Starting phenix.real_space_refine
on Fri Mar 15 12:23:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_16887_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_16887.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_16887.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_16887_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/03_2024/8oi6_16887_updated.pdb"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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
    Residue "A ASP   80": "OD1" <-> "OD2"
    Residue "A GLU  117": "OE1" <-> "OE2"
    Residue "A GLU  125": "OE1" <-> "OE2"
    Residue "A PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  262": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  292": "OD1" <-> "OD2"
    Residue "C GLU  125": "OE1" <-> "OE2"
    Residue "C TYR  166": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  167": "OE1" <-> "OE2"
    Residue "C PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  157": "OD1" <-> "OD2"
    Residue "D GLU  241": "OE1" <-> "OE2"
    Residue "D ASP  286": "OD1" <-> "OD2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 11573
  Number of models: 1
  Model: ""
    Number of chains: 11
    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: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "I"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "J"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 55
          Classifications: {'peptide': 7}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    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: 6.53, per 1000 atoms: 0.56
  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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.45
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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...
  running ksdssp...
    Secondary structure from input PDB file:
      71 helices and 19 sheets defined
      42.9% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 79 through 91
    Processing helix  chain 'A' and resid 113 through 125
      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 145
      removed outlier: 3.699A  pdb=" N   TYR A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 196
      removed outlier: 3.863A  pdb=" N   THR A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLU A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ARG A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 213
      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 223 through 232
    Processing helix  chain 'A' and resid 252 through 261
      removed outlier: 4.594A  pdb=" N   CYS A 257 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      Proline residue:  A 258  - end of helix
    Processing helix  chain 'A' and resid 264 through 267
    Processing helix  chain 'A' and resid 274 through 284
      removed outlier: 3.599A  pdb=" N   ILE A 282 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.748A  pdb=" N   LYS A 291 " --> pdb=" O   ASP A 288 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP A 292 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ALA A 295 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 305
    Processing helix  chain 'A' and resid 309 through 320
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 5.145A  pdb=" N   VAL A 339 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA A 347 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
      removed outlier: 3.531A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 351 through 354'
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 367 through 370
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 79 through 92
      removed outlier: 3.570A  pdb=" N   LYS B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 125
      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 145
      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 174
      No H-bonds generated for 'chain 'B' and resid 172 through 174'
    Processing helix  chain 'B' and resid 182 through 195
      removed outlier: 3.678A  pdb=" N   THR B 194 " --> pdb=" O   MET B 190 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   GLU B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 216
      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)
    Processing helix  chain 'B' and resid 223 through 232
      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 262
      removed outlier: 3.532A  pdb=" N   ARG B 256 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   CYS B 257 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      Proline residue:  B 258  - end of helix
    Processing helix  chain 'B' and resid 264 through 267
    Processing helix  chain 'B' and resid 274 through 284
    Processing helix  chain 'B' and resid 287 through 296
      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)
      removed outlier: 4.047A  pdb=" N   ASN B 296 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 305
    Processing helix  chain 'B' and resid 309 through 320
      removed outlier: 3.568A  pdb=" N   LEU B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 348
      removed outlier: 4.946A  pdb=" N   VAL B 339 " --> pdb=" O   LYS B 336 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B 341 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY B 342 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 354
      removed outlier: 3.908A  pdb=" N   GLN B 354 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 351 through 354'
    Processing helix  chain 'B' and resid 359 through 365
      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 60
      removed outlier: 3.545A  pdb=" N   SER C  60 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 64
      No H-bonds generated for 'chain 'C' and resid 62 through 64'
    Processing helix  chain 'C' and resid 79 through 91
      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 113 through 125
    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 172 through 174
      No H-bonds generated for 'chain 'C' and resid 172 through 174'
    Processing helix  chain 'C' and resid 182 through 195
      removed outlier: 4.554A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 216
      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 223 through 232
    Processing helix  chain 'C' and resid 252 through 261
      removed outlier: 3.744A  pdb=" N   ARG C 256 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   CYS C 257 " --> pdb=" O   ARG C 254 " (cutoff:3.500A)
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 264 through 267
    Processing helix  chain 'C' and resid 274 through 284
    Processing helix  chain 'C' and resid 289 through 296
      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 302 through 305
    Processing helix  chain 'C' and resid 309 through 320
    Processing helix  chain 'C' and resid 335 through 348
      removed outlier: 5.058A  pdb=" N   VAL C 339 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY C 342 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA C 347 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 355
    Processing helix  chain 'C' and resid 359 through 365
      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 370
    Processing helix  chain 'D' and resid 55 through 60
      removed outlier: 3.531A  pdb=" N   SER D  60 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 64
      No H-bonds generated for 'chain 'D' and resid 62 through 64'
    Processing helix  chain 'D' and resid 79 through 91
      removed outlier: 3.652A  pdb=" N   GLU D  83 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 125
      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 144
      removed outlier: 3.746A  pdb=" N   LEU D 142 " --> pdb=" O   ALA D 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 195
      removed outlier: 3.513A  pdb=" N   THR D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   GLU D 195 " --> pdb=" O   LYS D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 216
      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 223 through 232
      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 236
      No H-bonds generated for 'chain 'D' and resid 234 through 236'
    Processing helix  chain 'D' and resid 253 through 256
      No H-bonds generated for 'chain 'D' and resid 253 through 256'
    Processing helix  chain 'D' and resid 258 through 262
    Processing helix  chain 'D' and resid 264 through 267
    Processing helix  chain 'D' and resid 274 through 284
      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)
    Processing helix  chain 'D' and resid 287 through 295
      removed outlier: 4.852A  pdb=" N   LYS D 291 " --> pdb=" O   ASP D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 305
    Processing helix  chain 'D' and resid 309 through 320
    Processing helix  chain 'D' and resid 338 through 348
    Processing helix  chain 'D' and resid 350 through 353
      removed outlier: 4.011A  pdb=" N   GLN D 353 " --> pdb=" O   SER D 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 350 through 353'
    Processing sheet with id=  A, first strand: chain 'A' and resid 132 through 136
      removed outlier: 6.809A  pdb=" N   VAL A 103 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   ALA A 135 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 135 " (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)
      removed outlier: 3.969A  pdb=" N   VAL A   9 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   PHE A  31 " --> pdb=" O   CYS A  17 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 52 through 54
      removed outlier: 3.839A  pdb=" N   ARG A  37 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 297 through 300
      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)
    Processing sheet with id=  D, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=  E, first strand: chain 'B' and resid 16 through 19
      removed outlier: 3.667A  pdb=" N   PHE B  31 " --> pdb=" O   CYS B  17 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 52 through 54
      removed outlier: 3.698A  pdb=" N   ARG B  37 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 103 through 107
    Processing sheet with id=  H, first strand: chain 'B' and resid 298 through 300
    Processing sheet with id=  I, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=  J, first strand: chain 'C' and resid 8 through 10
      removed outlier: 4.024A  pdb=" N   THR C 106 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'C' and resid 16 through 19
      removed outlier: 3.654A  pdb=" N   PHE C  31 " --> pdb=" O   CYS C  17 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'C' and resid 65 through 69
      removed outlier: 3.815A  pdb=" N   ARG C  37 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'C' and resid 298 through 300
      removed outlier: 3.705A  pdb=" N   SER C 155 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=  O, first strand: chain 'D' and resid 8 through 10
      removed outlier: 3.524A  pdb=" N   THR D 106 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR D 133 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'D' and resid 16 through 19
    Processing sheet with id=  Q, first strand: chain 'D' and resid 52 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=  R, first strand: chain 'D' and resid 297 through 300
      removed outlier: 6.351A  pdb=" N   ILE D 151 " --> pdb=" O   VAL D 298 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   SER D 300 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   MET D 153 " --> pdb=" O   SER D 300 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'D' and resid 238 through 241

    412 hydrogen bonds defined for protein.
    978 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: 3.17

  Time building geometry restraints manager: 4.80 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: 3737
        1.34 -     1.46: 2694
        1.46 -     1.58: 5233
        1.58 -     1.70: 18
        1.70 -     1.82: 143
  Bond restraints: 11825
  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 11820 not shown)

  Histogram of bond angle deviations from ideal:
       98.48 -   106.01: 362
      106.01 -   113.55: 6546
      113.55 -   121.08: 5906
      121.08 -   128.62: 3159
      128.62 -   136.15: 81
  Bond angle restraints: 16054
  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 16049 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.98: 6867
       33.98 -    67.96: 220
       67.96 -   101.94: 17
      101.94 -   135.92: 4
      135.92 -   169.90: 3
  Dihedral angle restraints: 7111
    sinusoidal: 2873
      harmonic: 4238
  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 7108 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1562
       0.061 -    0.122: 226
       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: 2034
  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 2031 not shown)

  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 6
        2.03 -     2.75: 1205
        2.75 -     3.46: 16457
        3.46 -     4.18: 27649
        4.18 -     4.90: 50002
  Nonbonded interactions: 95319
  Sorted by model distance:
  nonbonded pdb=" N   TRP I   1 "
            pdb=" C   ALA I   7 "
     model   vdw
     1.310 3.350
  nonbonded pdb=" N   TRP J   1 "
            pdb=" C   ALA J   7 "
     model   vdw
     1.312 3.350
  nonbonded pdb=" N   TRP H   1 "
            pdb=" C   ALA H   7 "
     model   vdw
     1.313 3.350
  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
  ... (remaining 95314 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
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:             3.300
  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:          12.400
  Check model and map are aligned:         0.180
  Set scattering table:                    0.110
  Process input model:                     34.850
  Find NCS groups from input model:        0.750
  Set up NCS constraints:                  0.070
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.310
-------------------------------------------------------------------------------
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  11825  Z= 0.330
  Angle     :  0.640   8.991  16054  Z= 0.300
  Chirality :  0.043   0.306   1795
  Planarity :  0.003   0.040   2034
  Dihedral  : 16.968 169.900   4389
  Min Nonbonded Distance : 1.310

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (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
 TRP   0.014   0.001   TRP B  86 
 HIS   0.011   0.001   HIS B 371 
 PHE   0.008   0.001   PHE A 124 
 TYR   0.028   0.001   TYR C 166 
 ARG   0.003   0.000   ARG A 116 

*********************** 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 fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 1.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 88
  average time/residue: 0.2021
  time to fit residues: 27.8619
Evaluate side-chains
  84 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
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 120 optimal weight:   10.0000
   chunk 108 optimal weight:    9.9990
   chunk 60 optimal weight:    0.4980
   chunk 37 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  11825  Z= 0.417
  Angle     :  0.682   7.414  16054  Z= 0.328
  Chirality :  0.048   0.249   1795
  Planarity :  0.004   0.038   2034
  Dihedral  : 12.155 176.218   1676
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.82 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.22), residues: 1418
  helix: -0.08 (0.21), residues: 558
  sheet:  0.46 (0.33), residues: 250
  loop :  0.43 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP I   1 
 HIS   0.006   0.001   HIS B 101 
 PHE   0.020   0.002   PHE C 352 
 TYR   0.018   0.002   TYR B 143 
 ARG   0.003   0.001   ARG B 183 

*********************** 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
  111 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 1.248 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8005 (t0) cc_final: 0.7641 (t0)
REVERT: B  132 MET cc_start: 0.8428 (ttp) cc_final: 0.7690 (ttp)
REVERT: B  283 MET cc_start: 0.8611 (mmm) cc_final: 0.8349 (tpp)
REVERT: C  330 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9192 (tp)
REVERT: I    5 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7196 (p)
  outliers start: 34
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1803
  time to fit residues: 31.3266
Evaluate side-chains
  92 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASP
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  338 SER
Chi-restraints excluded: chain B residue  370 VAL
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 C residue  330 ILE
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 108 optimal weight:    7.9990
   chunk 88 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 130 optimal weight:   10.0000
   chunk 140 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11825  Z= 0.234
  Angle     :  0.581   7.417  16054  Z= 0.270
  Chirality :  0.045   0.209   1795
  Planarity :  0.004   0.037   2034
  Dihedral  : 11.268 167.852   1671
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.68 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.90 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.22), residues: 1418
  helix:  0.10 (0.22), residues: 560
  sheet:  0.43 (0.33), residues: 249
  loop :  0.45 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  87 
 PHE   0.013   0.001   PHE D  31 
 TYR   0.016   0.001   TYR B 143 
 ARG   0.002   0.000   ARG D 254 

*********************** 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
  105 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 1.241 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8028 (t0) cc_final: 0.7527 (t0)
REVERT: B  269 MET cc_start: 0.7777 (mtp) cc_final: 0.7537 (mtm)
REVERT: D  132 MET cc_start: 0.7480 (tmm) cc_final: 0.7056 (ppp)
REVERT: D  305 MET cc_start: 0.8097 (tpp) cc_final: 0.7806 (tpp)
REVERT: D  355 MET cc_start: 0.7783 (pmm) cc_final: 0.7406 (pmm)
REVERT: I    5 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6979 (p)
  outliers start: 27
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1892
  time to fit residues: 30.3525
Evaluate side-chains
  93 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   85 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  300 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  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue  129 THR
Chi-restraints excluded: chain D residue  314 GLN
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 128 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 138 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
A 137 GLN
B  12 ASN
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 280 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073  11825  Z= 0.400
  Angle     :  0.653   7.151  16054  Z= 0.308
  Chirality :  0.047   0.211   1795
  Planarity :  0.004   0.038   2034
  Dihedral  : 10.530 142.103   1671
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.67 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.98 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.23), residues: 1418
  helix:  0.06 (0.22), residues: 569
  sheet:  0.22 (0.34), residues: 253
  loop :  0.25 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 340 
 HIS   0.006   0.001   HIS B 101 
 PHE   0.015   0.002   PHE C 352 
 TYR   0.015   0.002   TYR B 143 
 ARG   0.005   0.001   ARG D 147 

*********************** 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
  115 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 1.392 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8028 (t0) cc_final: 0.7419 (t0)
REVERT: A  283 MET cc_start: 0.8916 (mmm) cc_final: 0.8569 (mmm)
REVERT: C   89 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9026 (t)
REVERT: D  132 MET cc_start: 0.7670 (tmm) cc_final: 0.7324 (ppp)
REVERT: D  180 LEU cc_start: 0.7784 (tp) cc_final: 0.7507 (tp)
REVERT: D  305 MET cc_start: 0.8083 (tpp) cc_final: 0.7749 (tpp)
REVERT: I    5 CYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7144 (p)
  outliers start: 39
  outliers final: 24
  residues processed: 108
  average time/residue: 0.1703
  time to fit residues: 30.1983
Evaluate side-chains
  102 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 1.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   25 ASP
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   85 ILE
Chi-restraints excluded: chain B residue   89 THR
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  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  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  199 SER
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain D residue  318 THR
Chi-restraints excluded: chain D residue  325 MET
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 115 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 117 optimal weight:    7.9990
   chunk 95 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   overall best weight:    0.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11825  Z= 0.204
  Angle     :  0.564   6.823  16054  Z= 0.259
  Chirality :  0.044   0.198   1795
  Planarity :  0.003   0.036   2034
  Dihedral  :  9.999 138.435   1671
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.40 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.23 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.23), residues: 1418
  helix:  0.26 (0.22), residues: 567
  sheet:  0.20 (0.34), residues: 252
  loop :  0.36 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 340 
 HIS   0.003   0.001   HIS B 275 
 PHE   0.011   0.001   PHE D  31 
 TYR   0.008   0.001   TYR A 169 
 ARG   0.002   0.000   ARG B 147 

*********************** 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
  111 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 1.469 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7992 (t0) cc_final: 0.7420 (t0)
REVERT: A  283 MET cc_start: 0.9006 (mmm) cc_final: 0.8796 (mmm)
REVERT: B  269 MET cc_start: 0.7769 (mtp) cc_final: 0.7532 (mtm)
REVERT: C   89 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9076 (t)
REVERT: D  132 MET cc_start: 0.7715 (tmm) cc_final: 0.7394 (ppp)
REVERT: D  305 MET cc_start: 0.8068 (tpp) cc_final: 0.7688 (tpp)
REVERT: I    5 CYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6913 (p)
  outliers start: 33
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1783
  time to fit residues: 30.8372
Evaluate side-chains
  99 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
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  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  292 ASP
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain D residue  199 SER
Chi-restraints excluded: chain D residue  278 THR
Chi-restraints excluded: chain D residue  314 GLN
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 46 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B  88 HIS
D 246 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11825  Z= 0.240
  Angle     :  0.575   6.849  16054  Z= 0.265
  Chirality :  0.044   0.193   1795
  Planarity :  0.004   0.036   2034
  Dihedral  :  9.733 133.349   1671
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.75 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.88 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.23), residues: 1418
  helix:  0.32 (0.22), residues: 569
  sheet:  0.13 (0.34), residues: 252
  loop :  0.32 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 356 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.012   0.001   PHE D  31 
 TYR   0.009   0.001   TYR C 294 
 ARG   0.002   0.000   ARG B 147 

*********************** 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
  112 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8050 (t0) cc_final: 0.7503 (t0)
REVERT: A  283 MET cc_start: 0.9020 (mmm) cc_final: 0.8610 (mmm)
REVERT: B  118 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7735 (tptt)
REVERT: B  132 MET cc_start: 0.8486 (tmm) cc_final: 0.8089 (ppp)
REVERT: B  269 MET cc_start: 0.7703 (mtp) cc_final: 0.7475 (mtm)
REVERT: C   89 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9133 (t)
REVERT: D  132 MET cc_start: 0.7814 (tmm) cc_final: 0.7524 (ppp)
REVERT: D  305 MET cc_start: 0.8232 (tpp) cc_final: 0.7848 (tpp)
REVERT: D  355 MET cc_start: 0.7672 (pmm) cc_final: 0.7008 (pmm)
REVERT: I    5 CYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6873 (p)
  outliers start: 35
  outliers final: 22
  residues processed: 108
  average time/residue: 0.1959
  time to fit residues: 33.1324
Evaluate side-chains
  100 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  371 HIS
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   89 THR
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  278 THR
Chi-restraints excluded: chain B residue  300 SER
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  292 ASP
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  199 SER
Chi-restraints excluded: chain D residue  278 THR
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 133 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 137 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11825  Z= 0.222
  Angle     :  0.568   8.660  16054  Z= 0.260
  Chirality :  0.044   0.191   1795
  Planarity :  0.003   0.036   2034
  Dihedral  :  9.431 132.809   1671
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.33 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 19.77 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.23), residues: 1418
  helix:  0.29 (0.22), residues: 575
  sheet:  0.11 (0.33), residues: 252
  loop :  0.33 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  79 
 HIS   0.013   0.001   HIS B 371 
 PHE   0.013   0.001   PHE D  31 
 TYR   0.008   0.001   TYR A  69 
 ARG   0.002   0.000   ARG B 147 

*********************** 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
  110 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 77
  time to evaluate  : 1.409 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8036 (t0) cc_final: 0.7472 (t0)
REVERT: A  283 MET cc_start: 0.9026 (mmm) cc_final: 0.8651 (mmm)
REVERT: B  118 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7628 (tptm)
REVERT: B  132 MET cc_start: 0.8550 (tmm) cc_final: 0.8110 (ppp)
REVERT: B  269 MET cc_start: 0.7772 (mtp) cc_final: 0.7540 (mtm)
REVERT: C   89 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9142 (t)
REVERT: D  305 MET cc_start: 0.8228 (tpp) cc_final: 0.7860 (tpp)
REVERT: D  355 MET cc_start: 0.7697 (pmm) cc_final: 0.7118 (pmm)
REVERT: I    5 CYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6815 (p)
  outliers start: 33
  outliers final: 23
  residues processed: 105
  average time/residue: 0.1884
  time to fit residues: 31.8472
Evaluate side-chains
  102 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   17 CYS
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue   89 THR
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  278 THR
Chi-restraints excluded: chain B residue  300 SER
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  292 ASP
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  199 SER
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   chunk 125 optimal weight:    3.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11825  Z= 0.182
  Angle     :  0.552  10.990  16054  Z= 0.250
  Chirality :  0.043   0.193   1795
  Planarity :  0.003   0.036   2034
  Dihedral  :  8.975 141.509   1671
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.47 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.34 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.23), residues: 1418
  helix:  0.44 (0.23), residues: 557
  sheet:  0.17 (0.33), residues: 252
  loop :  0.48 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  79 
 HIS   0.009   0.001   HIS B 371 
 PHE   0.013   0.001   PHE D  31 
 TYR   0.008   0.001   TYR B 143 
 ARG   0.002   0.000   ARG B 147 

*********************** 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
  103 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7973 (t0) cc_final: 0.7418 (t0)
REVERT: A  283 MET cc_start: 0.9013 (mmm) cc_final: 0.8752 (mmm)
REVERT: B  118 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7645 (tptm)
REVERT: B  132 MET cc_start: 0.8559 (tmm) cc_final: 0.8262 (ppp)
REVERT: B  269 MET cc_start: 0.7774 (mtp) cc_final: 0.7543 (mtm)
REVERT: D  305 MET cc_start: 0.8179 (tpp) cc_final: 0.7860 (tpp)
REVERT: D  355 MET cc_start: 0.7654 (pmm) cc_final: 0.7111 (pmm)
REVERT: I    5 CYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6759 (p)
  outliers start: 26
  outliers final: 19
  residues processed: 99
  average time/residue: 0.1870
  time to fit residues: 29.7338
Evaluate side-chains
  97 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  324 THR
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  272 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  300 SER
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  292 ASP
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  199 SER
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 120 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   chunk 127 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
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      :  0.003   0.038  11825  Z= 0.207
  Angle     :  0.570   9.887  16054  Z= 0.260
  Chirality :  0.044   0.192   1795
  Planarity :  0.003   0.036   2034
  Dihedral  :  8.751 146.175   1671
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.40 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.42 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.23), residues: 1418
  helix:  0.39 (0.23), residues: 563
  sheet:  0.14 (0.33), residues: 256
  loop :  0.49 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  79 
 HIS   0.009   0.001   HIS B 371 
 PHE   0.012   0.001   PHE D  31 
 TYR   0.017   0.001   TYR C 166 
 ARG   0.003   0.000   ARG A 116 

*********************** 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 fitting.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 1.546 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.8007 (t0) cc_final: 0.7488 (t0)
REVERT: A  283 MET cc_start: 0.9024 (mmm) cc_final: 0.8722 (mmm)
REVERT: B  118 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7800 (tptm)
REVERT: B  269 MET cc_start: 0.7788 (mtp) cc_final: 0.7553 (mtm)
REVERT: D  305 MET cc_start: 0.8183 (tpp) cc_final: 0.7859 (tpp)
REVERT: D  355 MET cc_start: 0.7675 (pmm) cc_final: 0.7157 (pmm)
REVERT: I    5 CYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6768 (p)
  outliers start: 25
  outliers final: 22
  residues processed: 99
  average time/residue: 0.1828
  time to fit residues: 29.4396
Evaluate side-chains
  101 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASP
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   17 CYS
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  272 CYS
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  300 SER
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  292 ASP
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  199 SER
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0070
   chunk 64 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0970
   chunk 142 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.3394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11825  Z= 0.131
  Angle     :  0.537   8.441  16054  Z= 0.244
  Chirality :  0.043   0.191   1795
  Planarity :  0.003   0.035   2034
  Dihedral  :  8.473 150.358   1671
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  1.90 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.67 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.23), residues: 1418
  helix:  0.53 (0.23), residues: 560
  sheet:  0.24 (0.33), residues: 254
  loop :  0.60 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  86 
 HIS   0.007   0.001   HIS B 371 
 PHE   0.012   0.001   PHE D  31 
 TYR   0.007   0.001   TYR A 143 
 ARG   0.002   0.000   ARG A 335 

********************** 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
  100 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 1.345 
Fit side-chains
REVERT: A   80 ASP cc_start: 0.7916 (t0) cc_final: 0.7379 (t0)
REVERT: A  283 MET cc_start: 0.8988 (mmm) cc_final: 0.8740 (mmm)
REVERT: B  118 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7575 (tptm)
REVERT: B  269 MET cc_start: 0.7785 (mtp) cc_final: 0.7547 (mtm)
REVERT: C  325 MET cc_start: 0.8097 (ppp) cc_final: 0.7305 (ppp)
REVERT: D  227 MET cc_start: 0.8796 (mmm) cc_final: 0.8478 (mmm)
REVERT: D  305 MET cc_start: 0.8183 (tpp) cc_final: 0.7935 (tpp)
REVERT: D  355 MET cc_start: 0.7614 (pmm) cc_final: 0.7189 (pmm)
REVERT: I    5 CYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6666 (p)
  outliers start: 20
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1904
  time to fit residues: 29.9501
Evaluate side-chains
  96 residues out of total 1229 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASN
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   17 CYS
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  278 THR
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  292 ASP
Chi-restraints excluded: chain D residue   89 THR
Chi-restraints excluded: chain D residue  314 GLN
Chi-restraints excluded: chain D residue  325 MET
Chi-restraints excluded: chain I residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0470
   chunk 104 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.3814

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.073480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.062625 restraints weight = 34173.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.064823 restraints weight = 17167.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.066274 restraints weight = 10479.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11825  Z= 0.128
  Angle     :  0.537   8.675  16054  Z= 0.241
  Chirality :  0.043   0.186   1795
  Planarity :  0.003   0.035   2034
  Dihedral  :  8.266 150.104   1671
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.12 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 20.67 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.23), residues: 1418
  helix:  0.57 (0.23), residues: 563
  sheet:  0.28 (0.33), residues: 254
  loop :  0.69 (0.27), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  86 
 HIS   0.006   0.001   HIS B 371 
 PHE   0.012   0.001   PHE D  31 
 TYR   0.018   0.001   TYR C 166 
 ARG   0.001   0.000   ARG D 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2023.35 seconds
wall clock time: 37 minutes 43.96 seconds (2263.96 seconds total)