Starting phenix.real_space_refine
on Tue Mar  3 21:21:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8guq_34276/03_2026/8guq_34276_neut.cif"
  }
  resolution = 3.08
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5602      2.51       5
     N    1499      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8789
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1721
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2250
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "S"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1760
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'KNF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.22, per 1000 atoms: 0.25
  Number of scatterers: 8789
  At special positions: 0
  Unit cell: (90.1334, 116.48, 131.733, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1622      8.00
     N    1499      7.00
     C    5602      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 174 " - pdb=" SG  CYS R 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 340.2 milliseconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      37.8% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.708A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.824A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.585A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.194A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.506A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.943A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.959A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 3.533A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.850A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.544A  pdb=" N   GLN B  17 " --> pdb=" O   GLN B  13 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 8 through 23
      removed outlier: 3.542A  pdb=" N   ARG C  13 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 44
      removed outlier: 3.502A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'R' and resid 32 through 62
      removed outlier: 3.614A  pdb=" N   LEU R  39 " --> pdb=" O   ALA R  35 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS R  40 " --> pdb=" O   VAL R  36 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR R  41 " --> pdb=" O   ALA R  37 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER R  47 " --> pdb=" O   LEU R  43 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU R  59 " --> pdb=" O   LEU R  55 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER R  61 " --> pdb=" O   LEU R  57 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   HIS R  62 " --> pdb=" O   ILE R  58 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 96
      removed outlier: 3.550A  pdb=" N   ILE R  73 " --> pdb=" O   SER R  69 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL R  92 " --> pdb=" O   ALA R  88 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASN R  93 " --> pdb=" O   CYS R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 117
      removed outlier: 3.712A  pdb=" N   VAL R 113 " --> pdb=" O   LYS R 109 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR R 114 " --> pdb=" O   ILE R 110 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR R 116 " --> pdb=" O   SER R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 118 through 137
      removed outlier: 3.502A  pdb=" N   CYS R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR R 137 " --> pdb=" O   LEU R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.602A  pdb=" N   VAL R 152 " --> pdb=" O   GLY R 148 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR R 153 " --> pdb=" O   ARG R 149 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU R 160 " --> pdb=" O   ILE R 156 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 224
      removed outlier: 3.702A  pdb=" N   LEU R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE R 200 " --> pdb=" O   LEU R 196 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ILE R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   THR R 208 " --> pdb=" O   GLY R 204 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS R 217 " --> pdb=" O   LEU R 213 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   HIS R 219 " --> pdb=" O   LYS R 215 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 271
      removed outlier: 3.665A  pdb=" N   THR R 246 " --> pdb=" O   ARG R 242 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU R 249 " --> pdb=" O   LYS R 245 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU R 255 " --> pdb=" O   LEU R 251 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   CYS R 257 " --> pdb=" O   VAL R 253 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE R 259 " --> pdb=" O   LEU R 255 " (cutoff:3.500A)
      Proline residue:  R 260  - end of helix
      removed outlier: 4.246A  pdb=" N   LEU R 264 " --> pdb=" O   PRO R 260 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU R 269 " --> pdb=" O   MET R 265 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ALA R 270 " --> pdb=" O   ALA R 266 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR R 271 " --> pdb=" O   HIS R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 285
      removed outlier: 3.727A  pdb=" N   ALA R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE R 283 " --> pdb=" O   LYS R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 286 through 299
      removed outlier: 3.834A  pdb=" N   SER R 292 " --> pdb=" O   CYS R 288 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL R 294 " --> pdb=" O   ILE R 290 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN R 295 " --> pdb=" O   ASN R 291 " (cutoff:3.500A)
      Proline residue:  R 296  - end of helix
    Processing helix  chain 'R' and resid 303 through 317
      removed outlier: 3.518A  pdb=" N   HIS R 311 " --> pdb=" O   ARG R 307 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU R 314 " --> pdb=" O   ALA R 310 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ALA R 315 " --> pdb=" O   HIS R 311 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS R 316 " --> pdb=" O   HIS R 312 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 4.003A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.529A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.414A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 8.888A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.734A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.734A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 3.691A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.006A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.565A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.431A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.506A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.518A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.582A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR S 231 " --> pdb=" O   TYR S 215 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148

    357 hydrogen bonds defined for protein.
    1008 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2819
        1.35 -     1.47: 2323
        1.47 -     1.60: 3740
        1.60 -     1.73: 0
        1.73 -     1.86: 95
  Bond restraints: 8977
  Sorted by residual:
  bond pdb=" C11 KNF R 401 "
       pdb=" C5  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.482  1.342  0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" C10 KNF R 401 "
       pdb=" C6  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.359  0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" C10 KNF R 401 "
       pdb=" C9  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.533  1.437  0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" C5  KNF R 401 "
       pdb=" C6  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.331  0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" C4  KNF R 401 "
       pdb=" N2  KNF R 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.399 -0.072 2.00e-02 2.50e+03 1.28e+01
  ... (remaining 8972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.00: 12115
        5.00 -    10.01: 47
       10.01 -    15.01: 4
       15.01 -    20.02: 1
       20.02 -    25.02: 1
  Bond angle restraints: 12168
  Sorted by residual:
  angle pdb=" C10 KNF R 401 "
        pdb=" C9  KNF R 401 "
        pdb=" C18 KNF R 401 "
      ideal   model   delta    sigma   weight residual
     118.74   93.72   25.02 3.00e+00 1.11e-01 6.96e+01
  angle pdb=" C18 KNF R 401 "
        pdb=" C8  KNF R 401 "
        pdb=" C7  KNF R 401 "
      ideal   model   delta    sigma   weight residual
     113.38  130.54  -17.16 3.00e+00 1.11e-01 3.27e+01
  angle pdb=" C   CYS A   3 "
        pdb=" N   THR A   4 "
        pdb=" CA  THR A   4 "
      ideal   model   delta    sigma   weight residual
     122.08  129.35   -7.27 1.47e+00 4.63e-01 2.45e+01
  angle pdb=" C   SER R  61 "
        pdb=" N   HIS R  62 "
        pdb=" CA  HIS R  62 "
      ideal   model   delta    sigma   weight residual
     122.08  129.33   -7.25 1.47e+00 4.63e-01 2.43e+01
  angle pdb=" CA  CYS R 174 "
        pdb=" CB  CYS R 174 "
        pdb=" SG  CYS R 174 "
      ideal   model   delta    sigma   weight residual
     114.40  124.73  -10.33 2.30e+00 1.89e-01 2.02e+01
  ... (remaining 12163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4706
       17.53 -    35.05: 502
       35.05 -    52.58: 97
       52.58 -    70.10: 18
       70.10 -    87.63: 5
  Dihedral angle restraints: 5328
    sinusoidal: 2044
      harmonic: 3284
  Sorted by residual:
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.22  -46.78     0      5.00e+00 4.00e-02 8.75e+01
  dihedral pdb=" CB  CYS R 174 "
           pdb=" SG  CYS R 174 "
           pdb=" SG  CYS R 179 "
           pdb=" CB  CYS R 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   21.31   71.69     1      1.00e+01 1.00e-02 6.58e+01
  dihedral pdb=" CA  HIS R  62 "
           pdb=" C   HIS R  62 "
           pdb=" N   GLN R  63 "
           pdb=" CA  GLN R  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 5325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.155: 1363
       0.155 -    0.310: 26
       0.310 -    0.465: 1
       0.465 -    0.619: 0
       0.619 -    0.774: 1
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" C8  KNF R 401 "
            pdb=" C18 KNF R 401 "
            pdb=" C7  KNF R 401 "
            pdb=" C9  KNF R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.65    1.88    0.77 2.00e-01 2.50e+01 1.50e+01
  chirality pdb=" C12 KNF R 401 "
            pdb=" C13 KNF R 401 "
            pdb=" C14 KNF R 401 "
            pdb=" N5  KNF R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.73    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1388 not shown)

  Planarity restraints: 1525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER S 172 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO S 173 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO S 173 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO S 173 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 173 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.69e+00
        pdb=" C   THR R 173 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   THR R 173 "    0.017 2.00e-02 2.50e+03
        pdb=" N   CYS R 174 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 259 "   -0.042 5.00e-02 4.00e+02   6.23e-02 6.21e+00
        pdb=" N   PRO R 260 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 260 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 260 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1522 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1966
        2.77 -     3.30: 7621
        3.30 -     3.84: 14430
        3.84 -     4.37: 17637
        4.37 -     4.90: 30843
  Nonbonded interactions: 72497
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.279 3.040
  ... (remaining 72492 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.560
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
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      :  0.009   0.140   8980  Z= 0.381
  Angle     :  0.980  25.021  12174  Z= 0.504
  Chirality :  0.061   0.774   1391
  Planarity :  0.006   0.066   1525
  Dihedral  : 14.931  87.628   3201
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.47 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.16 (0.19), residues: 1117
  helix: -4.53 (0.11), residues: 379
  sheet: -2.72 (0.27), residues: 269
  loop : -2.63 (0.24), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R  66 
 TYR   0.037   0.003   TYR S 178 
 PHE   0.026   0.003   PHE S  27 
 TRP   0.020   0.003   TRP B  63 
 HIS   0.009   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00893 ( 8977)
  covalent geometry    : angle       0.98034 (12168)
  SS BOND              : bond        0.00588 (    3)
  SS BOND              : angle       0.66365 (    6)
  hydrogen bonds       : bond        0.28849 (  357)
  hydrogen bonds       : angle      11.38282 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 183
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7478 (tp30)
REVERT: A  270 LYS cc_start: 0.7873 (mttt) cc_final: 0.7184 (mmtm)
REVERT: A  272 ASP cc_start: 0.7245 (m-30) cc_final: 0.6985 (p0)
REVERT: A  304 GLN cc_start: 0.7792 (tt0) cc_final: 0.7318 (tt0)
REVERT: A  331 ASN cc_start: 0.8276 (m-40) cc_final: 0.8042 (m110)
REVERT: A  346 ASN cc_start: 0.8438 (m-40) cc_final: 0.8047 (m-40)
REVERT: B   59 TYR cc_start: 0.8484 (m-80) cc_final: 0.7793 (m-80)
REVERT: B  232 ILE cc_start: 0.8415 (tt) cc_final: 0.7988 (tt)
REVERT: B  243 THR cc_start: 0.8717 (p) cc_final: 0.8363 (p)
REVERT: B  317 CYS cc_start: 0.7653 (p) cc_final: 0.7325 (p)
REVERT: B  335 PHE cc_start: 0.8278 (m-80) cc_final: 0.8077 (m-10)
REVERT: R   43 LEU cc_start: 0.8240 (mt) cc_final: 0.8018 (mt)
REVERT: R  302 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7492 (mmt90)
REVERT: S   18 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6933 (tpt170)
REVERT: S   46 GLU cc_start: 0.7783 (pt0) cc_final: 0.7511 (pt0)
REVERT: S   60 TYR cc_start: 0.8851 (m-80) cc_final: 0.8647 (m-80)
REVERT: S  190 ARG cc_start: 0.8206 (ptt-90) cc_final: 0.7996 (ptt90)
REVERT: S  198 THR cc_start: 0.7526 (t) cc_final: 0.6985 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 186
  average time/residue: 0.1237
  time to fit residues: 29.9411
Evaluate side-chains
  158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0040
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 213 HIS
A 255 ASN
B  62 HIS
B 340 ASN
C  24 ASN
R 295 ASN
R 316 HIS
S 130 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.187634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149220 restraints weight = 9460.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.04
r_work: 0.3467 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8980  Z= 0.142
  Angle     :  0.616  12.438  12174  Z= 0.320
  Chirality :  0.042   0.153   1391
  Planarity :  0.005   0.046   1525
  Dihedral  :  5.490  32.802   1246
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.28 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.71 (0.21), residues: 1117
  helix: -2.68 (0.19), residues: 377
  sheet: -2.25 (0.28), residues: 269
  loop : -2.18 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S  67 
 TYR   0.023   0.001   TYR A 296 
 PHE   0.015   0.002   PHE A 189 
 TRP   0.012   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8977)
  covalent geometry    : angle       0.61560 (12168)
  SS BOND              : bond        0.00499 (    3)
  SS BOND              : angle       0.81534 (    6)
  hydrogen bonds       : bond        0.04155 (  357)
  hydrogen bonds       : angle       5.61042 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 MET cc_start: 0.8021 (tpp) cc_final: 0.7691 (tpp)
REVERT: A  270 LYS cc_start: 0.7942 (mttt) cc_final: 0.7113 (mmtm)
REVERT: A  304 GLN cc_start: 0.7887 (tt0) cc_final: 0.7478 (tt0)
REVERT: A  346 ASN cc_start: 0.8444 (m-40) cc_final: 0.8136 (m-40)
REVERT: B    9 GLN cc_start: 0.7751 (tt0) cc_final: 0.7135 (tm-30)
REVERT: B   59 TYR cc_start: 0.8620 (m-80) cc_final: 0.8224 (m-80)
REVERT: B   61 MET cc_start: 0.8700 (ppp) cc_final: 0.8476 (ppp)
REVERT: B  188 MET cc_start: 0.8269 (mmm) cc_final: 0.8065 (mmm)
REVERT: B  232 ILE cc_start: 0.8499 (tt) cc_final: 0.8127 (tt)
REVERT: C   13 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6780 (ttm110)
REVERT: R   22 MET cc_start: 0.8257 (tpp) cc_final: 0.7986 (tpp)
REVERT: R   43 LEU cc_start: 0.8302 (mt) cc_final: 0.8097 (mt)
REVERT: R   51 ASN cc_start: 0.7309 (m-40) cc_final: 0.6930 (m110)
REVERT: R  193 SER cc_start: 0.7781 (t) cc_final: 0.7531 (t)
REVERT: R  196 LEU cc_start: 0.7717 (mm) cc_final: 0.7439 (mm)
REVERT: S   46 GLU cc_start: 0.8494 (pt0) cc_final: 0.8158 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 188
  average time/residue: 0.1127
  time to fit residues: 28.3417
Evaluate side-chains
  171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 107 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B  91 HIS
B 183 HIS
S 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.186287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.147720 restraints weight = 9449.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 1.98
r_work: 0.3455 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8980  Z= 0.154
  Angle     :  0.587  11.699  12174  Z= 0.302
  Chirality :  0.042   0.158   1391
  Planarity :  0.004   0.046   1525
  Dihedral  :  5.214  30.258   1246
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.66 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.23), residues: 1117
  helix: -1.32 (0.23), residues: 385
  sheet: -2.03 (0.29), residues: 263
  loop : -2.02 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 136 
 TYR   0.026   0.001   TYR S 178 
 PHE   0.017   0.002   PHE A 189 
 TRP   0.013   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8977)
  covalent geometry    : angle       0.58649 (12168)
  SS BOND              : bond        0.00496 (    3)
  SS BOND              : angle       0.76251 (    6)
  hydrogen bonds       : bond        0.03628 (  357)
  hydrogen bonds       : angle       5.02533 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6562 (m) cc_final: 0.6204 (t)
REVERT: A  243 MET cc_start: 0.8280 (tpp) cc_final: 0.8004 (tpp)
REVERT: A  270 LYS cc_start: 0.7884 (mttt) cc_final: 0.6988 (mmtm)
REVERT: A  272 ASP cc_start: 0.8041 (m-30) cc_final: 0.7708 (p0)
REVERT: A  304 GLN cc_start: 0.7831 (tt0) cc_final: 0.7396 (tt0)
REVERT: B    9 GLN cc_start: 0.7597 (tt0) cc_final: 0.6959 (tm-30)
REVERT: B   59 TYR cc_start: 0.8665 (m-80) cc_final: 0.8318 (m-80)
REVERT: B  188 MET cc_start: 0.8263 (mmm) cc_final: 0.7994 (mmm)
REVERT: B  234 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8481 (m-80)
REVERT: C   13 ARG cc_start: 0.7037 (ttm110) cc_final: 0.6688 (ttm110)
REVERT: R   22 MET cc_start: 0.8459 (tpp) cc_final: 0.8032 (tpp)
REVERT: R   51 ASN cc_start: 0.7086 (m-40) cc_final: 0.6650 (m110)
REVERT: R   70 TYR cc_start: 0.8679 (m-80) cc_final: 0.8232 (m-80)
REVERT: R  157 MET cc_start: 0.8109 (tmm) cc_final: 0.7607 (tmm)
REVERT: R  169 LEU cc_start: 0.7622 (pp) cc_final: 0.7127 (tt)
REVERT: R  286 MET cc_start: 0.7376 (mmm) cc_final: 0.6985 (mmm)
REVERT: R  302 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7207 (mtt90)
REVERT: S   46 GLU cc_start: 0.8458 (pt0) cc_final: 0.8242 (pt0)
REVERT: S   65 LYS cc_start: 0.7242 (tttp) cc_final: 0.6996 (tppt)
REVERT: S  190 ARG cc_start: 0.8194 (ptt-90) cc_final: 0.7983 (ptt90)
REVERT: S  212 VAL cc_start: 0.8963 (t) cc_final: 0.8598 (m)
  outliers start: 24
  outliers final: 17
  residues processed: 181
  average time/residue: 0.1128
  time to fit residues: 27.3923
Evaluate side-chains
  168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 108 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 306 GLN
B 183 HIS
B 340 ASN
C  59 ASN
S 130 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.185249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.149176 restraints weight = 9521.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.61
r_work: 0.3509 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8980  Z= 0.171
  Angle     :  0.598  13.230  12174  Z= 0.301
  Chirality :  0.043   0.163   1391
  Planarity :  0.004   0.045   1525
  Dihedral  :  5.090  30.077   1246
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.35 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.24), residues: 1117
  helix: -0.50 (0.25), residues: 385
  sheet: -1.99 (0.29), residues: 269
  loop : -1.87 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 136 
 TYR   0.027   0.002   TYR S 178 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.014   0.002   TRP S  47 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8977)
  covalent geometry    : angle       0.59821 (12168)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       0.81246 (    6)
  hydrogen bonds       : bond        0.03349 (  357)
  hydrogen bonds       : angle       4.78296 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6488 (m) cc_final: 0.6116 (t)
REVERT: A  243 MET cc_start: 0.8236 (tpp) cc_final: 0.7988 (tpp)
REVERT: A  270 LYS cc_start: 0.7937 (mttt) cc_final: 0.7143 (mmtm)
REVERT: A  272 ASP cc_start: 0.7938 (m-30) cc_final: 0.7525 (p0)
REVERT: A  304 GLN cc_start: 0.7814 (tt0) cc_final: 0.7436 (tt0)
REVERT: B   45 MET cc_start: 0.8272 (mtt) cc_final: 0.8030 (mtt)
REVERT: B   59 TYR cc_start: 0.8569 (m-80) cc_final: 0.8343 (m-80)
REVERT: B  188 MET cc_start: 0.8159 (mmm) cc_final: 0.7868 (mmm)
REVERT: B  232 ILE cc_start: 0.8548 (tt) cc_final: 0.8201 (tt)
REVERT: B  234 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8440 (m-80)
REVERT: C   13 ARG cc_start: 0.7170 (ttm110) cc_final: 0.6801 (ttm110)
REVERT: R   43 LEU cc_start: 0.8517 (mm) cc_final: 0.8271 (mm)
REVERT: R   51 ASN cc_start: 0.7223 (m-40) cc_final: 0.6884 (m110)
REVERT: R   70 TYR cc_start: 0.8691 (m-80) cc_final: 0.8285 (m-80)
REVERT: R  157 MET cc_start: 0.8231 (tmm) cc_final: 0.7547 (tmm)
REVERT: R  170 MET cc_start: 0.6341 (mpp) cc_final: 0.5670 (pmm)
REVERT: R  302 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7356 (mtt90)
REVERT: S  212 VAL cc_start: 0.8830 (t) cc_final: 0.8545 (m)
  outliers start: 32
  outliers final: 24
  residues processed: 176
  average time/residue: 0.1008
  time to fit residues: 23.9224
Evaluate side-chains
  179 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 99 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
B 183 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.186689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.148472 restraints weight = 9533.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.83
r_work: 0.3499 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8980  Z= 0.136
  Angle     :  0.568  12.265  12174  Z= 0.286
  Chirality :  0.042   0.158   1391
  Planarity :  0.003   0.044   1525
  Dihedral  :  4.941  29.134   1246
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.62 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.24), residues: 1117
  helix: -0.13 (0.26), residues: 388
  sheet: -1.82 (0.30), residues: 267
  loop : -1.76 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 136 
 TYR   0.026   0.001   TYR S 178 
 PHE   0.014   0.001   PHE S  27 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8977)
  covalent geometry    : angle       0.56792 (12168)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       0.70913 (    6)
  hydrogen bonds       : bond        0.03122 (  357)
  hydrogen bonds       : angle       4.59208 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6597 (m) cc_final: 0.6172 (t)
REVERT: A  270 LYS cc_start: 0.7858 (mttt) cc_final: 0.7018 (mmtm)
REVERT: A  272 ASP cc_start: 0.7984 (m-30) cc_final: 0.7455 (p0)
REVERT: A  304 GLN cc_start: 0.7724 (tt0) cc_final: 0.7363 (tt0)
REVERT: B   45 MET cc_start: 0.8323 (mtt) cc_final: 0.8098 (mtt)
REVERT: B  188 MET cc_start: 0.8183 (mmm) cc_final: 0.7918 (mmm)
REVERT: B  232 ILE cc_start: 0.8560 (tt) cc_final: 0.8206 (tt)
REVERT: B  234 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8503 (m-80)
REVERT: C   13 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6738 (ttm110)
REVERT: R   43 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8040 (mm)
REVERT: R   70 TYR cc_start: 0.8644 (m-80) cc_final: 0.8342 (m-80)
REVERT: R  157 MET cc_start: 0.8175 (tmm) cc_final: 0.7401 (tmm)
REVERT: R  170 MET cc_start: 0.6360 (mpp) cc_final: 0.5847 (pmm)
REVERT: R  286 MET cc_start: 0.7576 (mmm) cc_final: 0.7199 (mmm)
REVERT: R  302 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7304 (mtt90)
REVERT: S  211 ASP cc_start: 0.8615 (m-30) cc_final: 0.8316 (m-30)
REVERT: S  212 VAL cc_start: 0.8789 (t) cc_final: 0.8520 (m)
  outliers start: 29
  outliers final: 19
  residues processed: 176
  average time/residue: 0.0996
  time to fit residues: 23.8492
Evaluate side-chains
  172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 110 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.188280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.149013 restraints weight = 9379.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.83
r_work: 0.3503 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8980  Z= 0.136
  Angle     :  0.586  12.601  12174  Z= 0.290
  Chirality :  0.043   0.256   1391
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.840  28.470   1245
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.26 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.25), residues: 1117
  helix:  0.13 (0.26), residues: 394
  sheet: -1.77 (0.29), residues: 267
  loop : -1.66 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG S 190 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.013   0.001   PHE S  27 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8977)
  covalent geometry    : angle       0.58447 (12168)
  SS BOND              : bond        0.00504 (    3)
  SS BOND              : angle       2.26568 (    6)
  hydrogen bonds       : bond        0.02988 (  357)
  hydrogen bonds       : angle       4.45802 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  182 THR cc_start: 0.6624 (m) cc_final: 0.6197 (t)
REVERT: A  242 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7518 (mtm-85)
REVERT: A  243 MET cc_start: 0.8002 (tpp) cc_final: 0.7682 (mmm)
REVERT: A  270 LYS cc_start: 0.7867 (mttt) cc_final: 0.7123 (mmtm)
REVERT: A  304 GLN cc_start: 0.7734 (tt0) cc_final: 0.7338 (tt0)
REVERT: A  306 GLN cc_start: 0.7826 (mt0) cc_final: 0.7488 (mt0)
REVERT: B  188 MET cc_start: 0.8199 (mmm) cc_final: 0.7938 (mmm)
REVERT: B  232 ILE cc_start: 0.8586 (tt) cc_final: 0.8217 (tt)
REVERT: B  234 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8546 (m-80)
REVERT: C   13 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6708 (ttm110)
REVERT: R   43 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (mm)
REVERT: R   70 TYR cc_start: 0.8443 (m-80) cc_final: 0.8240 (m-80)
REVERT: R  157 MET cc_start: 0.8179 (tmm) cc_final: 0.7208 (tmm)
REVERT: R  170 MET cc_start: 0.6722 (mpp) cc_final: 0.6363 (pmm)
REVERT: R  286 MET cc_start: 0.7693 (mmm) cc_final: 0.7400 (mmm)
REVERT: R  302 ARG cc_start: 0.7652 (ttm170) cc_final: 0.7261 (mtt90)
REVERT: S  128 MET cc_start: 0.8321 (mmm) cc_final: 0.7333 (mmm)
REVERT: S  212 VAL cc_start: 0.8758 (t) cc_final: 0.8489 (m)
  outliers start: 29
  outliers final: 24
  residues processed: 174
  average time/residue: 0.1001
  time to fit residues: 23.7221
Evaluate side-chains
  176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 56 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.188976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149913 restraints weight = 9344.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.81
r_work: 0.3515 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8980  Z= 0.127
  Angle     :  0.572  11.970  12174  Z= 0.283
  Chirality :  0.042   0.217   1391
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.743  27.922   1245
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.00 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.25), residues: 1117
  helix:  0.39 (0.27), residues: 393
  sheet: -1.63 (0.29), residues: 262
  loop : -1.63 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 136 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.024   0.001   PHE A 189 
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8977)
  covalent geometry    : angle       0.57065 (12168)
  SS BOND              : bond        0.00457 (    3)
  SS BOND              : angle       1.66508 (    6)
  hydrogen bonds       : bond        0.02848 (  357)
  hydrogen bonds       : angle       4.34577 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6713 (m) cc_final: 0.6213 (t)
REVERT: A  270 LYS cc_start: 0.7767 (mttt) cc_final: 0.6969 (mmtm)
REVERT: A  276 GLU cc_start: 0.7429 (mp0) cc_final: 0.7215 (mp0)
REVERT: A  304 GLN cc_start: 0.7674 (tt0) cc_final: 0.7271 (tt0)
REVERT: A  306 GLN cc_start: 0.7911 (mt0) cc_final: 0.7543 (mt0)
REVERT: B  188 MET cc_start: 0.8221 (mmm) cc_final: 0.7957 (mmm)
REVERT: B  232 ILE cc_start: 0.8568 (tt) cc_final: 0.8212 (tt)
REVERT: B  234 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8551 (m-80)
REVERT: C   13 ARG cc_start: 0.7063 (ttm110) cc_final: 0.6693 (ttm110)
REVERT: R  157 MET cc_start: 0.8150 (tmm) cc_final: 0.7317 (tmm)
REVERT: R  170 MET cc_start: 0.6491 (mpp) cc_final: 0.6216 (pmm)
REVERT: R  302 ARG cc_start: 0.7630 (ttm170) cc_final: 0.7312 (mtt90)
REVERT: S  128 MET cc_start: 0.8304 (mmm) cc_final: 0.7328 (mmm)
REVERT: S  212 VAL cc_start: 0.8732 (t) cc_final: 0.8436 (m)
  outliers start: 26
  outliers final: 23
  residues processed: 179
  average time/residue: 0.0984
  time to fit residues: 24.1379
Evaluate side-chains
  174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    0.0270
   chunk 21 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
C  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.189945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150850 restraints weight = 9303.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.80
r_work: 0.3526 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8980  Z= 0.123
  Angle     :  0.584  12.189  12174  Z= 0.287
  Chirality :  0.043   0.299   1391
  Planarity :  0.003   0.043   1525
  Dihedral  :  4.693  27.840   1245
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.85 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.25), residues: 1117
  helix:  0.59 (0.27), residues: 393
  sheet: -1.63 (0.29), residues: 270
  loop : -1.58 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 136 
 TYR   0.024   0.001   TYR S 178 
 PHE   0.013   0.001   PHE S  27 
 TRP   0.010   0.001   TRP S  47 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8977)
  covalent geometry    : angle       0.58331 (12168)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       1.29106 (    6)
  hydrogen bonds       : bond        0.02809 (  357)
  hydrogen bonds       : angle       4.30525 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6689 (m) cc_final: 0.6183 (t)
REVERT: A  270 LYS cc_start: 0.7788 (mttt) cc_final: 0.7019 (mmtm)
REVERT: A  304 GLN cc_start: 0.7710 (tt0) cc_final: 0.7171 (tt0)
REVERT: A  306 GLN cc_start: 0.7945 (mt0) cc_final: 0.7597 (mt0)
REVERT: B   20 ASP cc_start: 0.6710 (m-30) cc_final: 0.6386 (m-30)
REVERT: B  188 MET cc_start: 0.8245 (mmm) cc_final: 0.7976 (mmm)
REVERT: B  232 ILE cc_start: 0.8550 (tt) cc_final: 0.8196 (tt)
REVERT: B  234 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8540 (m-80)
REVERT: C   13 ARG cc_start: 0.7046 (ttm110) cc_final: 0.6694 (ttm110)
REVERT: R  157 MET cc_start: 0.8148 (tmm) cc_final: 0.7365 (tmm)
REVERT: R  170 MET cc_start: 0.6666 (mpp) cc_final: 0.6336 (pmm)
REVERT: R  302 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7340 (mtt90)
REVERT: S  128 MET cc_start: 0.8296 (mmm) cc_final: 0.7330 (mmm)
REVERT: S  212 VAL cc_start: 0.8617 (t) cc_final: 0.8379 (m)
  outliers start: 26
  outliers final: 22
  residues processed: 172
  average time/residue: 0.1061
  time to fit residues: 24.6985
Evaluate side-chains
  172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 100 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.189181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149628 restraints weight = 9268.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.73
r_work: 0.3524 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8980  Z= 0.131
  Angle     :  0.579  12.675  12174  Z= 0.285
  Chirality :  0.043   0.277   1391
  Planarity :  0.003   0.042   1525
  Dihedral  :  4.666  28.469   1245
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.63 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.25), residues: 1117
  helix:  0.75 (0.27), residues: 394
  sheet: -1.62 (0.29), residues: 270
  loop : -1.57 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 136 
 TYR   0.025   0.001   TYR S 178 
 PHE   0.028   0.001   PHE A 189 
 TRP   0.010   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8977)
  covalent geometry    : angle       0.57862 (12168)
  SS BOND              : bond        0.00416 (    3)
  SS BOND              : angle       1.21506 (    6)
  hydrogen bonds       : bond        0.02783 (  357)
  hydrogen bonds       : angle       4.28607 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6700 (m) cc_final: 0.6194 (t)
REVERT: A  270 LYS cc_start: 0.7749 (mttt) cc_final: 0.6997 (mmtm)
REVERT: A  304 GLN cc_start: 0.7684 (tt0) cc_final: 0.7216 (tt0)
REVERT: B   20 ASP cc_start: 0.6700 (m-30) cc_final: 0.6378 (m-30)
REVERT: B  188 MET cc_start: 0.8252 (mmm) cc_final: 0.7972 (mmm)
REVERT: B  215 GLU cc_start: 0.8486 (tp30) cc_final: 0.8178 (tp30)
REVERT: B  232 ILE cc_start: 0.8562 (tt) cc_final: 0.8199 (tt)
REVERT: B  234 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8552 (m-80)
REVERT: B  255 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7409 (mt)
REVERT: C   13 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6687 (ttm110)
REVERT: R  157 MET cc_start: 0.8140 (tmm) cc_final: 0.7382 (tmm)
REVERT: R  170 MET cc_start: 0.6393 (mpp) cc_final: 0.6189 (pmm)
REVERT: R  293 MET cc_start: 0.7409 (ptp) cc_final: 0.6694 (mpp)
REVERT: R  302 ARG cc_start: 0.7665 (ttm170) cc_final: 0.7400 (mtt90)
REVERT: S  128 MET cc_start: 0.8275 (mmm) cc_final: 0.7335 (mmm)
REVERT: S  212 VAL cc_start: 0.8708 (t) cc_final: 0.8442 (m)
REVERT: S  225 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8337 (mt)
  outliers start: 30
  outliers final: 24
  residues processed: 173
  average time/residue: 0.1033
  time to fit residues: 24.5166
Evaluate side-chains
  178 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  137 VAL
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.187374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.148981 restraints weight = 9358.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.77
r_work: 0.3492 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8980  Z= 0.150
  Angle     :  0.591  13.534  12174  Z= 0.291
  Chirality :  0.043   0.270   1391
  Planarity :  0.003   0.040   1525
  Dihedral  :  4.704  28.971   1245
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.85 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.25), residues: 1117
  helix:  0.79 (0.27), residues: 394
  sheet: -1.66 (0.29), residues: 271
  loop : -1.57 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 136 
 TYR   0.027   0.001   TYR S 178 
 PHE   0.014   0.001   PHE S  27 
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8977)
  covalent geometry    : angle       0.59040 (12168)
  SS BOND              : bond        0.00439 (    3)
  SS BOND              : angle       1.05623 (    6)
  hydrogen bonds       : bond        0.02879 (  357)
  hydrogen bonds       : angle       4.31304 ( 1008)

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 THR cc_start: 0.6652 (m) cc_final: 0.6214 (t)
REVERT: A  270 LYS cc_start: 0.7857 (mttt) cc_final: 0.7126 (mmtm)
REVERT: A  304 GLN cc_start: 0.7711 (tt0) cc_final: 0.7317 (tt0)
REVERT: A  306 GLN cc_start: 0.7492 (mt0) cc_final: 0.7178 (mt0)
REVERT: B   20 ASP cc_start: 0.6729 (m-30) cc_final: 0.6409 (m-30)
REVERT: B   59 TYR cc_start: 0.8581 (m-80) cc_final: 0.8356 (m-80)
REVERT: B  188 MET cc_start: 0.8253 (mmm) cc_final: 0.7989 (mmm)
REVERT: B  215 GLU cc_start: 0.8498 (tp30) cc_final: 0.8244 (tp30)
REVERT: B  232 ILE cc_start: 0.8555 (tt) cc_final: 0.8202 (tt)
REVERT: B  234 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8570 (m-80)
REVERT: B  255 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7442 (mt)
REVERT: C   13 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6737 (ttm110)
REVERT: R  157 MET cc_start: 0.8161 (tmm) cc_final: 0.7455 (tmm)
REVERT: R  170 MET cc_start: 0.6534 (mpp) cc_final: 0.6303 (pmm)
REVERT: R  293 MET cc_start: 0.7672 (ptp) cc_final: 0.7011 (mpp)
REVERT: R  302 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7413 (mtt90)
REVERT: S  128 MET cc_start: 0.8296 (mmm) cc_final: 0.7366 (mmm)
REVERT: S  212 VAL cc_start: 0.8797 (t) cc_final: 0.8527 (m)
  outliers start: 26
  outliers final: 21
  residues processed: 172
  average time/residue: 0.1023
  time to fit residues: 24.0629
Evaluate side-chains
  173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   25 TYR
Chi-restraints excluded: chain R residue   27 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 ASN
Chi-restraints excluded: chain S residue    2 VAL
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  203 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 78 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0970
   chunk 108 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 59 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.187029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146239 restraints weight = 9585.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.16
r_work: 0.3511 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8980  Z= 0.110
  Angle     :  0.570  12.850  12174  Z= 0.279
  Chirality :  0.042   0.266   1391
  Planarity :  0.003   0.039   1525
  Dihedral  :  4.545  27.774   1245
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.38 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.25), residues: 1117
  helix:  0.91 (0.27), residues: 395
  sheet: -1.52 (0.29), residues: 269
  loop : -1.59 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 136 
 TYR   0.022   0.001   TYR A 230 
 PHE   0.025   0.001   PHE A 189 
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8977)
  covalent geometry    : angle       0.56918 (12168)
  SS BOND              : bond        0.00409 (    3)
  SS BOND              : angle       1.03887 (    6)
  hydrogen bonds       : bond        0.02687 (  357)
  hydrogen bonds       : angle       4.17513 ( 1008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2856.57 seconds
wall clock time: 49 minutes 35.15 seconds (2975.15 seconds total)