Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 19:17:49 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/02_2023/6whc_21671.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/02_2023/6whc_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_21671/02_2023/6whc_21671.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/02_2023/6whc_21671.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/02_2023/6whc_21671.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whc_21671/02_2023/6whc_21671.pdb"
  }
  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
-------------------------------------------------------------------------------
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
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-4877/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: 4.85, per 1000 atoms: 0.56
  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: 3.32
  Conformation dependent library (CDL) restraints added in 1.5 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: 0.43
  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: 2.31

  Time building geometry restraints manager: 3.59 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
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.
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:             2.330
  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:          4.340
  Check model and map are aligned:         0.130
  Process input model:                     24.670
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
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 : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer Outliers :  0.00 %
  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: -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

*********************** 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  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2265
  time to fit residues: 60.0584
Evaluate side-chains
  141 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.980 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4485
-------------------------------------------------------------------------------
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:    0.9990
   chunk 82 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   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:    6.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
C  18 GLN
C  59 ASN
E   3 GLN
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: 0.8244
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8897  Z= 0.250
  Angle     :  0.605   7.742  12062  Z= 0.315
  Chirality :  0.043   0.198   1345
  Planarity :  0.005   0.049   1548
  Dihedral  :  4.773  28.429   1216
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer Outliers :  1.67 %
  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 (0.22), residues: 1104
  helix: -2.15 (0.20), residues: 394
  sheet: -1.76 (0.34), residues: 211
  loop : -1.57 (0.26), residues: 499

*********************** 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
  163 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 11
  residues processed: 157
  average time/residue: 0.2155
  time to fit residues: 46.6470
Evaluate side-chains
  142 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 1.200 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.1332
  time to fit residues: 4.0659
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 259 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8897  Z= 0.269
  Angle     :  0.571   7.887  12062  Z= 0.299
  Chirality :  0.042   0.183   1345
  Planarity :  0.004   0.045   1548
  Dihedral  :  4.649  30.377   1216
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer Outliers :  2.22 %
  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: -0.78 (0.25), residues: 389
  sheet: -1.67 (0.34), residues: 210
  loop : -1.26 (0.27), residues: 505

*********************** 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
  157 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 11
  residues processed: 147
  average time/residue: 0.2067
  time to fit residues: 42.9621
Evaluate side-chains
  135 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.074 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0977
  time to fit residues: 3.6241
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0770
   chunk 10 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.7742

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8897  Z= 0.159
  Angle     :  0.523   8.340  12062  Z= 0.272
  Chirality :  0.041   0.183   1345
  Planarity :  0.003   0.045   1548
  Dihedral  :  4.406  30.475   1216
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer Outliers :  1.11 %
  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: -1.43 (0.25), residues: 1104
  helix: -0.26 (0.26), residues: 397
  sheet: -1.57 (0.34), residues: 212
  loop : -1.10 (0.28), residues: 495

*********************** 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
  151 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2055
  time to fit residues: 42.3408
Evaluate side-chains
  134 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.999 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0818
  time to fit residues: 1.9986
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
E  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2833

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= 0.200
  Angle     :  0.530   9.074  12062  Z= 0.274
  Chirality :  0.041   0.166   1345
  Planarity :  0.003   0.045   1548
  Dihedral  :  4.339  30.509   1216
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer Outliers :  1.11 %
  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: -1.18 (0.25), residues: 1104
  helix:  0.05 (0.27), residues: 396
  sheet: -1.54 (0.34), residues: 212
  loop : -1.00 (0.28), residues: 496

*********************** 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
  147 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 142
  average time/residue: 0.2083
  time to fit residues: 41.3833
Evaluate side-chains
  135 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 129
  time to evaluate  : 1.108 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0893
  time to fit residues: 2.5971
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:    8.9990
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8897  Z= 0.161
  Angle     :  0.527  10.078  12062  Z= 0.268
  Chirality :  0.041   0.156   1345
  Planarity :  0.003   0.048   1548
  Dihedral  :  4.203  30.151   1216
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer Outliers :  1.11 %
  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: -0.92 (0.26), residues: 1104
  helix:  0.35 (0.27), residues: 396
  sheet: -1.46 (0.34), residues: 210
  loop : -0.89 (0.28), residues: 498

*********************** 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
  149 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 4
  residues processed: 146
  average time/residue: 0.2033
  time to fit residues: 41.9811
Evaluate side-chains
  132 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.008 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0922
  time to fit residues: 2.1390
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:   40.0000
   chunk 59 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 105 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8897  Z= 0.206
  Angle     :  0.542  10.141  12062  Z= 0.275
  Chirality :  0.041   0.158   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  4.217  30.431   1216
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer Outliers :  0.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (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: -0.73 (0.26), residues: 1104
  helix:  0.56 (0.27), residues: 398
  sheet: -1.40 (0.34), residues: 210
  loop : -0.82 (0.29), residues: 496

*********************** 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
  138 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.971 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 137
  average time/residue: 0.2108
  time to fit residues: 40.4595
Evaluate side-chains
  128 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.033 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0811
  time to fit residues: 1.5451
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   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  32 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8897  Z= 0.234
  Angle     :  0.572  11.748  12062  Z= 0.290
  Chirality :  0.042   0.163   1345
  Planarity :  0.004   0.057   1548
  Dihedral  :  4.297  30.607   1216
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer Outliers :  0.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (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: -0.67 (0.26), residues: 1104
  helix:  0.65 (0.27), residues: 396
  sheet: -1.35 (0.35), residues: 210
  loop : -0.82 (0.29), residues: 498

*********************** 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
  142 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 1.093 
Fit side-chains
  outliers start: 8
  outliers final: 3
  residues processed: 138
  average time/residue: 0.1887
  time to fit residues: 37.7368
Evaluate side-chains
  130 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.957 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1863
  time to fit residues: 2.0886
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 103 optimal weight:    0.0030
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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: 0.8196
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8897  Z= 0.154
  Angle     :  0.564  10.476  12062  Z= 0.284
  Chirality :  0.042   0.230   1345
  Planarity :  0.003   0.048   1548
  Dihedral  :  4.120  29.475   1216
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer Outliers :  0.11 %
  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: -0.52 (0.26), residues: 1104
  helix:  0.80 (0.28), residues: 393
  sheet: -1.27 (0.34), residues: 210
  loop : -0.75 (0.29), residues: 501

*********************** 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
  139 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 1.001 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.1980
  time to fit residues: 39.7756
Evaluate side-chains
  128 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.043 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0917
  time to fit residues: 1.5692
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 179 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3388

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= 0.181
  Angle     :  0.588  14.619  12062  Z= 0.292
  Chirality :  0.042   0.158   1345
  Planarity :  0.003   0.047   1548
  Dihedral  :  4.113  29.428   1216
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer Outliers :  0.11 %
  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: -0.53 (0.26), residues: 1104
  helix:  0.76 (0.28), residues: 394
  sheet: -1.26 (0.33), residues: 222
  loop : -0.72 (0.29), residues: 488

********************** 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
  134 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 1.075 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.2046
  time to fit residues: 38.7693
Evaluate side-chains
  130 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.116 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0873
  time to fit residues: 1.6607
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.6980
   chunk 24 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0980
   chunk 76 optimal weight:    0.0070
   chunk 4 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.125229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.088407 restraints weight = 17053.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.35
r_work: 0.3272 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8897  Z= 0.147
  Angle     :  0.567  12.786  12062  Z= 0.282
  Chirality :  0.041   0.161   1345
  Planarity :  0.003   0.046   1548
  Dihedral  :  3.959  27.913   1216
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer Outliers :  0.33 %
  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: -0.46 (0.26), residues: 1104
  helix:  0.86 (0.28), residues: 393
  sheet: -1.19 (0.33), residues: 223
  loop : -0.72 (0.29), residues: 488

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Job complete
usr+sys time: 2011.22 seconds
wall clock time: 37 minutes 33.96 seconds (2253.96 seconds total)