Starting phenix.real_space_refine
on Thu Sep 18 04:12:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9izx_61045/09_2025/9izx_61045.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.037
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      91      5.16       5
     C    8986      2.51       5
     N    2451      2.21       5
     O    2624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14152
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3704
          Classifications: {'peptide': 485}
          Link IDs: {'PTRANS': 27, 'TRANS': 457}
    Chain: "B"
      Number of atoms: 3327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3327
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 26, 'TRANS': 412}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3589
          Classifications: {'peptide': 470}
          Link IDs: {'PTRANS': 27, 'TRANS': 442}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3532
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 26, 'TRANS': 436}
          Chain breaks: 2
  Time building chain proxies: 3.28, per 1000 atoms: 0.23
  Number of scatterers: 14152
  At special positions: 0
  Unit cell: (112.888, 116.184, 117.832, 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      91     16.00
     O    2624      8.00
     N    2451      7.00
     C    8986      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 661.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3392

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 14 sheets defined
      47.6% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 64
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 65 through 83
    Processing helix  chain 'A' and resid 83 through 95
    Processing helix  chain 'A' and resid 98 through 117
    Processing helix  chain 'A' and resid 119 through 124
      removed outlier: 3.627A  pdb=" N   MET A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 170
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 183 through 196
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 280 through 283
    Processing helix  chain 'A' and resid 296 through 299
    Processing helix  chain 'A' and resid 300 through 311
      removed outlier: 3.594A  pdb=" N   LEU A 311 " --> pdb=" O   HIS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 345
    Processing helix  chain 'A' and resid 379 through 384
      removed outlier: 3.654A  pdb=" N   LYS A 383 " --> pdb=" O   MET A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 409
      removed outlier: 3.510A  pdb=" N   ASN A 409 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'B' and resid 43 through 64
      Proline residue:  B  59  - end of helix
    Processing helix  chain 'B' and resid 65 through 83
    Processing helix  chain 'B' and resid 83 through 96
    Processing helix  chain 'B' and resid 98 through 118
      removed outlier: 3.590A  pdb=" N   SER B 118 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 170
      Proline residue:  B 165  - end of helix
    Processing helix  chain 'B' and resid 183 through 196
    Processing helix  chain 'B' and resid 209 through 219
      removed outlier: 3.571A  pdb=" N   VAL B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 245
    Processing helix  chain 'B' and resid 265 through 279
    Processing helix  chain 'B' and resid 280 through 283
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'B' and resid 300 through 311
      removed outlier: 3.603A  pdb=" N   LEU B 311 " --> pdb=" O   HIS B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 346
    Processing helix  chain 'B' and resid 379 through 384
    Processing helix  chain 'B' and resid 398 through 409
      removed outlier: 3.512A  pdb=" N   ALA B 402 " --> pdb=" O   THR B 398 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN B 409 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 432
    Processing helix  chain 'B' and resid 467 through 475
    Processing helix  chain 'C' and resid 43 through 64
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 65 through 83
      removed outlier: 3.585A  pdb=" N   VAL C  72 " --> pdb=" O   SER C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 95
    Processing helix  chain 'C' and resid 98 through 118
    Processing helix  chain 'C' and resid 157 through 170
      Proline residue:  C 165  - end of helix
    Processing helix  chain 'C' and resid 183 through 196
    Processing helix  chain 'C' and resid 209 through 219
    Processing helix  chain 'C' and resid 230 through 244
      removed outlier: 3.899A  pdb=" N   HIS C 244 " --> pdb=" O   ARG C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 279
    Processing helix  chain 'C' and resid 280 through 283
    Processing helix  chain 'C' and resid 296 through 299
    Processing helix  chain 'C' and resid 300 through 310
    Processing helix  chain 'C' and resid 328 through 345
    Processing helix  chain 'C' and resid 379 through 384
    Processing helix  chain 'C' and resid 398 through 409
      removed outlier: 3.513A  pdb=" N   ALA C 402 " --> pdb=" O   THR C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 432
    Processing helix  chain 'C' and resid 467 through 474
    Processing helix  chain 'D' and resid 43 through 64
      Proline residue:  D  59  - end of helix
    Processing helix  chain 'D' and resid 65 through 83
    Processing helix  chain 'D' and resid 83 through 95
    Processing helix  chain 'D' and resid 98 through 118
      removed outlier: 3.534A  pdb=" N   SER D 118 " --> pdb=" O   GLU D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 170
      Proline residue:  D 165  - end of helix
    Processing helix  chain 'D' and resid 183 through 196
    Processing helix  chain 'D' and resid 209 through 219
      removed outlier: 3.681A  pdb=" N   VAL D 213 " --> pdb=" O   GLN D 209 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 244
      removed outlier: 3.681A  pdb=" N   HIS D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 278
    Processing helix  chain 'D' and resid 279 through 283
    Processing helix  chain 'D' and resid 296 through 299
    Processing helix  chain 'D' and resid 300 through 311
    Processing helix  chain 'D' and resid 328 through 345
      removed outlier: 3.609A  pdb=" N   LYS D 332 " --> pdb=" O   THR D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 379 through 384
    Processing helix  chain 'D' and resid 398 through 409
      removed outlier: 3.515A  pdb=" N   ALA D 402 " --> pdb=" O   THR D 398 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 421 through 432
    Processing helix  chain 'D' and resid 467 through 474
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28
    Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 351
      removed outlier: 6.359A  pdb=" N   ILE B 371 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASN B 256 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL B 292 " --> pdb=" O   ASN B 256 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLY B 258 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   VAL B 294 " --> pdb=" O   GLY B 258 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL B 260 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LYS B 255 " --> pdb=" O   ARG B 414 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   ALA B 416 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   HIS B 257 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE B 418 " --> pdb=" O   HIS B 257 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B 259 " --> pdb=" O   PHE B 418 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ASN B 413 " --> pdb=" O   GLN B 436 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   GLY B 438 " --> pdb=" O   ASN B 413 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   THR B 415 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL B 437 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   THR A 479 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   VAL B 439 " --> pdb=" O   THR A 479 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   THR A 481 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   MET A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU A 137 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   SER A 139 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   THR A 127 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ARG A 141 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   GLY A 125 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   GLU C 126 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   MET C 135 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   VAL D 437 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   THR C 479 " --> pdb=" O   VAL D 437 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   VAL D 439 " --> pdb=" O   THR C 479 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   THR C 481 " --> pdb=" O   VAL D 439 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   THR D 415 " --> pdb=" O   GLY D 438 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   HIS D 257 " --> pdb=" O   ALA D 416 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   PHE D 418 " --> pdb=" O   HIS D 257 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   VAL D 259 " --> pdb=" O   PHE D 418 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY D 258 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   VAL D 294 " --> pdb=" O   GLY D 258 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL D 260 " --> pdb=" O   VAL D 294 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   THR D 370 " --> pdb=" O   LEU D 391 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   VAL D 393 " --> pdb=" O   THR D 370 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE D 372 " --> pdb=" O   VAL D 393 " (cutoff:3.500A)
      removed outlier: 8.325A  pdb=" N   GLU D 395 " --> pdb=" O   ILE D 372 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE D 371 " --> pdb=" O   LEU D 350 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205
      removed outlier: 6.552A  pdb=" N   CYS A 147 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LYS A 177 " --> pdb=" O   CYS A 147 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLY A 149 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   VAL A 146 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ALA A 148 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   PHE A 227 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE A 150 " --> pdb=" O   PHE A 227 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG A 247 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351
      removed outlier: 5.148A  pdb=" N   ILE A 349 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   SER A 373 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   THR A 370 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   VAL A 393 " --> pdb=" O   THR A 370 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A 372 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLU A 395 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   ASN A 374 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   HIS A 257 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   PHE A 418 " --> pdb=" O   HIS A 257 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 259 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 28
      removed outlier: 3.571A  pdb=" N   GLY B  37 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205
      removed outlier: 6.480A  pdb=" N   CYS B 147 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   LYS B 177 " --> pdb=" O   CYS B 147 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLY B 149 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 224 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL B 228 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   PHE B 227 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY B 229 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 28
    Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 205
      removed outlier: 7.186A  pdb=" N   VAL C 146 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 146 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ALA C 148 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   PHE C 227 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ILE C 150 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LYS C 223 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   GLN C 249 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE C 225 " --> pdb=" O   GLN C 249 " (cutoff:3.500A)
      removed outlier: 8.481A  pdb=" N   ASN C 251 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   PHE C 227 " --> pdb=" O   ASN C 251 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 351
      removed outlier: 6.362A  pdb=" N   ILE C 371 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   THR C 370 " --> pdb=" O   LEU C 391 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   VAL C 393 " --> pdb=" O   THR C 370 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE C 372 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
      removed outlier: 8.153A  pdb=" N   GLU C 395 " --> pdb=" O   ILE C 372 " (cutoff:3.500A)
      removed outlier: 9.730A  pdb=" N   ALA C 287 " --> pdb=" O   VAL C 390 " (cutoff:3.500A)
      removed outlier: 9.230A  pdb=" N   VAL C 392 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   SER C 289 " --> pdb=" O   VAL C 392 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU C 394 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ALA C 291 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   THR C 396 " --> pdb=" O   ALA C 291 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   LEU C 293 " --> pdb=" O   THR C 396 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ASN C 256 " --> pdb=" O   THR C 290 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   VAL C 292 " --> pdb=" O   ASN C 256 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLY C 258 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   VAL C 294 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   VAL C 260 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   LYS C 255 " --> pdb=" O   ARG C 414 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   ALA C 416 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   HIS C 257 " --> pdb=" O   ALA C 416 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   PHE C 418 " --> pdb=" O   HIS C 257 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL C 259 " --> pdb=" O   PHE C 418 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12
    Processing sheet with id=AB3, first strand: chain 'D' and resid 24 through 28
    Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 143
    Processing sheet with id=AB5, first strand: chain 'D' and resid 203 through 205
      removed outlier: 7.582A  pdb=" N   VAL D 146 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE D 225 " --> pdb=" O   VAL D 146 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ALA D 148 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   PHE D 227 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ILE D 150 " --> pdb=" O   PHE D 227 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY D 229 " --> pdb=" O   ILE D 150 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LYS D 223 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   GLN D 249 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ILE D 225 " --> pdb=" O   GLN D 249 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ASN D 251 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   PHE D 227 " --> pdb=" O   ASN D 251 " (cutoff:3.500A)

    695 hydrogen bonds defined for protein.
    2019 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: 2.35

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4416
        1.34 -     1.45: 1635
        1.45 -     1.57: 8231
        1.57 -     1.69: 0
        1.69 -     1.81: 150
  Bond restraints: 14432
  Sorted by residual:
  bond pdb=" C   MET D 158 "
       pdb=" N   ILE D 159 "
    ideal  model  delta    sigma   weight residual
    1.329  1.369 -0.040 1.13e-02 7.83e+03 1.27e+01
  bond pdb=" CA  MET D 158 "
       pdb=" C   MET D 158 "
    ideal  model  delta    sigma   weight residual
    1.531  1.487  0.044 1.35e-02 5.49e+03 1.06e+01
  bond pdb=" CA  ILE D 150 "
       pdb=" C   ILE D 150 "
    ideal  model  delta    sigma   weight residual
    1.522  1.488  0.033 1.27e-02 6.20e+03 6.83e+00
  bond pdb=" N   ILE D 150 "
       pdb=" CA  ILE D 150 "
    ideal  model  delta    sigma   weight residual
    1.458  1.429  0.029 1.21e-02 6.83e+03 5.84e+00
  bond pdb=" CA  ILE D 150 "
       pdb=" CB  ILE D 150 "
    ideal  model  delta    sigma   weight residual
    1.541  1.512  0.029 1.30e-02 5.92e+03 4.91e+00
  ... (remaining 14427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 19378
        2.09 -     4.18: 158
        4.18 -     6.27: 15
        6.27 -     8.36: 2
        8.36 -    10.45: 3
  Bond angle restraints: 19556
  Sorted by residual:
  angle pdb=" CA  MET D 158 "
        pdb=" C   MET D 158 "
        pdb=" O   MET D 158 "
      ideal   model   delta    sigma   weight residual
     120.71  111.92    8.79 1.34e+00 5.57e-01 4.31e+01
  angle pdb=" N   PRO D 152 "
        pdb=" CA  PRO D 152 "
        pdb=" C   PRO D 152 "
      ideal   model   delta    sigma   weight residual
     111.11  121.42  -10.31 1.59e+00 3.96e-01 4.21e+01
  angle pdb=" C   MET D 158 "
        pdb=" CA  MET D 158 "
        pdb=" CB  MET D 158 "
      ideal   model   delta    sigma   weight residual
     115.89  109.66    6.23 1.32e+00 5.74e-01 2.23e+01
  angle pdb=" C   PHE D 155 "
        pdb=" N   PRO D 156 "
        pdb=" CA  PRO D 156 "
      ideal   model   delta    sigma   weight residual
     119.84  114.45    5.39 1.25e+00 6.40e-01 1.86e+01
  angle pdb=" N   MET D 158 "
        pdb=" CA  MET D 158 "
        pdb=" C   MET D 158 "
      ideal   model   delta    sigma   weight residual
     109.02  102.41    6.61 1.68e+00 3.54e-01 1.55e+01
  ... (remaining 19551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 8475
       17.11 -    34.22: 204
       34.22 -    51.33: 43
       51.33 -    68.45: 14
       68.45 -    85.56: 7
  Dihedral angle restraints: 8743
    sinusoidal: 3465
      harmonic: 5278
  Sorted by residual:
  dihedral pdb=" C   ILE D 150 "
           pdb=" N   ILE D 150 "
           pdb=" CA  ILE D 150 "
           pdb=" CB  ILE D 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -114.15   -7.85     0      2.50e+00 1.60e-01 9.87e+00
  dihedral pdb=" CB  GLU A 103 "
           pdb=" CG  GLU A 103 "
           pdb=" CD  GLU A 103 "
           pdb=" OE1 GLU A 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.56  -85.56     1      3.00e+01 1.11e-03 9.84e+00
  dihedral pdb=" CB  GLU A  18 "
           pdb=" CG  GLU A  18 "
           pdb=" CD  GLU A  18 "
           pdb=" OE1 GLU A  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.41   84.41     1      3.00e+01 1.11e-03 9.63e+00
  ... (remaining 8740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1901
       0.060 -    0.121: 305
       0.121 -    0.181: 14
       0.181 -    0.242: 2
       0.242 -    0.302: 1
  Chirality restraints: 2223
  Sorted by residual:
  chirality pdb=" CA  PRO D 152 "
            pdb=" N   PRO D 152 "
            pdb=" C   PRO D 152 "
            pdb=" CB  PRO D 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CA  ILE D 150 "
            pdb=" N   ILE D 150 "
            pdb=" C   ILE D 150 "
            pdb=" CB  ILE D 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  MET D 158 "
            pdb=" N   MET D 158 "
            pdb=" C   MET D 158 "
            pdb=" CB  MET D 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.27e-01
  ... (remaining 2220 not shown)

  Planarity restraints: 2545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 151 "   -0.037 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO D 152 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D 152 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 152 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 155 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO D 156 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 156 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 156 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET D 158 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.78e+00
        pdb=" C   MET D 158 "    0.029 2.00e-02 2.50e+03
        pdb=" O   MET D 158 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE D 159 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 2542 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     2.05: 2
        2.05 -     2.76: 2175
        2.76 -     3.47: 21054
        3.47 -     4.19: 34023
        4.19 -     4.90: 61728
  Nonbonded interactions: 118982
  Sorted by model distance:
  nonbonded pdb=" CZ  PHE D 155 "
            pdb=" CD1 PHE D 387 "
     model   vdw
     1.332 3.640
  nonbonded pdb=" CZ  PHE D 155 "
            pdb=" CE1 PHE D 387 "
     model   vdw
     1.944 3.640
  nonbonded pdb=" ND2 ASN D 409 "
            pdb=" O   TYR D 411 "
     model   vdw
     2.108 3.120
  nonbonded pdb=" CE2 PHE D 155 "
            pdb=" CD1 PHE D 387 "
     model   vdw
     2.127 3.640
  nonbonded pdb=" O   LEU A 193 "
            pdb=" OG  SER A 196 "
     model   vdw
     2.128 3.040
  ... (remaining 118977 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ 
h 476))
  selection = chain 'B'
  selection = (chain 'C' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ 
h 476))
  selection = (chain 'D' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ 
h 476))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     13.730
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
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      :  0.002   0.047  14432  Z= 0.132
  Angle     :  0.506  10.453  19556  Z= 0.290
  Chirality :  0.042   0.302   2223
  Planarity :  0.003   0.055   2545
  Dihedral  :  8.946  85.557   5351
  Min Nonbonded Distance : 1.332

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.34 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  3.48 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.19), residues: 1839
  helix:  1.17 (0.18), residues: 807
  sheet: -0.75 (0.27), residues: 315
  loop : -1.39 (0.23), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 460 
 TYR   0.007   0.001   TYR A  76 
 PHE   0.014   0.001   PHE D 155 
 TRP   0.006   0.001   TRP C 162 
 HIS   0.002   0.000   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (14432)
  covalent geometry    : angle       0.50581 (19556)
  hydrogen bonds       : bond        0.15295 (  695)
  hydrogen bonds       : angle       6.09603 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 298
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6772 (pm20)
REVERT: B   76 TYR cc_start: 0.6551 (t80) cc_final: 0.6257 (t80)
REVERT: B  123 MET cc_start: 0.1737 (tmm) cc_final: 0.0420 (tpt)
  outliers start: 7
  outliers final: 0
  residues processed: 303
  average time/residue: 0.6201
  time to fit residues: 204.8965
Evaluate side-chains
  168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    7.9990
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 204 ASN
A 207 HIS
A 210 HIS
A 214 ASN
A 272 GLN
A 430 HIS
A 476 GLN
B  41 GLN
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 257 HIS
C  28 HIS
C 251 ASN
C 307 HIS
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 365 ASN
C 472 GLN
D  77 GLN
D 115 HIS
D 251 ASN
D 256 ASN
** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.079104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.050344 restraints weight = 51712.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 4.51
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.095  14432  Z= 0.290
  Angle     :  0.750  10.677  19556  Z= 0.372
  Chirality :  0.048   0.199   2223
  Planarity :  0.005   0.059   2545
  Dihedral  :  4.592  87.458   1954
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.10 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.09 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.20), residues: 1839
  helix:  1.83 (0.18), residues: 825
  sheet: -0.08 (0.28), residues: 318
  loop : -0.84 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 243 
 TYR   0.020   0.002   TYR D  76 
 PHE   0.030   0.002   PHE B 164 
 TRP   0.022   0.002   TRP B  24 
 HIS   0.009   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 (14432)
  covalent geometry    : angle       0.75030 (19556)
  hydrogen bonds       : bond        0.03916 (  695)
  hydrogen bonds       : angle       5.06368 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 173
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8718 (mm-30)
REVERT: A   86 GLU cc_start: 0.9679 (tp30) cc_final: 0.9471 (tm-30)
REVERT: A  449 MET cc_start: 0.7652 (ppp) cc_final: 0.7372 (ppp)
REVERT: B    9 LYS cc_start: 0.9256 (mttp) cc_final: 0.8538 (mtpp)
REVERT: B   24 TRP cc_start: 0.8418 (m100) cc_final: 0.8082 (m100)
REVERT: B   70 GLN cc_start: 0.9763 (tt0) cc_final: 0.9531 (mt0)
REVERT: B  123 MET cc_start: 0.2960 (tmm) cc_final: 0.1444 (tpt)
REVERT: B  164 PHE cc_start: 0.8992 (p90) cc_final: 0.8653 (p90)
REVERT: B  168 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8725 (mpt)
REVERT: B  176 MET cc_start: 0.8642 (tpp) cc_final: 0.8412 (tpp)
REVERT: B  200 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8141 (t0)
REVERT: B  252 MET cc_start: 0.8909 (pp-130) cc_final: 0.8480 (pp-130)
REVERT: B  379 MET cc_start: 0.9243 (mtp) cc_final: 0.8994 (mtt)
REVERT: C   76 TYR cc_start: 0.9426 (t80) cc_final: 0.9174 (t80)
REVERT: C  252 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7360 (ppp)
REVERT: D  114 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8670 (pp20)
REVERT: D  162 TRP cc_start: 0.8375 (m-10) cc_final: 0.8175 (m100)
REVERT: D  306 GLU cc_start: 0.8926 (tp30) cc_final: 0.8640 (tp30)
REVERT: D  357 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9041 (mmtt)
REVERT: D  384 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7989 (pm20)
REVERT: D  395 GLU cc_start: 0.8758 (pm20) cc_final: 0.8524 (mp0)
REVERT: D  468 LYS cc_start: 0.8898 (mptt) cc_final: 0.8076 (pptt)
  outliers start: 47
  outliers final: 11
  residues processed: 203
  average time/residue: 0.5707
  time to fit residues: 127.3705
Evaluate side-chains
  160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  357 LYS
Chi-restraints excluded: chain D residue  384 GLU
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  413 ASN
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 123 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0870
   chunk 107 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 165 optimal weight:    0.9980
   chunk 1 optimal weight:    8.9990
   chunk 121 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 136 optimal weight:    0.7980
   overall best weight:    1.1762

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 GLN
B 209 GLN
B 219 HIS
** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 436 GLN
D 172 ASN
** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.081187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.052452 restraints weight = 51312.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 4.62
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14432  Z= 0.121
  Angle     :  0.642  11.943  19556  Z= 0.306
  Chirality :  0.045   0.173   2223
  Planarity :  0.004   0.051   2545
  Dihedral  :  3.996  16.997   1951
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.56 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.39 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.20), residues: 1839
  helix:  2.09 (0.18), residues: 818
  sheet:  0.10 (0.28), residues: 317
  loop : -0.58 (0.25), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 243 
 TYR   0.021   0.002   TYR D  76 
 PHE   0.023   0.001   PHE D 164 
 TRP   0.012   0.001   TRP B  24 
 HIS   0.012   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (14432)
  covalent geometry    : angle       0.64180 (19556)
  hydrogen bonds       : bond        0.03189 (  695)
  hydrogen bonds       : angle       4.55126 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 167
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8560 (ptpt)
REVERT: A   82 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8664 (mm-30)
REVERT: A  168 MET cc_start: 0.9348 (mtt) cc_final: 0.9137 (mtt)
REVERT: B   24 TRP cc_start: 0.8484 (m100) cc_final: 0.7959 (m100)
REVERT: B   26 ASP cc_start: 0.9469 (OUTLIER) cc_final: 0.9182 (p0)
REVERT: B  107 PHE cc_start: 0.9428 (t80) cc_final: 0.9056 (t80)
REVERT: B  123 MET cc_start: 0.2788 (tmm) cc_final: 0.1311 (tpt)
REVERT: B  166 MET cc_start: 0.9314 (tpp) cc_final: 0.9059 (tpt)
REVERT: B  168 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8750 (mmt)
REVERT: B  200 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8345 (t0)
REVERT: B  252 MET cc_start: 0.8959 (pp-130) cc_final: 0.8374 (pp-130)
REVERT: B  361 TYR cc_start: 0.9121 (m-80) cc_final: 0.8901 (m-80)
REVERT: B  379 MET cc_start: 0.9291 (mtp) cc_final: 0.8812 (mtp)
REVERT: C  176 MET cc_start: 0.9305 (mmm) cc_final: 0.9096 (mmm)
REVERT: C  206 ILE cc_start: 0.9223 (pp) cc_final: 0.8997 (pp)
REVERT: C  252 MET cc_start: 0.7850 (ppp) cc_final: 0.7349 (ppp)
REVERT: D  114 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8514 (pp20)
REVERT: D  123 MET cc_start: 0.9242 (tmm) cc_final: 0.9017 (tmm)
REVERT: D  162 TRP cc_start: 0.8229 (m-10) cc_final: 0.7896 (m100)
REVERT: D  252 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6396 (mmm)
REVERT: D  306 GLU cc_start: 0.8907 (tp30) cc_final: 0.8513 (tp30)
REVERT: D  384 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8070 (pm20)
REVERT: D  395 GLU cc_start: 0.8691 (pm20) cc_final: 0.8475 (mp0)
REVERT: D  411 TYR cc_start: 0.6758 (t80) cc_final: 0.6133 (t80)
REVERT: D  413 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7402 (p0)
REVERT: D  468 LYS cc_start: 0.8891 (mptt) cc_final: 0.8113 (pptt)
  outliers start: 41
  outliers final: 15
  residues processed: 193
  average time/residue: 0.5658
  time to fit residues: 120.9040
Evaluate side-chains
  168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  219 HIS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   77 GLN
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  413 ASN
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:   30.0000
   chunk 100 optimal weight:    9.9990
   chunk 164 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 140 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 180 optimal weight:    0.0670
   chunk 67 optimal weight:   10.0000
   chunk 158 optimal weight:    8.9990
   overall best weight:    5.6126

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 204 ASN
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.078489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.049348 restraints weight = 51825.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 4.50
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080  14432  Z= 0.278
  Angle     :  0.685  11.370  19556  Z= 0.338
  Chirality :  0.046   0.202   2223
  Planarity :  0.004   0.069   2545
  Dihedral  :  4.238  20.745   1951
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.15 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 14.44 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.20), residues: 1839
  helix:  2.03 (0.18), residues: 824
  sheet:  0.24 (0.28), residues: 319
  loop : -0.60 (0.25), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 312 
 TYR   0.032   0.002   TYR C  76 
 PHE   0.023   0.002   PHE D 164 
 TRP   0.020   0.001   TRP D 162 
 HIS   0.013   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (14432)
  covalent geometry    : angle       0.68542 (19556)
  hydrogen bonds       : bond        0.03414 (  695)
  hydrogen bonds       : angle       4.73699 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 150
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8824 (mm-30)
REVERT: B   26 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9183 (p0)
REVERT: B   81 LYS cc_start: 0.9669 (mtpp) cc_final: 0.9453 (mtmm)
REVERT: B  107 PHE cc_start: 0.9435 (t80) cc_final: 0.9118 (t80)
REVERT: B  123 MET cc_start: 0.2814 (tmm) cc_final: 0.1049 (tpt)
REVERT: B  158 MET cc_start: 0.8194 (mpp) cc_final: 0.7960 (mmp)
REVERT: B  166 MET cc_start: 0.9333 (tpp) cc_final: 0.9098 (tpt)
REVERT: B  168 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8821 (mmt)
REVERT: B  176 MET cc_start: 0.8663 (tpp) cc_final: 0.8074 (tpp)
REVERT: B  200 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8277 (t0)
REVERT: B  252 MET cc_start: 0.8984 (pp-130) cc_final: 0.8354 (pp-130)
REVERT: B  379 MET cc_start: 0.9369 (mtp) cc_final: 0.8973 (mtp)
REVERT: C   76 TYR cc_start: 0.9509 (t80) cc_final: 0.9286 (t80)
REVERT: C  164 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8493 (t80)
REVERT: C  168 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8528 (mpt)
REVERT: C  176 MET cc_start: 0.9385 (mmm) cc_final: 0.9171 (mmm)
REVERT: C  206 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9048 (pp)
REVERT: C  252 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7151 (ppp)
REVERT: D  114 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8681 (pp20)
REVERT: D  123 MET cc_start: 0.9336 (tmm) cc_final: 0.9039 (tmm)
REVERT: D  162 TRP cc_start: 0.8387 (m-10) cc_final: 0.7889 (m100)
REVERT: D  252 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6439 (mtt)
REVERT: D  306 GLU cc_start: 0.8972 (tp30) cc_final: 0.8659 (tp30)
REVERT: D  357 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9090 (mmtt)
REVERT: D  395 GLU cc_start: 0.8755 (pm20) cc_final: 0.8522 (mp0)
REVERT: D  411 TYR cc_start: 0.6780 (t80) cc_final: 0.6175 (t80)
REVERT: D  468 LYS cc_start: 0.8927 (mptt) cc_final: 0.8145 (pptt)
  outliers start: 49
  outliers final: 17
  residues processed: 178
  average time/residue: 0.5505
  time to fit residues: 108.5276
Evaluate side-chains
  167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 TYR
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  206 ILE
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  357 LYS
Chi-restraints excluded: chain D residue  384 GLU
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 108 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 136 optimal weight:    0.9990
   chunk 48 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 141 optimal weight:    0.1980
   chunk 128 optimal weight:    6.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A  77 GLN
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  70 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 = 0.3697 r_free = 0.3697 target = 0.079930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.051080 restraints weight = 51577.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 4.55
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14432  Z= 0.140
  Angle     :  0.633  13.247  19556  Z= 0.304
  Chirality :  0.044   0.185   2223
  Planarity :  0.004   0.040   2545
  Dihedral  :  4.123  18.525   1951
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.94 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.11 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.20), residues: 1839
  helix:  2.14 (0.18), residues: 822
  sheet:  0.30 (0.29), residues: 319
  loop : -0.50 (0.25), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 312 
 TYR   0.030   0.002   TYR D  76 
 PHE   0.027   0.001   PHE B 164 
 TRP   0.009   0.001   TRP D 162 
 HIS   0.013   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14432)
  covalent geometry    : angle       0.63319 (19556)
  hydrogen bonds       : bond        0.03044 (  695)
  hydrogen bonds       : angle       4.44062 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 157
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8738 (mm-30)
REVERT: A  124 MET cc_start: 0.8145 (mpm) cc_final: 0.7834 (mpm)
REVERT: A  163 MET cc_start: 0.8541 (mtm) cc_final: 0.8336 (mtm)
REVERT: B   26 ASP cc_start: 0.9480 (OUTLIER) cc_final: 0.9197 (p0)
REVERT: B   81 LYS cc_start: 0.9666 (mtpp) cc_final: 0.9430 (mtpt)
REVERT: B  111 GLN cc_start: 0.9580 (mt0) cc_final: 0.9250 (mm110)
REVERT: B  123 MET cc_start: 0.3023 (tmm) cc_final: 0.1264 (tpt)
REVERT: B  164 PHE cc_start: 0.8951 (p90) cc_final: 0.8654 (p90)
REVERT: B  166 MET cc_start: 0.9349 (tpp) cc_final: 0.9091 (tpt)
REVERT: B  200 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8279 (t0)
REVERT: B  252 MET cc_start: 0.9056 (pp-130) cc_final: 0.8434 (pp-130)
REVERT: B  311 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9158 (mm)
REVERT: B  379 MET cc_start: 0.9361 (mtp) cc_final: 0.8999 (mtp)
REVERT: C   76 TYR cc_start: 0.9504 (t80) cc_final: 0.9217 (t80)
REVERT: C  164 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8685 (t80)
REVERT: C  168 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8447 (mpt)
REVERT: C  252 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7234 (ppp)
REVERT: D  114 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8643 (pp20)
REVERT: D  123 MET cc_start: 0.9331 (tmm) cc_final: 0.9011 (tmm)
REVERT: D  162 TRP cc_start: 0.8249 (m-10) cc_final: 0.8031 (m100)
REVERT: D  252 MET cc_start: 0.7508 (mtt) cc_final: 0.6279 (mtt)
REVERT: D  286 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8718 (mtp)
REVERT: D  306 GLU cc_start: 0.8955 (tp30) cc_final: 0.8539 (tp30)
REVERT: D  395 GLU cc_start: 0.8700 (pm20) cc_final: 0.8418 (mp0)
REVERT: D  411 TYR cc_start: 0.6890 (t80) cc_final: 0.6304 (t80)
REVERT: D  468 LYS cc_start: 0.8929 (mptt) cc_final: 0.8156 (pptt)
  outliers start: 54
  outliers final: 20
  residues processed: 192
  average time/residue: 0.5037
  time to fit residues: 107.7962
Evaluate side-chains
  167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  286 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 1 optimal weight:   40.0000
   chunk 118 optimal weight:   10.0000
   chunk 173 optimal weight:    9.9990
   chunk 107 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A  71 GLN
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 GLN
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 476 GLN
** C  70 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 = 0.3657 r_free = 0.3657 target = 0.077981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.048812 restraints weight = 52750.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.54
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.088  14432  Z= 0.288
  Angle     :  0.730  13.397  19556  Z= 0.354
  Chirality :  0.047   0.237   2223
  Planarity :  0.005   0.113   2545
  Dihedral  :  4.347  17.376   1951
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.86 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.22 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.20), residues: 1839
  helix:  1.95 (0.18), residues: 831
  sheet:  0.22 (0.29), residues: 312
  loop : -0.57 (0.25), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  69 
 TYR   0.038   0.002   TYR D  76 
 PHE   0.026   0.002   PHE D 155 
 TRP   0.026   0.002   TRP B  24 
 HIS   0.013   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 (14432)
  covalent geometry    : angle       0.73027 (19556)
  hydrogen bonds       : bond        0.03468 (  695)
  hydrogen bonds       : angle       4.77122 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 150
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8925 (mm-30)
REVERT: A  163 MET cc_start: 0.8637 (mtm) cc_final: 0.7985 (mtm)
REVERT: A  252 MET cc_start: 0.8078 (tpp) cc_final: 0.7487 (tpp)
REVERT: B   26 ASP cc_start: 0.9474 (OUTLIER) cc_final: 0.9216 (p0)
REVERT: B   81 LYS cc_start: 0.9690 (mtpp) cc_final: 0.9461 (mtmm)
REVERT: B  123 MET cc_start: 0.2637 (tmm) cc_final: 0.0927 (tpt)
REVERT: B  158 MET cc_start: 0.8127 (mpp) cc_final: 0.7547 (tpt)
REVERT: B  166 MET cc_start: 0.9332 (tpp) cc_final: 0.9094 (tpt)
REVERT: B  200 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8274 (t0)
REVERT: B  252 MET cc_start: 0.9055 (pp-130) cc_final: 0.8424 (pp-130)
REVERT: B  379 MET cc_start: 0.9377 (mtp) cc_final: 0.8998 (mtp)
REVERT: C  164 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8508 (t80)
REVERT: C  168 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8253 (mpt)
REVERT: C  252 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7497 (ppp)
REVERT: C  449 MET cc_start: 0.6920 (mpp) cc_final: 0.6694 (pmm)
REVERT: D  114 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8749 (pp20)
REVERT: D  123 MET cc_start: 0.9329 (tmm) cc_final: 0.8984 (tmm)
REVERT: D  162 TRP cc_start: 0.8330 (m-10) cc_final: 0.7871 (m100)
REVERT: D  252 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6521 (mtt)
REVERT: D  306 GLU cc_start: 0.9011 (tp30) cc_final: 0.8631 (tp30)
REVERT: D  395 GLU cc_start: 0.8782 (pm20) cc_final: 0.8473 (mp0)
REVERT: D  411 TYR cc_start: 0.6839 (t80) cc_final: 0.6157 (t80)
  outliers start: 52
  outliers final: 24
  residues processed: 181
  average time/residue: 0.5229
  time to fit residues: 105.7634
Evaluate side-chains
  164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  155 PHE
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 107 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 161 optimal weight:    8.9990
   chunk 154 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:   50.0000
   chunk 31 optimal weight:    8.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 GLN
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 476 GLN
** C  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.080062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.051195 restraints weight = 50960.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 4.51
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14432  Z= 0.132
  Angle     :  0.702  14.339  19556  Z= 0.327
  Chirality :  0.045   0.211   2223
  Planarity :  0.004   0.105   2545
  Dihedral  :  4.193  17.420   1951
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.15 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.01 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.20), residues: 1839
  helix:  2.06 (0.18), residues: 826
  sheet:  0.32 (0.29), residues: 312
  loop : -0.48 (0.25), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.039   0.002   TYR D  76 
 PHE   0.023   0.001   PHE B 164 
 TRP   0.022   0.001   TRP B  24 
 HIS   0.012   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (14432)
  covalent geometry    : angle       0.70230 (19556)
  hydrogen bonds       : bond        0.03069 (  695)
  hydrogen bonds       : angle       4.53363 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 149
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLN cc_start: 0.9465 (mm-40) cc_final: 0.9220 (mm-40)
REVERT: B   26 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9231 (p0)
REVERT: B   81 LYS cc_start: 0.9692 (mtpp) cc_final: 0.9440 (mtmm)
REVERT: B  111 GLN cc_start: 0.9576 (mt0) cc_final: 0.9250 (mm110)
REVERT: B  123 MET cc_start: 0.2691 (tmm) cc_final: 0.1078 (tpt)
REVERT: B  166 MET cc_start: 0.9365 (tpp) cc_final: 0.9066 (tpt)
REVERT: B  176 MET cc_start: 0.8804 (tpp) cc_final: 0.8314 (tpp)
REVERT: B  200 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8252 (t0)
REVERT: B  252 MET cc_start: 0.9090 (pp-130) cc_final: 0.8486 (pp-130)
REVERT: B  379 MET cc_start: 0.9343 (mtp) cc_final: 0.9001 (mtp)
REVERT: C  124 MET cc_start: 0.8154 (mpm) cc_final: 0.7916 (mpm)
REVERT: C  252 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7584 (ppp)
REVERT: D  114 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8631 (pp20)
REVERT: D  123 MET cc_start: 0.9317 (tmm) cc_final: 0.8966 (tmm)
REVERT: D  252 MET cc_start: 0.7589 (mtt) cc_final: 0.6494 (mtt)
REVERT: D  286 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8654 (mtp)
REVERT: D  306 GLU cc_start: 0.8975 (tp30) cc_final: 0.8554 (tp30)
REVERT: D  411 TYR cc_start: 0.6772 (t80) cc_final: 0.6146 (t80)
REVERT: D  468 LYS cc_start: 0.8877 (mptt) cc_final: 0.8113 (pptt)
  outliers start: 48
  outliers final: 25
  residues processed: 179
  average time/residue: 0.5199
  time to fit residues: 103.9195
Evaluate side-chains
  166 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  158 MET
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  155 PHE
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  398 THR
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  286 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 22 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 115 optimal weight:    7.9990
   chunk 143 optimal weight:    0.3980
   chunk 65 optimal weight:    8.9990
   chunk 153 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   chunk 28 optimal weight:    9.9990
   overall best weight:    3.8964

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 476 GLN
** C  70 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 = 0.3674 r_free = 0.3674 target = 0.078857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.049898 restraints weight = 51634.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 4.50
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  14432  Z= 0.202
  Angle     :  0.726  14.895  19556  Z= 0.343
  Chirality :  0.046   0.239   2223
  Planarity :  0.005   0.105   2545
  Dihedral  :  4.253  17.252   1951
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.48 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.06 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.20), residues: 1839
  helix:  1.97 (0.18), residues: 834
  sheet:  0.34 (0.29), residues: 312
  loop : -0.49 (0.25), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 414 
 TYR   0.045   0.002   TYR D  76 
 PHE   0.022   0.001   PHE D 164 
 TRP   0.014   0.001   TRP B  24 
 HIS   0.005   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (14432)
  covalent geometry    : angle       0.72594 (19556)
  hydrogen bonds       : bond        0.03260 (  695)
  hydrogen bonds       : angle       4.69821 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 145
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.9433 (ptp) cc_final: 0.9103 (pmm)
REVERT: A   71 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9219 (mm-40)
REVERT: A  110 LEU cc_start: 0.9176 (mt) cc_final: 0.8962 (pp)
REVERT: A  133 LYS cc_start: 0.9659 (tppp) cc_final: 0.9119 (tmmt)
REVERT: B   26 ASP cc_start: 0.9486 (OUTLIER) cc_final: 0.9233 (p0)
REVERT: B   81 LYS cc_start: 0.9670 (mtpp) cc_final: 0.9410 (mtmm)
REVERT: B  111 GLN cc_start: 0.9579 (mt0) cc_final: 0.9251 (mm110)
REVERT: B  123 MET cc_start: 0.2810 (tmm) cc_final: 0.1176 (tpt)
REVERT: B  166 MET cc_start: 0.9355 (tpp) cc_final: 0.9059 (tpt)
REVERT: B  168 MET cc_start: 0.9235 (ppp) cc_final: 0.9016 (ppp)
REVERT: B  200 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (t0)
REVERT: B  252 MET cc_start: 0.9092 (pp-130) cc_final: 0.8604 (pp-130)
REVERT: B  379 MET cc_start: 0.9358 (mtp) cc_final: 0.8992 (mtp)
REVERT: C   90 LEU cc_start: 0.9791 (OUTLIER) cc_final: 0.9480 (tm)
REVERT: C  134 ASP cc_start: 0.8239 (t0) cc_final: 0.7949 (t0)
REVERT: C  252 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7574 (ppp)
REVERT: C  449 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6738 (pmm)
REVERT: D  114 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8684 (pp20)
REVERT: D  123 MET cc_start: 0.9322 (tmm) cc_final: 0.8960 (tmm)
REVERT: D  176 MET cc_start: 0.9482 (tpp) cc_final: 0.9219 (tpt)
REVERT: D  252 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6524 (mtt)
REVERT: D  306 GLU cc_start: 0.9013 (tp30) cc_final: 0.8599 (tp30)
REVERT: D  411 TYR cc_start: 0.6789 (t80) cc_final: 0.6108 (t80)
REVERT: D  468 LYS cc_start: 0.8890 (mptt) cc_final: 0.8080 (pptt)
  outliers start: 43
  outliers final: 24
  residues processed: 168
  average time/residue: 0.5280
  time to fit residues: 98.8548
Evaluate side-chains
  166 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  285 CYS
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  155 PHE
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  288 LEU
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 80 optimal weight:   20.0000
   chunk 180 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 165 optimal weight:    6.9990
   chunk 166 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 139 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 476 GLN
** C  70 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 = 0.3688 r_free = 0.3688 target = 0.079724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.050688 restraints weight = 51349.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 4.54
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14432  Z= 0.157
  Angle     :  0.726  15.495  19556  Z= 0.342
  Chirality :  0.046   0.218   2223
  Planarity :  0.005   0.110   2545
  Dihedral  :  4.251  18.111   1951
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.26 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.13 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.20), residues: 1839
  helix:  1.92 (0.18), residues: 833
  sheet:  0.36 (0.30), residues: 312
  loop : -0.47 (0.25), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 312 
 TYR   0.045   0.002   TYR D  76 
 PHE   0.021   0.001   PHE D 164 
 TRP   0.012   0.001   TRP B  24 
 HIS   0.007   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (14432)
  covalent geometry    : angle       0.72600 (19556)
  hydrogen bonds       : bond        0.03188 (  695)
  hydrogen bonds       : angle       4.66314 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 143
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.9371 (ptp) cc_final: 0.9069 (pmm)
REVERT: A   71 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9213 (mm-40)
REVERT: A  110 LEU cc_start: 0.9165 (mt) cc_final: 0.8948 (pp)
REVERT: A  128 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7347 (mtp)
REVERT: A  163 MET cc_start: 0.8957 (mtm) cc_final: 0.8631 (ptm)
REVERT: A  187 MET cc_start: 0.9329 (tpp) cc_final: 0.9104 (tpt)
REVERT: B   26 ASP cc_start: 0.9487 (OUTLIER) cc_final: 0.9244 (p0)
REVERT: B  111 GLN cc_start: 0.9569 (mt0) cc_final: 0.9241 (mm110)
REVERT: B  123 MET cc_start: 0.2778 (tmm) cc_final: 0.1171 (tpt)
REVERT: B  166 MET cc_start: 0.9356 (tpp) cc_final: 0.9057 (tpt)
REVERT: B  168 MET cc_start: 0.9223 (ppp) cc_final: 0.8984 (ppp)
REVERT: B  200 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8252 (t0)
REVERT: B  252 MET cc_start: 0.9092 (pp-130) cc_final: 0.8602 (pp-130)
REVERT: B  379 MET cc_start: 0.9353 (mtp) cc_final: 0.8953 (mtp)
REVERT: C   90 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9483 (tm)
REVERT: C  134 ASP cc_start: 0.8264 (t0) cc_final: 0.8001 (t0)
REVERT: C  164 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8636 (t80)
REVERT: C  168 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8362 (mpt)
REVERT: C  252 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7542 (ppp)
REVERT: C  449 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6656 (pmm)
REVERT: D  114 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8620 (pp20)
REVERT: D  123 MET cc_start: 0.9314 (tmm) cc_final: 0.9018 (tmm)
REVERT: D  252 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6508 (mtt)
REVERT: D  306 GLU cc_start: 0.8989 (tp30) cc_final: 0.8568 (tp30)
REVERT: D  411 TYR cc_start: 0.6792 (t80) cc_final: 0.6113 (t80)
REVERT: D  468 LYS cc_start: 0.8847 (mptt) cc_final: 0.8069 (pptt)
  outliers start: 40
  outliers final: 22
  residues processed: 167
  average time/residue: 0.4907
  time to fit residues: 92.0805
Evaluate side-chains
  168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  285 CYS
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  155 PHE
Chi-restraints excluded: chain C residue  164 PHE
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  114 GLU
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 171 optimal weight:    9.9990
   chunk 151 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 166 optimal weight:    3.9990
   chunk 31 optimal weight:    0.2980
   chunk 103 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 167 optimal weight:    0.0970
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
B 115 HIS
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  77 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.081000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.052377 restraints weight = 51775.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 4.61
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14432  Z= 0.121
  Angle     :  0.741  16.116  19556  Z= 0.344
  Chirality :  0.046   0.237   2223
  Planarity :  0.005   0.103   2545
  Dihedral  :  4.209  18.219   1951
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.10 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.04 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.20), residues: 1839
  helix:  1.84 (0.18), residues: 833
  sheet:  0.47 (0.30), residues: 311
  loop : -0.47 (0.25), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 312 
 TYR   0.035   0.002   TYR D  76 
 PHE   0.021   0.001   PHE D 164 
 TRP   0.012   0.001   TRP B 162 
 HIS   0.004   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (14432)
  covalent geometry    : angle       0.74087 (19556)
  hydrogen bonds       : bond        0.02977 (  695)
  hydrogen bonds       : angle       4.56320 ( 2019)

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

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

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3678 Ramachandran restraints generated.
    1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.9362 (ptp) cc_final: 0.9027 (pmm)
REVERT: A   71 GLN cc_start: 0.9454 (mm-40) cc_final: 0.9215 (mm-40)
REVERT: A  110 LEU cc_start: 0.9068 (mt) cc_final: 0.8868 (pp)
REVERT: A  123 MET cc_start: 0.8747 (mmm) cc_final: 0.8501 (tpp)
REVERT: A  163 MET cc_start: 0.9015 (mtm) cc_final: 0.8524 (ptm)
REVERT: A  187 MET cc_start: 0.9301 (tpp) cc_final: 0.9009 (tpt)
REVERT: B   26 ASP cc_start: 0.9468 (OUTLIER) cc_final: 0.9197 (p0)
REVERT: B   77 GLN cc_start: 0.9500 (tm-30) cc_final: 0.9294 (tm-30)
REVERT: B  166 MET cc_start: 0.9358 (tpp) cc_final: 0.9107 (tpt)
REVERT: B  168 MET cc_start: 0.9188 (ppp) cc_final: 0.8945 (ppp)
REVERT: B  200 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (t0)
REVERT: B  252 MET cc_start: 0.9119 (pp-130) cc_final: 0.8526 (pp-130)
REVERT: B  379 MET cc_start: 0.9316 (mtp) cc_final: 0.8994 (mtp)
REVERT: C   90 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9512 (tm)
REVERT: C  134 ASP cc_start: 0.8237 (t0) cc_final: 0.7970 (t0)
REVERT: C  164 PHE cc_start: 0.9202 (t80) cc_final: 0.8588 (t80)
REVERT: C  168 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8466 (mpt)
REVERT: C  252 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7574 (ppp)
REVERT: C  449 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6790 (pmm)
REVERT: D  114 GLU cc_start: 0.9277 (pt0) cc_final: 0.8572 (pp20)
REVERT: D  123 MET cc_start: 0.9213 (tmm) cc_final: 0.8694 (tmm)
REVERT: D  124 MET cc_start: 0.7293 (pmm) cc_final: 0.6987 (pmm)
REVERT: D  252 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6405 (mtt)
REVERT: D  306 GLU cc_start: 0.8961 (tp30) cc_final: 0.8532 (tp30)
REVERT: D  411 TYR cc_start: 0.6711 (t80) cc_final: 0.6169 (t80)
REVERT: D  468 LYS cc_start: 0.8791 (mptt) cc_final: 0.8037 (pptt)
  outliers start: 32
  outliers final: 20
  residues processed: 175
  average time/residue: 0.5512
  time to fit residues: 107.2504
Evaluate side-chains
  165 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  430 HIS
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain B residue    8 VAL
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  186 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  381 CYS
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  119 VAL
Chi-restraints excluded: chain C residue  168 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  381 CYS
Chi-restraints excluded: chain C residue  449 MET
Chi-restraints excluded: chain D residue  164 PHE
Chi-restraints excluded: chain D residue  252 MET
Chi-restraints excluded: chain D residue  398 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  434 VAL
Chi-restraints excluded: chain D residue  445 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 172 optimal weight:    0.0870
   chunk 33 optimal weight:    0.1980
   chunk 129 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 135 optimal weight:    2.9990
   chunk 155 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    2.6564

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 476 GLN
D  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.080137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.051303 restraints weight = 51287.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 4.53
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14432  Z= 0.161
  Angle     :  0.760  16.162  19556  Z= 0.358
  Chirality :  0.046   0.228   2223
  Planarity :  0.005   0.102   2545
  Dihedral  :  4.229  24.478   1951
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.21 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.18 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.21), residues: 1839
  helix:  1.89 (0.18), residues: 832
  sheet:  0.55 (0.30), residues: 311
  loop : -0.45 (0.25), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 312 
 TYR   0.037   0.002   TYR D  76 
 PHE   0.021   0.001   PHE D 164 
 TRP   0.012   0.001   TRP D 162 
 HIS   0.004   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (14432)
  covalent geometry    : angle       0.76008 (19556)
  hydrogen bonds       : bond        0.03043 (  695)
  hydrogen bonds       : angle       4.66341 ( 2019)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4098.12 seconds
wall clock time: 71 minutes 5.17 seconds (4265.17 seconds total)