118 (mt0)
REVERT: N   86 LEU cc_start: 0.8980 (mm) cc_final: 0.8697 (tp)
REVERT: R  231 MET cc_start: 0.8692 (tmm) cc_final: 0.8378 (tmm)
REVERT: R  241 TRP cc_start: 0.8283 (t-100) cc_final: 0.7649 (m-90)
REVERT: R  290 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7933 (mm-30)
REVERT: R  298 ASN cc_start: 0.7974 (t0) cc_final: 0.7392 (t0)
REVERT: R  301 MET cc_start: 0.7480 (mmm) cc_final: 0.7109 (mmp)
  outliers start: 20
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1925
  time to fit residues: 40.3926
Evaluate side-chains
  149 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  379 CYS
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  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  317 CYS
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   93 VAL
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  214 THR
Chi-restraints excluded: chain R residue  244 VAL
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 79 optimal weight:   50.0000
   chunk 12 optimal weight:    0.0980
   chunk 24 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0770
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0470
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.3436

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.125206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.088392 restraints weight = 16875.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.34
r_work: 0.3265 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8897  Z= 0.139
  Angle     :  0.561   9.909  12062  Z= 0.283
  Chirality :  0.042   0.269   1345
  Planarity :  0.003   0.045   1548
  Dihedral  :  4.070  27.893   1216
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 25.22 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.26), residues: 1104
  helix:  0.89 (0.27), residues: 395
  sheet: -1.28 (0.34), residues: 209
  loop : -0.72 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.000   HIS E   1 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.019   0.001   TYR E  10 
 ARG   0.011   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2153.76 seconds
wall clock time: 40 minutes 39.46 seconds (2439.46 seconds total)