Starting phenix.real_space_refine
on Sun May  3 08:09:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oi6_16887/05_2026/8oi6_16887.map"
  }
  resolution = 3.59
  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=  -0.002 sd=   0.214
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: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      4      5.21       5
     S      83      5.16       5
     C    7304      2.51       5
     N    1945      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11573
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2843
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 19, 'TRANS': 344}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2843
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 19, 'TRANS': 344}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2843
          Classifications: {'peptide': 364}
          Link IDs: {'PTRANS': 19, 'TRANS': 344}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 2767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2767
          Classifications: {'peptide': 354}
          Link IDs: {'PTRANS': 18, 'TRANS': 335}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "J"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "J"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.73, per 1000 atoms: 0.24
  Number of scatterers: 11573
  At special positions: 0
  Unit cell: (94.38, 89.54, 165.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      83     16.00
     P       8     15.00
     Mg      4     11.99
     O    2229      8.00
     N    1945      7.00
     C    7304      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
      " TRP I   1 " - " ALA I   7 "
      " DTH I   4 " - " ALA I   3 "
      " TRP J   1 " - " ALA J   7 "
      " DTH J   4 " - " ALA J   3 "
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 495.3 milliseconds
  

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
        pdb=" CB  DTH I   4 "
        pdb=" CB  DTH J   4 "
  Number of C-beta restraints generated:  2722

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 22 sheets defined
      49.4% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.569A  pdb=" N   GLN A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.864A  pdb=" N   ARG A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET A 123 " --> pdb=" O   MET A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
      removed outlier: 3.699A  pdb=" N   TYR A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 193
    Processing helix  chain 'A' and resid 194 through 197
    Processing helix  chain 'A' and resid 202 through 214
      removed outlier: 4.041A  pdb=" N   GLU A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ILE A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 233
      removed outlier: 3.783A  pdb=" N   GLU A 226 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 256
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.599A  pdb=" N   ILE A 282 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 295
      removed outlier: 4.050A  pdb=" N   ALA A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 4.007A  pdb=" N   TYR A 306 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.531A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 78 through 93
      removed outlier: 3.570A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 4.293A  pdb=" N   ARG B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLU B 117 " --> pdb=" O   LYS B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
      removed outlier: 3.518A  pdb=" N   LEU B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TYR B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 175
    Processing helix  chain 'B' and resid 181 through 194
      removed outlier: 3.678A  pdb=" N   THR B 194 " --> pdb=" O   MET B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 217
      removed outlier: 3.797A  pdb=" N   GLU B 207 " --> pdb=" O   THR B 203 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE B 208 " --> pdb=" O   ALA B 204 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   CYS B 217 " --> pdb=" O   LYS B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 233
      removed outlier: 3.518A  pdb=" N   ALA B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 257
    Processing helix  chain 'B' and resid 258 through 262
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 273 through 285
    Processing helix  chain 'B' and resid 286 through 295
      removed outlier: 4.165A  pdb=" N   LYS B 291 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ASP B 292 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ALA B 295 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 306
      removed outlier: 3.958A  pdb=" N   TYR B 306 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 321
      removed outlier: 3.568A  pdb=" N   LEU B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 336
      No H-bonds generated for 'chain 'B' and resid 334 through 336'
    Processing helix  chain 'B' and resid 337 through 349
    Processing helix  chain 'B' and resid 350 through 356
      removed outlier: 3.908A  pdb=" N   GLN B 354 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   TRP B 356 " --> pdb=" O   GLN B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 366
      removed outlier: 3.680A  pdb=" N   SER B 365 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 61
      removed outlier: 3.500A  pdb=" N   LYS C  61 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.691A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   HIS C  87 " --> pdb=" O   GLU C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 3.810A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 145
      removed outlier: 3.507A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 175
    Processing helix  chain 'C' and resid 181 through 194
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.549A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 257
      removed outlier: 3.733A  pdb=" N   CYS C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 263 through 268
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 4.430A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR C 294 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 3.501A  pdb=" N   THR C 304 " --> pdb=" O   GLY C 301 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 349
    Processing helix  chain 'C' and resid 351 through 356
      removed outlier: 3.916A  pdb=" N   TRP C 356 " --> pdb=" O   GLN C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
      removed outlier: 3.585A  pdb=" N   GLU C 364 " --> pdb=" O   GLN C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 371
    Processing helix  chain 'D' and resid 55 through 61
      removed outlier: 3.567A  pdb=" N   LYS D  61 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 92
      removed outlier: 3.652A  pdb=" N   GLU D  83 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 112 through 126
      removed outlier: 3.585A  pdb=" N   ARG D 116 " --> pdb=" O   PRO D 112 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   MET D 123 " --> pdb=" O   MET D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 145
      removed outlier: 3.746A  pdb=" N   LEU D 142 " --> pdb=" O   ALA D 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 194
      removed outlier: 3.513A  pdb=" N   THR D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
      removed outlier: 3.851A  pdb=" N   GLU D 207 " --> pdb=" O   THR D 203 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE D 208 " --> pdb=" O   ALA D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 233
      removed outlier: 3.550A  pdb=" N   ALA D 228 " --> pdb=" O   GLU D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 237
    Processing helix  chain 'D' and resid 252 through 257
      removed outlier: 3.658A  pdb=" N   CYS D 257 " --> pdb=" O   GLU D 253 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 261
    Processing helix  chain 'D' and resid 263 through 268
    Processing helix  chain 'D' and resid 273 through 285
      removed outlier: 3.602A  pdb=" N   MET D 283 " --> pdb=" O   PHE D 279 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS D 284 " --> pdb=" O   ASN D 280 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   CYS D 285 " --> pdb=" O   SER D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 288
      No H-bonds generated for 'chain 'D' and resid 286 through 288'
    Processing helix  chain 'D' and resid 289 through 296
    Processing helix  chain 'D' and resid 301 through 306
      removed outlier: 4.019A  pdb=" N   TYR D 306 " --> pdb=" O   THR D 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 321
    Processing helix  chain 'D' and resid 337 through 349
    Processing helix  chain 'D' and resid 350 through 354
      removed outlier: 4.011A  pdb=" N   GLN D 353 " --> pdb=" O   SER D 350 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.565A  pdb=" N   PHE A  31 " --> pdb=" O   CYS A  17 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL A   9 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.624A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.839A  pdb=" N   ARG A  37 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170
      removed outlier: 7.171A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   ILE A 151 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   SER A 300 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   MET A 153 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   THR A 297 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32
      removed outlier: 3.667A  pdb=" N   PHE B  31 " --> pdb=" O   CYS B  17 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LEU B   8 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   THR B 106 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   VAL B  10 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.698A  pdb=" N   ARG B  37 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170
    Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170
      removed outlier: 6.574A  pdb=" N   THR B 297 " --> pdb=" O   ILE B 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.654A  pdb=" N   PHE C  31 " --> pdb=" O   CYS C  17 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   THR C 106 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.815A  pdb=" N   ARG C  37 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178
      removed outlier: 3.705A  pdb=" N   SER C 155 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10
      removed outlier: 6.071A  pdb=" N   LEU D   8 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   THR D 106 " --> pdb=" O   LEU D   8 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   VAL D  10 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR D 133 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19
    Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54
      removed outlier: 3.755A  pdb=" N   LYS D  68 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG D  37 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178
      removed outlier: 5.947A  pdb=" N   THR D 297 " --> pdb=" O   ILE D 330 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241

    529 hydrogen bonds defined for protein.
    1329 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: 1.84

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3734
        1.34 -     1.46: 2694
        1.46 -     1.58: 5233
        1.58 -     1.70: 18
        1.70 -     1.82: 143
  Bond restraints: 11822
  Sorted by residual:
  bond pdb=" N   HYP I   6 "
       pdb=" CD  HYP I   6 "
    ideal  model  delta    sigma   weight residual
    1.473  1.636 -0.163 1.40e-02 5.10e+03 1.36e+02
  bond pdb=" N   HYP H   6 "
       pdb=" CD  HYP H   6 "
    ideal  model  delta    sigma   weight residual
    1.473  1.635 -0.162 1.40e-02 5.10e+03 1.35e+02
  bond pdb=" N   HYP J   6 "
       pdb=" CD  HYP J   6 "
    ideal  model  delta    sigma   weight residual
    1.473  1.635 -0.162 1.40e-02 5.10e+03 1.33e+02
  bond pdb=" CG  HYP H   6 "
       pdb=" CD  HYP H   6 "
    ideal  model  delta    sigma   weight residual
    1.530  1.371  0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" CG  HYP J   6 "
       pdb=" CD  HYP J   6 "
    ideal  model  delta    sigma   weight residual
    1.530  1.372  0.158 2.00e-02 2.50e+03 6.23e+01
  ... (remaining 11817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 15707
        1.85 -     3.69: 247
        3.69 -     5.54: 60
        5.54 -     7.39: 23
        7.39 -     9.23: 8
  Bond angle restraints: 16045
  Sorted by residual:
  angle pdb=" N   HYP H   6 "
        pdb=" CA  HYP H   6 "
        pdb=" CB  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.00  107.42   -4.42 1.10e+00 8.26e-01 1.61e+01
  angle pdb=" N   HYP H   6 "
        pdb=" CD  HYP H   6 "
        pdb=" CG  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.20  109.04   -5.84 1.50e+00 4.44e-01 1.52e+01
  angle pdb=" N   HIC D  73 "
        pdb=" CA  HIC D  73 "
        pdb=" CB  HIC D  73 "
      ideal   model   delta    sigma   weight residual
     110.50  116.88   -6.38 1.70e+00 3.46e-01 1.41e+01
  angle pdb=" N   HYP J   6 "
        pdb=" CA  HYP J   6 "
        pdb=" CB  HYP J   6 "
      ideal   model   delta    sigma   weight residual
     103.00  106.86   -3.86 1.10e+00 8.26e-01 1.23e+01
  angle pdb=" N   HYP I   6 "
        pdb=" CA  HYP I   6 "
        pdb=" CB  HYP I   6 "
      ideal   model   delta    sigma   weight residual
     103.00  106.84   -3.84 1.10e+00 8.26e-01 1.22e+01
  ... (remaining 16040 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.98: 6878
       33.98 -    67.96: 224
       67.96 -   101.94: 17
      101.94 -   135.92: 4
      135.92 -   169.90: 3
  Dihedral angle restraints: 7126
    sinusoidal: 2885
      harmonic: 4241
  Sorted by residual:
  dihedral pdb=" O1B ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PB  ADP B 401 "
           pdb=" PA  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  130.10  169.90     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  131.78  168.22     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" O1B ADP A 401 "
           pdb=" O3A ADP A 401 "
           pdb=" PB  ADP A 401 "
           pdb=" PA  ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  137.14  162.86     1      2.00e+01 2.50e-03 4.69e+01
  ... (remaining 7123 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1565
       0.061 -    0.122: 223
       0.122 -    0.184: 4
       0.184 -    0.245: 0
       0.245 -    0.306: 3
  Chirality restraints: 1795
  Sorted by residual:
  chirality pdb=" CA  HYP I   6 "
            pdb=" N   HYP I   6 "
            pdb=" C   HYP I   6 "
            pdb=" CB  HYP I   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CA  HYP J   6 "
            pdb=" N   HYP J   6 "
            pdb=" C   HYP J   6 "
            pdb=" CB  HYP J   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  HYP H   6 "
            pdb=" N   HYP H   6 "
            pdb=" C   HYP H   6 "
            pdb=" CB  HYP H   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 1792 not shown)

  Planarity restraints: 2037
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 117 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" CD  GLU A 117 "    0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 117 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 117 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 166 "   -0.011 2.00e-02 2.50e+03   1.15e-02 2.63e+00
        pdb=" CG  TYR C 166 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 166 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 166 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 166 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 166 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 166 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 166 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 366 "   -0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO B 367 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 367 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 367 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2034 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 45
        2.43 -     3.04: 7139
        3.04 -     3.66: 17282
        3.66 -     4.28: 26390
        4.28 -     4.90: 43999
  Nonbonded interactions: 94855
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.808 3.620
  nonbonded pdb=" CD1 TRP I   1 "
            pdb=" SG  CYS I   5 "
     model   vdw
     1.810 3.620
  nonbonded pdb=" CD1 TRP J   1 "
            pdb=" SG  CYS J   5 "
     model   vdw
     1.820 3.620
  nonbonded pdb=" O1B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     2.126 2.170
  nonbonded pdb=" O1B ADP D 401 "
            pdb="MG    MG D 402 "
     model   vdw
     2.137 2.170
  ... (remaining 94850 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 362 or resid 401 through 402))
  selection = (chain 'B' and (resid 6 through 362 or resid 401 through 402))
  selection = (chain 'C' and (resid 6 through 362 or resid 401 through 402))
  selection = chain 'D'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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 group one per residue
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:             3.710
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.910
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.163  11828  Z= 0.301
  Angle     :  0.638  10.099  16063  Z= 0.303
  Chirality :  0.043   0.306   1795
  Planarity :  0.003   0.040   2031
  Dihedral  : 16.962 169.900   4386
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.83 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 17.74 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.23), residues: 1418
  helix:  0.06 (0.22), residues: 538
  sheet:  0.56 (0.37), residues: 212
  loop :  0.49 (0.25), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.028   0.001   TYR C 166 
 PHE   0.008   0.001   PHE A 124 
 TRP   0.014   0.001   TRP B  86 
 HIS   0.011   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (11822)
  covalent geometry    : angle       0.63067 (16045)
  hydrogen bonds       : bond        0.30317 (  525)
  hydrogen bonds       : angle       8.74333 ( 1329)
  link_TRANS           : bond        0.01252 (    6)
  link_TRANS           : angle       2.98562 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 88
  average time/residue: 0.0826
  time to fit residues: 11.7026
Evaluate side-chains
  84 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain J residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B  12 ASN
B 173 HIS
B 225 GLN
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 HIS
D 111 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.075049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.064290 restraints weight = 34045.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.066426 restraints weight = 17294.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.067857 restraints weight = 10665.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068807 restraints weight = 7463.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.069462 restraints weight = 5739.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11828  Z= 0.197
  Angle     :  0.636   7.070  16063  Z= 0.309
  Chirality :  0.045   0.152   1795
  Planarity :  0.004   0.035   2031
  Dihedral  : 11.998 178.507   1673
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.69 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.11 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.22), residues: 1418
  helix:  0.33 (0.22), residues: 580
  sheet:  0.48 (0.34), residues: 235
  loop :  0.63 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 183 
 TYR   0.017   0.001   TYR B 143 
 PHE   0.015   0.001   PHE C 352 
 TRP   0.025   0.002   TRP I   1 
 HIS   0.004   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (11822)
  covalent geometry    : angle       0.63579 (16045)
  hydrogen bonds       : bond        0.04791 (  525)
  hydrogen bonds       : angle       5.75989 ( 1329)
  link_TRANS           : bond        0.00304 (    6)
  link_TRANS           : angle       0.73455 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7948 (t0) cc_final: 0.7683 (t0)
REVERT: B  123 MET cc_start: 0.8277 (mmm) cc_final: 0.7978 (mmt)
REVERT: B  314 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7882 (tt0)
REVERT: D  355 MET cc_start: 0.7760 (pmm) cc_final: 0.6925 (pmm)
  outliers start: 23
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0734
  time to fit residues: 12.0386
Evaluate side-chains
  88 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  324 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 109 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  12 ASN
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.074303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.063367 restraints weight = 33956.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.065567 restraints weight = 17227.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.067031 restraints weight = 10637.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.068000 restraints weight = 7454.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.068666 restraints weight = 5725.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11828  Z= 0.147
  Angle     :  0.572   7.105  16063  Z= 0.271
  Chirality :  0.044   0.212   1795
  Planarity :  0.004   0.035   2031
  Dihedral  : 10.889 159.704   1668
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.97 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.60 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.23), residues: 1418
  helix:  0.46 (0.22), residues: 591
  sheet:  0.46 (0.34), residues: 253
  loop :  0.65 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 116 
 TYR   0.015   0.001   TYR B 143 
 PHE   0.011   0.001   PHE D  31 
 TRP   0.012   0.001   TRP C 340 
 HIS   0.003   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (11822)
  covalent geometry    : angle       0.57236 (16045)
  hydrogen bonds       : bond        0.03628 (  525)
  hydrogen bonds       : angle       5.25910 ( 1329)
  link_TRANS           : bond        0.00244 (    6)
  link_TRANS           : angle       0.35669 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7968 (t0) cc_final: 0.7538 (t0)
REVERT: B  132 MET cc_start: 0.8161 (ttp) cc_final: 0.7534 (ttp)
REVERT: B  314 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7758 (tt0)
REVERT: C  132 MET cc_start: 0.8150 (tmm) cc_final: 0.7948 (tmm)
REVERT: D  355 MET cc_start: 0.7718 (pmm) cc_final: 0.7132 (pmm)
REVERT: I    5 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8029 (p)
  outliers start: 28
  outliers final: 15
  residues processed: 102
  average time/residue: 0.0786
  time to fit residues: 13.2969
Evaluate side-chains
  94 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue   89 THR
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue   82 MET
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 139 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 127 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  12 ASN
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 280 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.072574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.061617 restraints weight = 34314.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063769 restraints weight = 17539.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.065214 restraints weight = 10885.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.066193 restraints weight = 7658.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.066854 restraints weight = 5891.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  11828  Z= 0.223
  Angle     :  0.616   6.956  16063  Z= 0.292
  Chirality :  0.046   0.207   1795
  Planarity :  0.004   0.037   2031
  Dihedral  : 10.232 149.315   1668
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.97 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.41 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.23), residues: 1418
  helix:  0.55 (0.23), residues: 585
  sheet:  0.41 (0.34), residues: 250
  loop :  0.53 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 290 
 TYR   0.015   0.001   TYR B 143 
 PHE   0.014   0.002   PHE C 352 
 TRP   0.012   0.002   TRP C 340 
 HIS   0.004   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (11822)
  covalent geometry    : angle       0.61625 (16045)
  hydrogen bonds       : bond        0.03518 (  525)
  hydrogen bonds       : angle       5.15017 ( 1329)
  link_TRANS           : bond        0.00334 (    6)
  link_TRANS           : angle       0.44298 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 78
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8011 (t0) cc_final: 0.7486 (t0)
REVERT: B  269 MET cc_start: 0.7791 (mtp) cc_final: 0.7527 (mtm)
REVERT: B  314 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7804 (tt0)
REVERT: D  180 LEU cc_start: 0.7679 (tp) cc_final: 0.7378 (tp)
REVERT: D  355 MET cc_start: 0.7624 (pmm) cc_final: 0.7101 (pmm)
REVERT: I    5 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8063 (p)
  outliers start: 35
  outliers final: 17
  residues processed: 107
  average time/residue: 0.0806
  time to fit residues: 13.9873
Evaluate side-chains
  95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   12 ASN
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 129 optimal weight:    4.9990
   chunk 138 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 109 optimal weight:    7.9990
   chunk 75 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  12 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.073793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.062873 restraints weight = 33908.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.065061 restraints weight = 17202.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.066538 restraints weight = 10610.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.067515 restraints weight = 7428.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.068174 restraints weight = 5699.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11828  Z= 0.125
  Angle     :  0.554   6.665  16063  Z= 0.259
  Chirality :  0.044   0.200   1795
  Planarity :  0.004   0.036   2031
  Dihedral  :  9.936 145.433   1668
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.90 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.14 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.23), residues: 1418
  helix:  0.73 (0.23), residues: 582
  sheet:  0.35 (0.34), residues: 253
  loop :  0.66 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 116 
 TYR   0.007   0.001   TYR C  69 
 PHE   0.011   0.001   PHE D  31 
 TRP   0.012   0.001   TRP C 340 
 HIS   0.003   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11822)
  covalent geometry    : angle       0.55380 (16045)
  hydrogen bonds       : bond        0.03003 (  525)
  hydrogen bonds       : angle       4.94787 ( 1329)
  link_TRANS           : bond        0.00195 (    6)
  link_TRANS           : angle       0.31495 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7999 (t0) cc_final: 0.7430 (t0)
REVERT: B  314 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7759 (tt0)
REVERT: D  355 MET cc_start: 0.7658 (pmm) cc_final: 0.7429 (pmm)
REVERT: H    5 CYS cc_start: 0.6795 (t) cc_final: 0.5803 (m)
REVERT: I    5 CYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7979 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0746
  time to fit residues: 11.7889
Evaluate side-chains
  93 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 30 optimal weight:    0.0070
   chunk 74 optimal weight:    0.0570
   chunk 0 optimal weight:    6.9990
   chunk 140 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.0122

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
D  12 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.072220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.061256 restraints weight = 34639.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.063377 restraints weight = 17806.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.064811 restraints weight = 11047.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.065773 restraints weight = 7788.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.066393 restraints weight = 6006.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  11828  Z= 0.235
  Angle     :  0.638   6.790  16063  Z= 0.302
  Chirality :  0.046   0.208   1795
  Planarity :  0.004   0.046   2031
  Dihedral  :  9.523 138.652   1668
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.61 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 17.90 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.23), residues: 1418
  helix:  0.60 (0.23), residues: 582
  sheet:  0.27 (0.34), residues: 252
  loop :  0.53 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 290 
 TYR   0.010   0.001   TYR A 198 
 PHE   0.015   0.002   PHE C 352 
 TRP   0.012   0.002   TRP A  79 
 HIS   0.005   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (11822)
  covalent geometry    : angle       0.63790 (16045)
  hydrogen bonds       : bond        0.03415 (  525)
  hydrogen bonds       : angle       5.03071 ( 1329)
  link_TRANS           : bond        0.00332 (    6)
  link_TRANS           : angle       0.45697 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8097 (t0) cc_final: 0.7570 (t0)
REVERT: B  118 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7817 (tptt)
REVERT: B  269 MET cc_start: 0.7734 (mtp) cc_final: 0.7473 (mtm)
REVERT: B  314 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7772 (tt0)
REVERT: D  180 LEU cc_start: 0.7794 (tp) cc_final: 0.7530 (tp)
REVERT: D  355 MET cc_start: 0.7945 (pmm) cc_final: 0.7681 (pmm)
REVERT: I    5 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7984 (p)
  outliers start: 32
  outliers final: 23
  residues processed: 104
  average time/residue: 0.0773
  time to fit residues: 13.2345
Evaluate side-chains
  101 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 131 optimal weight:    0.7980
   chunk 140 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.074115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.063175 restraints weight = 33995.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.065313 restraints weight = 17475.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.066755 restraints weight = 10879.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.067727 restraints weight = 7668.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.068294 restraints weight = 5916.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11828  Z= 0.121
  Angle     :  0.566   8.183  16063  Z= 0.262
  Chirality :  0.044   0.198   1795
  Planarity :  0.004   0.037   2031
  Dihedral  :  9.155 134.204   1668
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.83 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.28 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.23), residues: 1418
  helix:  0.79 (0.23), residues: 589
  sheet:  0.24 (0.33), residues: 253
  loop :  0.66 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 116 
 TYR   0.010   0.001   TYR B 143 
 PHE   0.012   0.001   PHE D  31 
 TRP   0.012   0.002   TRP C 340 
 HIS   0.003   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11822)
  covalent geometry    : angle       0.56588 (16045)
  hydrogen bonds       : bond        0.02834 (  525)
  hydrogen bonds       : angle       4.81988 ( 1329)
  link_TRANS           : bond        0.00191 (    6)
  link_TRANS           : angle       0.30261 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7992 (t0) cc_final: 0.7462 (t0)
REVERT: A  132 MET cc_start: 0.7098 (ptt) cc_final: 0.6819 (ptt)
REVERT: A  283 MET cc_start: 0.8870 (mmm) cc_final: 0.8629 (mmm)
REVERT: B  314 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7625 (tt0)
REVERT: C   82 MET cc_start: 0.8458 (tpt) cc_final: 0.8214 (tpt)
REVERT: H    5 CYS cc_start: 0.6770 (t) cc_final: 0.5783 (m)
  outliers start: 19
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0789
  time to fit residues: 12.6041
Evaluate side-chains
  95 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  314 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 125 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
D  12 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.072560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.061601 restraints weight = 34102.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063761 restraints weight = 17423.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.065212 restraints weight = 10820.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.066183 restraints weight = 7608.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066842 restraints weight = 5860.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11828  Z= 0.170
  Angle     :  0.601   7.990  16063  Z= 0.277
  Chirality :  0.044   0.212   1795
  Planarity :  0.004   0.037   2031
  Dihedral  :  8.939 135.673   1668
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.54 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.80 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.23), residues: 1418
  helix:  0.74 (0.23), residues: 593
  sheet:  0.18 (0.34), residues: 250
  loop :  0.55 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 177 
 TYR   0.016   0.001   TYR C 166 
 PHE   0.011   0.001   PHE D  31 
 TRP   0.011   0.002   TRP C 340 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (11822)
  covalent geometry    : angle       0.60149 (16045)
  hydrogen bonds       : bond        0.02979 (  525)
  hydrogen bonds       : angle       4.83043 ( 1329)
  link_TRANS           : bond        0.00254 (    6)
  link_TRANS           : angle       0.35960 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.8029 (t0) cc_final: 0.7546 (t0)
REVERT: A  132 MET cc_start: 0.7300 (ptt) cc_final: 0.7012 (ptt)
REVERT: B  314 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: H    5 CYS cc_start: 0.7064 (t) cc_final: 0.5876 (m)
  outliers start: 28
  outliers final: 23
  residues processed: 103
  average time/residue: 0.0791
  time to fit residues: 13.4370
Evaluate side-chains
  103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   17 CYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  314 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0370
   chunk 77 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 114 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 140 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.074701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.063688 restraints weight = 33691.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.065860 restraints weight = 17231.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.067315 restraints weight = 10693.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068302 restraints weight = 7523.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.068806 restraints weight = 5788.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11828  Z= 0.104
  Angle     :  0.563   8.797  16063  Z= 0.258
  Chirality :  0.043   0.204   1795
  Planarity :  0.003   0.036   2031
  Dihedral  :  8.684 142.664   1668
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.97 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.37 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.23), residues: 1418
  helix:  0.87 (0.23), residues: 590
  sheet:  0.22 (0.33), residues: 250
  loop :  0.75 (0.27), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 116 
 TYR   0.011   0.001   TYR B 143 
 PHE   0.012   0.001   PHE D  31 
 TRP   0.012   0.002   TRP C 340 
 HIS   0.003   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11822)
  covalent geometry    : angle       0.56346 (16045)
  hydrogen bonds       : bond        0.02619 (  525)
  hydrogen bonds       : angle       4.69682 ( 1329)
  link_TRANS           : bond        0.00153 (    6)
  link_TRANS           : angle       0.24832 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7963 (t0) cc_final: 0.7444 (t0)
REVERT: A  132 MET cc_start: 0.7291 (ptt) cc_final: 0.7020 (ptt)
REVERT: B  314 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7617 (tt0)
REVERT: D   44 MET cc_start: 0.7017 (ttp) cc_final: 0.6577 (ttp)
REVERT: D  132 MET cc_start: 0.6821 (tmm) cc_final: 0.6580 (tmm)
REVERT: D  227 MET cc_start: 0.8870 (mmm) cc_final: 0.8568 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 99
  average time/residue: 0.0813
  time to fit residues: 13.2265
Evaluate side-chains
  98 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  272 CYS
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  314 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 114 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 133 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0670
   chunk 121 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
D  12 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.075254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064497 restraints weight = 33795.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.066670 restraints weight = 17093.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.068108 restraints weight = 10505.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.069079 restraints weight = 7339.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.069735 restraints weight = 5609.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11828  Z= 0.097
  Angle     :  0.558   9.056  16063  Z= 0.255
  Chirality :  0.043   0.202   1795
  Planarity :  0.003   0.038   2031
  Dihedral  :  8.424 145.350   1668
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.97 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.53 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.23), residues: 1418
  helix:  0.85 (0.22), residues: 600
  sheet:  0.37 (0.32), residues: 268
  loop :  0.66 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 116 
 TYR   0.020   0.001   TYR C 166 
 PHE   0.012   0.001   PHE D  31 
 TRP   0.016   0.002   TRP A  86 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (11822)
  covalent geometry    : angle       0.55872 (16045)
  hydrogen bonds       : bond        0.02542 (  525)
  hydrogen bonds       : angle       4.60765 ( 1329)
  link_TRANS           : bond        0.00126 (    6)
  link_TRANS           : angle       0.23761 (   18)

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

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

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2836 Ramachandran restraints generated.
    1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 ASP cc_start: 0.7993 (t0) cc_final: 0.7470 (t0)
REVERT: A  132 MET cc_start: 0.7177 (ptt) cc_final: 0.6912 (ptt)
REVERT: B  118 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7575 (tptm)
REVERT: B  314 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7611 (tt0)
REVERT: D   44 MET cc_start: 0.7040 (ttp) cc_final: 0.6430 (ttp)
REVERT: D  132 MET cc_start: 0.6943 (tmm) cc_final: 0.6724 (tmm)
REVERT: D  227 MET cc_start: 0.8825 (mmm) cc_final: 0.8500 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0871
  time to fit residues: 14.0669
Evaluate side-chains
  99 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  118 LYS
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 GLN
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  314 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 131 optimal weight:    0.4980
   chunk 142 optimal weight:    0.8980
   chunk 31 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0270
   chunk 110 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 138 optimal weight:    0.9990
   overall best weight:    0.5440

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.075365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.064587 restraints weight = 33935.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.066762 restraints weight = 17221.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.068217 restraints weight = 10583.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.069198 restraints weight = 7375.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.069847 restraints weight = 5634.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11828  Z= 0.098
  Angle     :  0.556   8.661  16063  Z= 0.253
  Chirality :  0.043   0.200   1795
  Planarity :  0.003   0.040   2031
  Dihedral  :  8.212 143.807   1668
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.69 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.53 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.23), residues: 1418
  helix:  0.88 (0.22), residues: 600
  sheet:  0.42 (0.32), residues: 262
  loop :  0.71 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 116 
 TYR   0.008   0.001   TYR B 143 
 PHE   0.012   0.001   PHE D  31 
 TRP   0.021   0.002   TRP A  86 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11822)
  covalent geometry    : angle       0.55651 (16045)
  hydrogen bonds       : bond        0.02488 (  525)
  hydrogen bonds       : angle       4.56559 ( 1329)
  link_TRANS           : bond        0.00128 (    6)
  link_TRANS           : angle       0.22884 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1588.09 seconds
wall clock time: 28 minutes 33.34 seconds (1713.34 seconds total)