Starting phenix.real_space_refine
on Sun May 11 23:18:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhi_36266/05_2025/8jhi_36266.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5454      2.51       5
     N    1479      2.21       5
     O    1566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8562
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1953
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2592
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 962
          Classifications: {'peptide': 126}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2619
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 322, 2614
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306}
          Unresolved chain links: 1
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "C"
        Number of residues, atoms: 322, 2614
          Classifications: {'peptide': 322}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306}
          Unresolved chain links: 1
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 2680
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  BALA R 392 " occ=0.33
      ... (8 atoms not shown)
      pdb=" CB CALA R 392 " occ=0.67
  Time building chain proxies: 6.26, per 1000 atoms: 0.73
  Number of scatterers: 8562
  At special positions: 0
  Unit cell: (78.208, 98.176, 151.424, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1566      8.00
     N    1479      7.00
     C    5454      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  45 " - pdb=" SG  CYS N 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 122 " - pdb=" SG  CYS N 130 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 165 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 189 " - pdb=" SG  CYS R 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 286 " - pdb=" SG  CYS R 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 458 " - pdb=" SG  CYS R 465 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      38.3% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 35
      removed outlier: 4.146A  pdb=" N   MET A  30 " --> pdb=" O   GLN A  26 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLY A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR A  35 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 253 through 278
      removed outlier: 4.100A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.539A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.790A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.908A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.687A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   GLN A 390 " --> pdb=" O   MET A 386 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.550A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 45
    Processing helix  chain 'C' and resid 53 through 68
    Processing helix  chain 'N' and resid 51 through 55
      removed outlier: 3.757A  pdb=" N   TYR N  55 " --> pdb=" O   PHE N  52 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 85 through 88
      removed outlier: 3.514A  pdb=" N   LYS N  88 " --> pdb=" O   GLY N  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 85 through 88'
    Processing helix  chain 'N' and resid 110 through 114
      removed outlier: 3.677A  pdb=" N   THR N 114 " --> pdb=" O   PRO N 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 225
      removed outlier: 4.313A  pdb=" N   ILE R 212 " --> pdb=" O   LEU R 208 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER R 215 " --> pdb=" O   ILE R 211 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA R 216 " --> pdb=" O   ILE R 212 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   THR R 217 " --> pdb=" O   CYS R 213 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR R 220 " --> pdb=" O   ALA R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 236
    Processing helix  chain 'R' and resid 237 through 264
      removed outlier: 3.941A  pdb=" N   VAL R 248 " --> pdb=" O   CYS R 244 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ASP R 260 " --> pdb=" O   PHE R 256 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ARG R 261 " --> pdb=" O   LEU R 257 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ALA R 263 " --> pdb=" O   GLU R 259 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 292
      removed outlier: 3.909A  pdb=" N   THR R 287 " --> pdb=" O   ASN R 283 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET R 288 " --> pdb=" O   LYS R 284 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU R 289 " --> pdb=" O   ALA R 285 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 316
    Processing helix  chain 'R' and resid 324 through 326
      No H-bonds generated for 'chain 'R' and resid 324 through 326'
    Processing helix  chain 'R' and resid 327 through 336
    Processing helix  chain 'R' and resid 336 through 341
    Processing helix  chain 'R' and resid 344 through 348
    Processing helix  chain 'R' and resid 375 through 408
      removed outlier: 3.808A  pdb=" N   VAL R 400 " --> pdb=" O   SER R 396 " (cutoff:3.500A)
      Proline residue:  R 405  - end of helix
    Processing helix  chain 'R' and resid 413 through 457
      Proline residue:  R 431  - end of helix
      removed outlier: 5.363A  pdb=" N   GLY R 447 " --> pdb=" O   GLN R 443 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   ILE R 448 " --> pdb=" O   ALA R 444 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 476 through 490
      removed outlier: 3.512A  pdb=" N   PHE R 480 " --> pdb=" O   ASP R 476 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 492 through 497
      removed outlier: 3.772A  pdb=" N   PHE R 496 " --> pdb=" O   ILE R 492 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.243A  pdb=" N   HIS A  36 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  36 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ARG A  37 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  37 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LEU A  39 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.505A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.913A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.128A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.599A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.940A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.710A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.664A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 26 through 30
    Processing sheet with id=AB1, first strand: chain 'N' and resid 81 through 83
      removed outlier: 3.669A  pdb=" N   SER N  82 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   TRP N  70 " --> pdb=" O   ARG N  61 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   ARG N  61 " --> pdb=" O   TRP N  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 352 through 354

    376 hydrogen bonds defined for protein.
    1054 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2782
        1.35 -     1.48: 2214
        1.48 -     1.60: 3659
        1.60 -     1.73: 0
        1.73 -     1.86: 90
  Bond restraints: 8745
  Sorted by residual:
  bond pdb=" C   ARG R 236 "
       pdb=" N   PRO R 237 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.47e+00
  bond pdb=" CB  ILE R 292 "
       pdb=" CG1 ILE R 292 "
    ideal  model  delta    sigma   weight residual
    1.530  1.563 -0.033 2.00e-02 2.50e+03 2.68e+00
  bond pdb=" CA  ILE R 292 "
       pdb=" CB  ILE R 292 "
    ideal  model  delta    sigma   weight residual
    1.540  1.583 -0.043 2.70e-02 1.37e+03 2.48e+00
  bond pdb=" CB  CYS R 286 "
       pdb=" SG  CYS R 286 "
    ideal  model  delta    sigma   weight residual
    1.808  1.856 -0.048 3.30e-02 9.18e+02 2.11e+00
  bond pdb=" CB  CYS N 122 "
       pdb=" SG  CYS N 122 "
    ideal  model  delta    sigma   weight residual
    1.808  1.767  0.041 3.30e-02 9.18e+02 1.57e+00
  ... (remaining 8740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 11476
        1.79 -     3.57: 298
        3.57 -     5.36: 36
        5.36 -     7.14: 20
        7.14 -     8.93: 4
  Bond angle restraints: 11834
  Sorted by residual:
  angle pdb=" CA  CYS R 286 "
        pdb=" CB  CYS R 286 "
        pdb=" SG  CYS R 286 "
      ideal   model   delta    sigma   weight residual
     114.40  123.33   -8.93 2.30e+00 1.89e-01 1.51e+01
  angle pdb=" C   LEU R 258 "
        pdb=" N   GLU R 259 "
        pdb=" CA  GLU R 259 "
      ideal   model   delta    sigma   weight residual
     121.76  128.43   -6.67 2.19e+00 2.09e-01 9.27e+00
  angle pdb=" C   TYR R 461 "
        pdb=" N   HIS R 462 "
        pdb=" CA  HIS R 462 "
      ideal   model   delta    sigma   weight residual
     121.54  127.35   -5.81 1.91e+00 2.74e-01 9.24e+00
  angle pdb=" C   LYS R 408 "
        pdb=" N   GLU R 409 "
        pdb=" CA  GLU R 409 "
      ideal   model   delta    sigma   weight residual
     121.54  127.08   -5.54 1.91e+00 2.74e-01 8.42e+00
  angle pdb=" N   GLU B  10 "
        pdb=" CA  GLU B  10 "
        pdb=" CB  GLU B  10 "
      ideal   model   delta    sigma   weight residual
     110.39  115.19   -4.80 1.66e+00 3.63e-01 8.35e+00
  ... (remaining 11829 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 4684
       17.77 -    35.55: 439
       35.55 -    53.32: 74
       53.32 -    71.09: 15
       71.09 -    88.87: 9
  Dihedral angle restraints: 5221
    sinusoidal: 2094
      harmonic: 3127
  Sorted by residual:
  dihedral pdb=" CB  CYS N 122 "
           pdb=" SG  CYS N 122 "
           pdb=" SG  CYS N 130 "
           pdb=" CB  CYS N 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.41   54.41     1      1.00e+01 1.00e-02 4.01e+01
  dihedral pdb=" CB  CYS R 165 "
           pdb=" SG  CYS R 165 "
           pdb=" SG  CYS R 185 "
           pdb=" CB  CYS R 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.85   51.85     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CA  SER R 215 "
           pdb=" C   SER R 215 "
           pdb=" N   ALA R 216 "
           pdb=" CA  ALA R 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.08  -22.92     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 5218 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 823
       0.037 -    0.074: 361
       0.074 -    0.110: 100
       0.110 -    0.147: 28
       0.147 -    0.184: 5
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CG  LEU A 291 "
            pdb=" CB  LEU A 291 "
            pdb=" CD1 LEU A 291 "
            pdb=" CD2 LEU A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.47e-01
  chirality pdb=" CA  TYR R 233 "
            pdb=" N   TYR R 233 "
            pdb=" C   TYR R 233 "
            pdb=" CB  TYR R 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.85e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.33e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 121 "    0.194 9.50e-02 1.11e+02   8.70e-02 4.70e+00
        pdb=" NE  ARG N 121 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 121 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 121 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 121 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 463 "    0.035 5.00e-02 4.00e+02   5.35e-02 4.58e+00
        pdb=" N   PRO R 464 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO R 464 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 464 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR N 140 "    0.014 2.00e-02 2.50e+03   1.51e-02 4.54e+00
        pdb=" CG  TYR N 140 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR N 140 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR N 140 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR N 140 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR N 140 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR N 140 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR N 140 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 271
        2.71 -     3.26: 8446
        3.26 -     3.80: 14003
        3.80 -     4.35: 17259
        4.35 -     4.90: 28633
  Nonbonded interactions: 68612
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 241 "
            pdb=" O   VAL R 490 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   GLU B 226 "
            pdb=" NH2 ARG N 121 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.285 3.040
  ... (remaining 68607 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.33 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.250
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8751  Z= 0.166
  Angle     :  0.711   8.929  11846  Z= 0.364
  Chirality :  0.045   0.184   1317
  Planarity :  0.006   0.087   1505
  Dihedral  : 14.305  88.867   3185
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.87 (0.25), residues: 1060
  helix:  0.24 (0.27), residues: 361
  sheet:  0.14 (0.35), residues: 219
  loop : -1.55 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 453 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.019   0.002   PHE R 480 
 TYR   0.037   0.002   TYR N 140 
 ARG   0.005   0.000   ARG R 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13107 (  376)
  hydrogen bonds       : angle       5.52726 ( 1054)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       2.62952 (   12)
  covalent geometry    : bond        0.00371 ( 8745)
  covalent geometry    : angle       0.70653 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 TYR cc_start: 0.8762 (m-10) cc_final: 0.8512 (m-10)
REVERT: B  292 PHE cc_start: 0.8266 (m-10) cc_final: 0.7893 (m-10)
REVERT: C   41 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8419 (tm-30)
REVERT: R  192 MET cc_start: 0.6198 (pmm) cc_final: 0.5666 (pmm)
REVERT: R  298 MET cc_start: 0.7031 (mmp) cc_final: 0.6673 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2591
  time to fit residues: 79.0851
Evaluate side-chains
  170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 44 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 220 GLN
B 340 ASN
N 105 GLN
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.161873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.121440 restraints weight = 13576.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 3.57
r_work: 0.3471 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8751  Z= 0.137
  Angle     :  0.626   7.139  11846  Z= 0.322
  Chirality :  0.043   0.166   1317
  Planarity :  0.005   0.049   1505
  Dihedral  :  4.603  30.764   1183
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.43 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.47 (0.26), residues: 1060
  helix:  0.81 (0.29), residues: 359
  sheet:  0.15 (0.36), residues: 213
  loop : -1.38 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 453 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.044   0.002   PHE R 219 
 TYR   0.020   0.001   TYR R 241 
 ARG   0.006   0.000   ARG R 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  376)
  hydrogen bonds       : angle       4.64029 ( 1054)
  SS BOND              : bond        0.00153 (    6)
  SS BOND              : angle       1.70795 (   12)
  covalent geometry    : bond        0.00310 ( 8745)
  covalent geometry    : angle       0.62368 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8725 (tt0)
REVERT: A  390 GLN cc_start: 0.8217 (mp10) cc_final: 0.7838 (mp10)
REVERT: B  111 TYR cc_start: 0.9147 (m-10) cc_final: 0.8869 (m-10)
REVERT: B  262 MET cc_start: 0.8158 (tpp) cc_final: 0.7486 (tpp)
REVERT: B  292 PHE cc_start: 0.8660 (m-10) cc_final: 0.8242 (m-10)
REVERT: C   41 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: C   51 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6485 (mtm180)
REVERT: R  298 MET cc_start: 0.7817 (mmp) cc_final: 0.7481 (mmm)
  outliers start: 23
  outliers final: 17
  residues processed: 194
  average time/residue: 0.2368
  time to fit residues: 61.8234
Evaluate side-chains
  188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 101 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 110 ASN
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.155133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.113648 restraints weight = 13570.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 3.53
r_work: 0.3422 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8751  Z= 0.172
  Angle     :  0.632   8.735  11846  Z= 0.323
  Chirality :  0.044   0.160   1317
  Planarity :  0.004   0.051   1505
  Dihedral  :  4.531  30.313   1183
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 13.70 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.33 (0.27), residues: 1060
  helix:  0.99 (0.29), residues: 360
  sheet:  0.19 (0.37), residues: 204
  loop : -1.32 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.034   0.002   PHE R 219 
 TYR   0.022   0.002   TYR R 241 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  376)
  hydrogen bonds       : angle       4.42616 ( 1054)
  SS BOND              : bond        0.00145 (    6)
  SS BOND              : angle       1.79310 (   12)
  covalent geometry    : bond        0.00398 ( 8745)
  covalent geometry    : angle       0.62959 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8341 (mm-30)
REVERT: A  220 HIS cc_start: 0.8023 (m-70) cc_final: 0.7766 (m-70)
REVERT: B   19 ARG cc_start: 0.7442 (tmm-80) cc_final: 0.7226 (ttp-110)
REVERT: B   61 MET cc_start: 0.8980 (ppp) cc_final: 0.8515 (ppp)
REVERT: B  260 GLU cc_start: 0.8612 (tt0) cc_final: 0.8221 (tm-30)
REVERT: B  262 MET cc_start: 0.8233 (tpp) cc_final: 0.7256 (tpp)
REVERT: B  289 TYR cc_start: 0.9173 (m-80) cc_final: 0.8898 (m-80)
REVERT: C   41 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8372 (tm-30)
REVERT: C   51 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7170 (mtm180)
REVERT: N   28 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8367 (mm-40)
  outliers start: 30
  outliers final: 23
  residues processed: 196
  average time/residue: 0.2203
  time to fit residues: 57.9807
Evaluate side-chains
  198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 175
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Chi-restraints excluded: chain R residue  387 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 90 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.155273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.114021 restraints weight = 13479.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 3.55
r_work: 0.3438 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8751  Z= 0.129
  Angle     :  0.607   8.026  11846  Z= 0.307
  Chirality :  0.042   0.157   1317
  Planarity :  0.004   0.049   1505
  Dihedral  :  4.417  29.660   1183
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.15 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.27 (0.27), residues: 1060
  helix:  1.15 (0.29), residues: 360
  sheet:  0.11 (0.37), residues: 207
  loop : -1.33 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.048   0.002   PHE R 219 
 TYR   0.016   0.001   TYR R 204 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  376)
  hydrogen bonds       : angle       4.28213 ( 1054)
  SS BOND              : bond        0.00111 (    6)
  SS BOND              : angle       1.55064 (   12)
  covalent geometry    : bond        0.00299 ( 8745)
  covalent geometry    : angle       0.60534 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 182
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8325 (mm-30)
REVERT: A  220 HIS cc_start: 0.7980 (m-70) cc_final: 0.7708 (m-70)
REVERT: B   19 ARG cc_start: 0.7440 (tmm-80) cc_final: 0.7195 (ttp-110)
REVERT: B   61 MET cc_start: 0.8990 (ppp) cc_final: 0.8489 (ppp)
REVERT: B  262 MET cc_start: 0.8215 (tpp) cc_final: 0.7550 (tpp)
REVERT: B  292 PHE cc_start: 0.8765 (m-80) cc_final: 0.8360 (m-80)
REVERT: C   41 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: C   51 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7073 (mtm180)
REVERT: R  221 PHE cc_start: 0.6825 (m-80) cc_final: 0.6258 (m-80)
REVERT: R  246 MET cc_start: 0.7660 (mmt) cc_final: 0.7255 (tpp)
REVERT: R  298 MET cc_start: 0.7845 (mmp) cc_final: 0.7290 (mmm)
  outliers start: 24
  outliers final: 20
  residues processed: 188
  average time/residue: 0.2111
  time to fit residues: 53.8534
Evaluate side-chains
  190 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** R 411 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.155233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.113770 restraints weight = 13514.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 3.56
r_work: 0.3429 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8751  Z= 0.125
  Angle     :  0.588   8.019  11846  Z= 0.299
  Chirality :  0.042   0.158   1317
  Planarity :  0.004   0.048   1505
  Dihedral  :  4.316  29.132   1183
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.02 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 (0.26), residues: 1060
  helix:  1.17 (0.29), residues: 365
  sheet:  0.11 (0.37), residues: 207
  loop : -1.36 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.002   0.001   HIS R 181 
 PHE   0.040   0.001   PHE R 219 
 TYR   0.015   0.001   TYR R 245 
 ARG   0.003   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  376)
  hydrogen bonds       : angle       4.18248 ( 1054)
  SS BOND              : bond        0.00520 (    6)
  SS BOND              : angle       1.41165 (   12)
  covalent geometry    : bond        0.00288 ( 8745)
  covalent geometry    : angle       0.58667 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7757 (tt0)
REVERT: A  220 HIS cc_start: 0.7989 (m-70) cc_final: 0.7744 (m-70)
REVERT: B   19 ARG cc_start: 0.7498 (tmm-80) cc_final: 0.7215 (ttp-110)
REVERT: B   61 MET cc_start: 0.8922 (ppp) cc_final: 0.8456 (ppp)
REVERT: B  111 TYR cc_start: 0.9150 (m-80) cc_final: 0.8876 (m-10)
REVERT: B  260 GLU cc_start: 0.8639 (tt0) cc_final: 0.8236 (tm-30)
REVERT: B  262 MET cc_start: 0.8254 (tpp) cc_final: 0.7340 (tpp)
REVERT: B  292 PHE cc_start: 0.8712 (m-80) cc_final: 0.8332 (m-80)
REVERT: C   41 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8338 (tm-30)
REVERT: R  184 ASP cc_start: 0.6977 (t0) cc_final: 0.6617 (t70)
REVERT: R  221 PHE cc_start: 0.6802 (m-80) cc_final: 0.6421 (m-80)
REVERT: R  298 MET cc_start: 0.7869 (mmp) cc_final: 0.7414 (mmm)
  outliers start: 22
  outliers final: 21
  residues processed: 182
  average time/residue: 0.2081
  time to fit residues: 51.7313
Evaluate side-chains
  188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  130 CYS
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 99 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.154609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.113293 restraints weight = 13482.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 3.56
r_work: 0.3428 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3436 r_free = 0.3436    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   8751  Z= 0.131
  Angle     :  0.603   9.006  11846  Z= 0.304
  Chirality :  0.042   0.167   1317
  Planarity :  0.004   0.048   1505
  Dihedral  :  4.270  28.945   1183
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.48 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.18 (0.27), residues: 1060
  helix:  1.25 (0.29), residues: 365
  sheet:  0.06 (0.36), residues: 212
  loop : -1.28 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.002   0.001   HIS R 181 
 PHE   0.031   0.001   PHE R 219 
 TYR   0.021   0.001   TYR R 441 
 ARG   0.005   0.000   ARG N  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03383 (  376)
  hydrogen bonds       : angle       4.16622 ( 1054)
  SS BOND              : bond        0.00102 (    6)
  SS BOND              : angle       1.39494 (   12)
  covalent geometry    : bond        0.00314 ( 8745)
  covalent geometry    : angle       0.60130 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 173
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7759 (tt0)
REVERT: A  220 HIS cc_start: 0.7929 (m-70) cc_final: 0.7656 (m-70)
REVERT: B  215 GLU cc_start: 0.8576 (pm20) cc_final: 0.8310 (pm20)
REVERT: B  260 GLU cc_start: 0.8715 (tt0) cc_final: 0.8231 (tm-30)
REVERT: B  262 MET cc_start: 0.8244 (tpp) cc_final: 0.7281 (tpp)
REVERT: B  292 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8327 (m-80)
REVERT: C   41 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: C   51 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7228 (mtm180)
REVERT: R  184 ASP cc_start: 0.6958 (t0) cc_final: 0.6599 (t70)
REVERT: R  298 MET cc_start: 0.7895 (mmp) cc_final: 0.7478 (mmm)
  outliers start: 35
  outliers final: 26
  residues processed: 188
  average time/residue: 0.2028
  time to fit residues: 52.0082
Evaluate side-chains
  193 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  100 ASN
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  110 LYS
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Chi-restraints excluded: chain R residue  433 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 279 GLN
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.155807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.114800 restraints weight = 13618.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 3.52
r_work: 0.3428 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8751  Z= 0.135
  Angle     :  0.611   8.420  11846  Z= 0.307
  Chirality :  0.042   0.166   1317
  Planarity :  0.004   0.047   1505
  Dihedral  :  4.276  28.918   1183
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.66 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.16 (0.27), residues: 1060
  helix:  1.23 (0.29), residues: 367
  sheet:  0.03 (0.36), residues: 212
  loop : -1.22 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.002   0.001   HIS R 181 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.020   0.001   TYR R 441 
 ARG   0.004   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  376)
  hydrogen bonds       : angle       4.18311 ( 1054)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       1.36172 (   12)
  covalent geometry    : bond        0.00322 ( 8745)
  covalent geometry    : angle       0.60947 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7794 (tt0)
REVERT: A  220 HIS cc_start: 0.7958 (m-70) cc_final: 0.7693 (m-70)
REVERT: B   61 MET cc_start: 0.8970 (ppp) cc_final: 0.8460 (ppp)
REVERT: B  260 GLU cc_start: 0.8708 (tt0) cc_final: 0.8241 (tm-30)
REVERT: B  262 MET cc_start: 0.8224 (tpp) cc_final: 0.7262 (tpp)
REVERT: B  273 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8217 (mp)
REVERT: B  292 PHE cc_start: 0.8781 (m-80) cc_final: 0.8318 (m-80)
REVERT: C   41 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8343 (tm-30)
REVERT: C   53 LYS cc_start: 0.8670 (tptt) cc_final: 0.8408 (tptt)
REVERT: R  184 ASP cc_start: 0.6960 (t0) cc_final: 0.6593 (t70)
  outliers start: 29
  outliers final: 25
  residues processed: 186
  average time/residue: 0.2027
  time to fit residues: 52.0597
Evaluate side-chains
  195 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 169
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  100 ASN
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  130 CYS
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Chi-restraints excluded: chain R residue  433 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0470
   chunk 92 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0870
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.157293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.115973 restraints weight = 13654.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 3.54
r_work: 0.3448 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8751  Z= 0.119
  Angle     :  0.623   8.728  11846  Z= 0.312
  Chirality :  0.042   0.168   1317
  Planarity :  0.004   0.047   1505
  Dihedral  :  4.272  28.452   1183
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.88 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.15 (0.27), residues: 1060
  helix:  1.23 (0.29), residues: 367
  sheet:  0.06 (0.36), residues: 211
  loop : -1.22 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.002   0.000   HIS R 181 
 PHE   0.029   0.001   PHE R 219 
 TYR   0.018   0.001   TYR R 441 
 ARG   0.004   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03257 (  376)
  hydrogen bonds       : angle       4.08757 ( 1054)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       1.67238 (   12)
  covalent geometry    : bond        0.00281 ( 8745)
  covalent geometry    : angle       0.62110 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7896 (tt0)
REVERT: B  105 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8120 (t80)
REVERT: B  260 GLU cc_start: 0.8680 (tt0) cc_final: 0.8234 (tm-30)
REVERT: B  262 MET cc_start: 0.8212 (tpp) cc_final: 0.7260 (tpp)
REVERT: B  273 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8162 (mp)
REVERT: B  292 PHE cc_start: 0.8688 (m-80) cc_final: 0.8282 (m-80)
REVERT: C   53 LYS cc_start: 0.8608 (tptt) cc_final: 0.8368 (tptt)
REVERT: N   28 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8446 (mm-40)
REVERT: N  109 LEU cc_start: 0.8502 (tt) cc_final: 0.8132 (mp)
REVERT: R  184 ASP cc_start: 0.6986 (t0) cc_final: 0.6616 (t70)
REVERT: R  246 MET cc_start: 0.7649 (mmt) cc_final: 0.7282 (mmm)
REVERT: R  298 MET cc_start: 0.7817 (mmp) cc_final: 0.7307 (mmm)
  outliers start: 33
  outliers final: 25
  residues processed: 194
  average time/residue: 0.2128
  time to fit residues: 56.2801
Evaluate side-chains
  199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   43 LEU
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  130 CYS
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.160231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.118823 restraints weight = 13794.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 3.59
r_work: 0.3413 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8751  Z= 0.146
  Angle     :  0.661   9.553  11846  Z= 0.329
  Chirality :  0.043   0.205   1317
  Planarity :  0.004   0.045   1505
  Dihedral  :  4.320  28.844   1183
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.99 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.15 (0.27), residues: 1060
  helix:  1.28 (0.29), residues: 367
  sheet: -0.02 (0.36), residues: 217
  loop : -1.24 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.027   0.002   PHE R 496 
 TYR   0.019   0.001   TYR R 441 
 ARG   0.003   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03367 (  376)
  hydrogen bonds       : angle       4.12185 ( 1054)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       2.21995 (   12)
  covalent geometry    : bond        0.00348 ( 8745)
  covalent geometry    : angle       0.65708 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8145 (t80)
REVERT: B  260 GLU cc_start: 0.8663 (tt0) cc_final: 0.8261 (tm-30)
REVERT: B  273 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8224 (mp)
REVERT: B  280 LYS cc_start: 0.8651 (tttm) cc_final: 0.8440 (ttmm)
REVERT: C   53 LYS cc_start: 0.8673 (tptt) cc_final: 0.8436 (tptt)
REVERT: N  109 LEU cc_start: 0.8546 (tt) cc_final: 0.8173 (mp)
REVERT: R  184 ASP cc_start: 0.7006 (t0) cc_final: 0.6634 (t70)
REVERT: R  246 MET cc_start: 0.7643 (mmt) cc_final: 0.7337 (mmm)
REVERT: R  298 MET cc_start: 0.7917 (mmp) cc_final: 0.7353 (mmm)
  outliers start: 31
  outliers final: 24
  residues processed: 184
  average time/residue: 0.2061
  time to fit residues: 52.0308
Evaluate side-chains
  194 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   43 LEU
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  130 CYS
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    1.2302

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

Flipped N/Q/H residues before XYZ refinement:
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.157676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.117020 restraints weight = 13662.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 3.53
r_work: 0.3408 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8751  Z= 0.156
  Angle     :  0.673   9.367  11846  Z= 0.335
  Chirality :  0.043   0.219   1317
  Planarity :  0.004   0.043   1505
  Dihedral  :  4.351  29.047   1183
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.63 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.18 (0.27), residues: 1060
  helix:  1.24 (0.29), residues: 368
  sheet: -0.04 (0.36), residues: 217
  loop : -1.24 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 211 
 HIS   0.002   0.001   HIS R 181 
 PHE   0.027   0.002   PHE R 496 
 TYR   0.020   0.001   TYR R 245 
 ARG   0.003   0.000   ARG A  12 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  376)
  hydrogen bonds       : angle       4.15984 ( 1054)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       2.02794 (   12)
  covalent geometry    : bond        0.00371 ( 8745)
  covalent geometry    : angle       0.67036 (11834)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 172
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ARG cc_start: 0.8069 (mmp80) cc_final: 0.7313 (mpt180)
REVERT: A   28 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7782 (mt-10)
REVERT: B   22 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8329 (mmt90)
REVERT: B  105 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8231 (t80)
REVERT: B  260 GLU cc_start: 0.8662 (tt0) cc_final: 0.8284 (tm-30)
REVERT: B  262 MET cc_start: 0.8263 (tpp) cc_final: 0.7336 (tpp)
REVERT: B  273 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8233 (mp)
REVERT: B  280 LYS cc_start: 0.8671 (tttm) cc_final: 0.8457 (ttmm)
REVERT: C   53 LYS cc_start: 0.8736 (tptt) cc_final: 0.8479 (tptt)
REVERT: N   28 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8368 (mm-40)
REVERT: N  109 LEU cc_start: 0.8580 (tt) cc_final: 0.8203 (mp)
REVERT: R  184 ASP cc_start: 0.7030 (t0) cc_final: 0.6631 (t70)
REVERT: R  246 MET cc_start: 0.7670 (mmt) cc_final: 0.7403 (mmm)
REVERT: R  298 MET cc_start: 0.7880 (mmp) cc_final: 0.7329 (mmm)
  outliers start: 28
  outliers final: 23
  residues processed: 183
  average time/residue: 0.1983
  time to fit residues: 49.7898
Evaluate side-chains
  194 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 169
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   65 CYS
Chi-restraints excluded: chain N residue   43 LEU
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue  102 LEU
Chi-restraints excluded: chain N residue  107 ASN
Chi-restraints excluded: chain N residue  116 VAL
Chi-restraints excluded: chain N residue  130 CYS
Chi-restraints excluded: chain N residue  134 THR
Chi-restraints excluded: chain R residue  356 ASN
Chi-restraints excluded: chain R residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 443 GLN ** 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 = 0.4037 r_free = 0.4037 target = 0.152958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.111678 restraints weight = 13524.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 3.47
r_work: 0.3356 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8751  Z= 0.196
  Angle     :  0.705  10.384  11846  Z= 0.353
  Chirality :  0.044   0.219   1317
  Planarity :  0.004   0.043   1505
  Dihedral  :  4.463  29.969   1183
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.06 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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: -0.25 (0.26), residues: 1060
  helix:  1.23 (0.29), residues: 368
  sheet: -0.07 (0.36), residues: 212
  loop : -1.33 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.025   0.002   PHE R 496 
 TYR   0.021   0.002   TYR R 245 
 ARG   0.003   0.000   ARG R 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  376)
  hydrogen bonds       : angle       4.27466 ( 1054)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       1.91709 (   12)
  covalent geometry    : bond        0.00465 ( 8745)
  covalent geometry    : angle       0.70226 (11834)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4764.27 seconds
wall clock time: 83 minutes 16.03 seconds (4996.03 seconds total)