Starting phenix.real_space_refine
on Wed Mar  4 05:33:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sgz_10191/03_2026/6sgz_10191.map"
  }
  resolution = 3.9
  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=   0.004 sd=   0.119
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      29      5.16       5
     C    7171      2.51       5
     N    1997      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11177
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 3120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 3120
          Classifications: {'peptide': 435}
          Link IDs: {'PTRANS': 24, 'TRANS': 410}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 3168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3168
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 27, 'TRANS': 414}
          Chain breaks: 3
    Chain: "I"
      Number of atoms: 461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 461
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 1, 'TRANS': 57}
    Chain: "J"
      Number of atoms: 2603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2603
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 26, 'TRANS': 301}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1825
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 16, 'TRANS': 224}
          Chain breaks: 7
  Time building chain proxies: 2.60, per 1000 atoms: 0.23
  Number of scatterers: 11177
  At special positions: 0
  Unit cell: (132.938, 116.985, 101.033, 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      29     16.00
     O    1980      8.00
     N    1997      7.00
     C    7171      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: 0.87
  Conformation dependent library (CDL) restraints added in 568.1 milliseconds
  

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2804

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      58.9% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'E' and resid 34 through 47
      removed outlier: 3.660A  pdb=" N   ILE E  38 " --> pdb=" O   PRO E  34 " (cutoff:3.500A)
      Proline residue:  E  40  - end of helix
    Processing helix  chain 'E' and resid 82 through 87
      removed outlier: 3.631A  pdb=" N   GLY E  87 " --> pdb=" O   LEU E  83 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 119
    Processing helix  chain 'E' and resid 127 through 158
      removed outlier: 3.748A  pdb=" N   HIS E 131 " --> pdb=" O   TRP E 127 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE E 132 " --> pdb=" O   GLY E 128 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   ALA E 133 " --> pdb=" O   PRO E 129 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG E 134 " --> pdb=" O   THR E 130 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE E 157 " --> pdb=" O   ALA E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 181
      removed outlier: 4.230A  pdb=" N   GLN E 164 " --> pdb=" O   ASP E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 196
    Processing helix  chain 'E' and resid 196 through 204
      removed outlier: 3.522A  pdb=" N   ALA E 201 " --> pdb=" O   LEU E 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 233
      removed outlier: 3.562A  pdb=" N   ALA E 233 " --> pdb=" O   LEU E 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 240 through 264
      removed outlier: 3.656A  pdb=" N   PHE E 244 " --> pdb=" O   GLY E 240 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LEU E 255 " --> pdb=" O   GLY E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 285
      removed outlier: 4.157A  pdb=" N   CYS E 273 " --> pdb=" O   ASP E 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 293
      removed outlier: 3.610A  pdb=" N   TRP E 293 " --> pdb=" O   LEU E 289 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 294 through 296
      No H-bonds generated for 'chain 'E' and resid 294 through 296'
    Processing helix  chain 'E' and resid 319 through 350
      removed outlier: 3.715A  pdb=" N   ARG E 323 " --> pdb=" O   ASP E 319 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ALA E 336 " --> pdb=" O   THR E 332 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLY E 342 " --> pdb=" O   GLY E 338 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER E 346 " --> pdb=" O   GLY E 342 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ALA E 348 " --> pdb=" O   ALA E 344 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU E 349 " --> pdb=" O   GLY E 345 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 356 through 373
      removed outlier: 3.819A  pdb=" N   TRP E 360 " --> pdb=" O   SER E 356 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL E 364 " --> pdb=" O   TRP E 360 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 373 through 378
      removed outlier: 4.203A  pdb=" N   TRP E 377 " --> pdb=" O   ARG E 373 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASP E 378 " --> pdb=" O   ALA E 374 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 373 through 378'
    Processing helix  chain 'E' and resid 379 through 404
      removed outlier: 4.833A  pdb=" N   SER E 390 " --> pdb=" O   LEU E 386 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   TYR E 391 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 409 through 430
    Processing helix  chain 'E' and resid 440 through 456
      removed outlier: 4.309A  pdb=" N   ALA E 456 " --> pdb=" O   THR E 452 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 457 through 467
      removed outlier: 4.313A  pdb=" N   VAL E 461 " --> pdb=" O   SER E 457 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 37
      removed outlier: 3.727A  pdb=" N   GLU H  37 " --> pdb=" O   PRO H  34 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 34 through 37'
    Processing helix  chain 'H' and resid 38 through 47
    Processing helix  chain 'H' and resid 82 through 87
    Processing helix  chain 'H' and resid 115 through 124
      removed outlier: 3.533A  pdb=" N   PHE H 119 " --> pdb=" O   ALA H 115 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 129 through 159
      removed outlier: 3.747A  pdb=" N   ARG H 134 " --> pdb=" O   THR H 130 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 160 through 179
      removed outlier: 4.014A  pdb=" N   GLN H 164 " --> pdb=" O   ASP H 160 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 187 through 206
      removed outlier: 3.652A  pdb=" N   LEU H 197 " --> pdb=" O   ALA H 193 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   VAL H 198 " --> pdb=" O   VAL H 194 " (cutoff:3.500A)
      Proline residue:  H 199  - end of helix
    Processing helix  chain 'H' and resid 215 through 234
      removed outlier: 3.609A  pdb=" N   GLY H 234 " --> pdb=" O   ILE H 230 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 241 through 264
      removed outlier: 3.902A  pdb=" N   THR H 245 " --> pdb=" O   ILE H 241 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ALA H 260 " --> pdb=" O   LEU H 256 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 267 through 285
      removed outlier: 3.526A  pdb=" N   ILE H 271 " --> pdb=" O   SER H 267 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 287 through 294
      removed outlier: 3.506A  pdb=" N   ALA H 294 " --> pdb=" O   SER H 290 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 313 through 345
      Proline residue:  H 321  - end of helix
      removed outlier: 4.093A  pdb=" N   ARG H 325 " --> pdb=" O   PRO H 321 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 345 through 350
      removed outlier: 3.932A  pdb=" N   VAL H 350 " --> pdb=" O   SER H 346 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 356 through 373
      removed outlier: 3.583A  pdb=" N   TRP H 360 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 374 through 376
      No H-bonds generated for 'chain 'H' and resid 374 through 376'
    Processing helix  chain 'H' and resid 379 through 404
      removed outlier: 3.714A  pdb=" N   HIS H 389 " --> pdb=" O   TRP H 385 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   SER H 390 " --> pdb=" O   LEU H 386 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   TYR H 391 " --> pdb=" O   LEU H 387 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 408 through 429
      removed outlier: 3.702A  pdb=" N   TRP H 412 " --> pdb=" O   GLN H 408 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 435 through 439
    Processing helix  chain 'H' and resid 440 through 467
      removed outlier: 3.885A  pdb=" N   ASP H 455 " --> pdb=" O   ALA H 451 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   ILE H 459 " --> pdb=" O   ASP H 455 " (cutoff:3.500A)
      Proline residue:  H 460  - end of helix
    Processing helix  chain 'H' and resid 468 through 471
    Processing helix  chain 'I' and resid 34 through 55
    Processing helix  chain 'I' and resid 62 through 90
    Processing helix  chain 'J' and resid 93 through 130
      removed outlier: 3.546A  pdb=" N   VAL J  97 " --> pdb=" O   ARG J  93 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 134 through 139
      removed outlier: 3.775A  pdb=" N   ALA J 137 " --> pdb=" O   GLU J 134 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 183 through 197
      removed outlier: 4.025A  pdb=" N   LEU J 190 " --> pdb=" O   ALA J 186 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 210 through 212
      No H-bonds generated for 'chain 'J' and resid 210 through 212'
    Processing helix  chain 'J' and resid 220 through 237
      removed outlier: 4.305A  pdb=" N   ALA J 226 " --> pdb=" O   ASP J 222 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 257 through 263
    Processing helix  chain 'J' and resid 285 through 294
    Processing helix  chain 'J' and resid 295 through 297
      No H-bonds generated for 'chain 'J' and resid 295 through 297'
    Processing helix  chain 'J' and resid 386 through 399
      removed outlier: 4.080A  pdb=" N   ARG J 399 " --> pdb=" O   ARG J 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 17
      removed outlier: 3.571A  pdb=" N   LEU D  17 " --> pdb=" O   VAL D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 38
    Processing helix  chain 'D' and resid 49 through 62
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 89 through 95
    Processing helix  chain 'D' and resid 96 through 98
      No H-bonds generated for 'chain 'D' and resid 96 through 98'
    Processing helix  chain 'D' and resid 131 through 140
      removed outlier: 3.922A  pdb=" N   SER D 139 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 163
    Processing helix  chain 'D' and resid 207 through 212
    Processing helix  chain 'D' and resid 265 through 270
    Processing sheet with id=AA1, first strand: chain 'E' and resid 67 through 71
      removed outlier: 8.700A  pdb=" N   LEU E  94 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ALA E  13 " --> pdb=" O   LEU E  94 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   LEU E  96 " --> pdb=" O   ALA E  13 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU E  15 " --> pdb=" O   LEU E  96 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   ALA E  98 " --> pdb=" O   LEU E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 24 through 30
      removed outlier: 8.577A  pdb=" N   LEU H  94 " --> pdb=" O   ARG H  11 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   ALA H  13 " --> pdb=" O   LEU H  94 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   LEU H  96 " --> pdb=" O   ALA H  13 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   LEU H  15 " --> pdb=" O   LEU H  96 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   ALA H  98 " --> pdb=" O   LEU H  15 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24
      removed outlier: 3.823A  pdb=" N   ILE J  24 " --> pdb=" O   LYS J 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'J' and resid 157 through 165
      removed outlier: 7.152A  pdb=" N   THR J 205 " --> pdb=" O   ALA J 160 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ARG J 162 " --> pdb=" O   ALA J 203 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   ALA J 203 " --> pdb=" O   ARG J 162 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ASP J 164 " --> pdb=" O   ARG J 201 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ARG J 201 " --> pdb=" O   ASP J 164 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 244 through 249
      removed outlier: 6.139A  pdb=" N   GLY J 245 " --> pdb=" O   LEU J 315 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   VAL J 317 " --> pdb=" O   GLY J 245 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ALA J 247 " --> pdb=" O   VAL J 317 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   LEU J 314 " --> pdb=" O   THR J 338 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   ILE J 340 " --> pdb=" O   LEU J 314 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL J 316 " --> pdb=" O   ILE J 340 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   ARG J 342 " --> pdb=" O   VAL J 316 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU J 318 " --> pdb=" O   ARG J 342 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   LEU J 360 " --> pdb=" O   ARG J 214 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR J 216 " --> pdb=" O   LEU J 360 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL J 362 " --> pdb=" O   THR J 216 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ILE J 218 " --> pdb=" O   VAL J 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 167 through 168
      removed outlier: 3.844A  pdb=" N   LYS D 106 " --> pdb=" O   THR D 125 " (cutoff:3.500A)

    654 hydrogen bonds defined for protein.
    1920 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3727
        1.34 -     1.46: 2139
        1.46 -     1.58: 5473
        1.58 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 11389
  Sorted by residual:
  bond pdb=" CA  ARG J 357 "
       pdb=" CB  ARG J 357 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 8.90e-03 1.26e+04 1.26e+00
  bond pdb=" CA  VAL H  99 "
       pdb=" C   VAL H  99 "
    ideal  model  delta    sigma   weight residual
    1.526  1.535 -0.009 7.90e-03 1.60e+04 1.25e+00
  bond pdb=" CB  ASP E 378 "
       pdb=" CG  ASP E 378 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  ASN E 354 "
       pdb=" CG  ASN E 354 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.10e+00
  bond pdb=" CA  THR D 103 "
       pdb=" CB  THR D 103 "
    ideal  model  delta    sigma   weight residual
    1.527  1.544 -0.017 1.61e-02 3.86e+03 1.10e+00
  ... (remaining 11384 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 15312
        2.20 -     4.41: 254
        4.41 -     6.61: 28
        6.61 -     8.81: 3
        8.81 -    11.02: 1
  Bond angle restraints: 15598
  Sorted by residual:
  angle pdb=" N   GLY J 256 "
        pdb=" CA  GLY J 256 "
        pdb=" C   GLY J 256 "
      ideal   model   delta    sigma   weight residual
     115.42  111.22    4.20 1.27e+00 6.20e-01 1.09e+01
  angle pdb=" CA  TYR D  96 "
        pdb=" C   TYR D  96 "
        pdb=" N   LEU D  97 "
      ideal   model   delta    sigma   weight residual
     118.27  123.38   -5.11 1.59e+00 3.96e-01 1.03e+01
  angle pdb=" CA  LEU D 278 "
        pdb=" CB  LEU D 278 "
        pdb=" CG  LEU D 278 "
      ideal   model   delta    sigma   weight residual
     116.30  127.32  -11.02 3.50e+00 8.16e-02 9.91e+00
  angle pdb=" N   THR J 344 "
        pdb=" CA  THR J 344 "
        pdb=" C   THR J 344 "
      ideal   model   delta    sigma   weight residual
     114.04  110.15    3.89 1.24e+00 6.50e-01 9.84e+00
  angle pdb=" CA  GLY J 256 "
        pdb=" C   GLY J 256 "
        pdb=" N   ASP J 257 "
      ideal   model   delta    sigma   weight residual
     118.52  114.71    3.81 1.22e+00 6.72e-01 9.77e+00
  ... (remaining 15593 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 6208
       17.86 -    35.72: 497
       35.72 -    53.58: 87
       53.58 -    71.44: 16
       71.44 -    89.30: 6
  Dihedral angle restraints: 6814
    sinusoidal: 2511
      harmonic: 4303
  Sorted by residual:
  dihedral pdb=" CA  ALA J 323 "
           pdb=" C   ALA J 323 "
           pdb=" N   ASP J 324 "
           pdb=" CA  ASP J 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.08   28.92     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  LEU J 297 "
           pdb=" C   LEU J 297 "
           pdb=" N   ALA J 298 "
           pdb=" CA  ALA J 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.05   24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL E  99 "
           pdb=" C   VAL E  99 "
           pdb=" N   PRO E 100 "
           pdb=" CA  PRO E 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 6811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1248
       0.032 -    0.065: 472
       0.065 -    0.097: 152
       0.097 -    0.129: 58
       0.129 -    0.161: 11
  Chirality restraints: 1941
  Sorted by residual:
  chirality pdb=" CA  TRP J 231 "
            pdb=" N   TRP J 231 "
            pdb=" C   TRP J 231 "
            pdb=" CB  TRP J 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" CA  THR D 103 "
            pdb=" N   THR D 103 "
            pdb=" C   THR D 103 "
            pdb=" CB  THR D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CB  THR D 103 "
            pdb=" CA  THR D 103 "
            pdb=" OG1 THR D 103 "
            pdb=" CG2 THR D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.76e-01
  ... (remaining 1938 not shown)

  Planarity restraints: 1969
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J 165 "   -0.041 5.00e-02 4.00e+02   6.22e-02 6.18e+00
        pdb=" N   PRO J 166 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO J 166 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO J 166 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E 298 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO E 299 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO E 299 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 299 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J 269 "    0.031 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO J 270 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO J 270 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO J 270 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1966 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1297
        2.74 -     3.28: 12184
        3.28 -     3.82: 18136
        3.82 -     4.36: 20059
        4.36 -     4.90: 33731
  Nonbonded interactions: 85407
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 347 "
            pdb=" OG  SER H 351 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ALA J 233 "
            pdb=" OG1 THR J 237 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   ASN J 348 "
            pdb=" NH1 ARG J 349 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   TRP J 128 "
            pdb=" NH2 ARG J 144 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OD2 ASP J 240 "
            pdb=" OG  SER J 402 "
     model   vdw
     2.243 3.040
  ... (remaining 85402 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 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 
1 or resid 214 through 471))
  selection = (chain 'H' and (resid 8 through 299 or resid 315 through 471))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.91 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.030
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.380
  Find NCS groups from input model:        0.120
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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      :  0.003   0.036  11389  Z= 0.170
  Angle     :  0.696  11.017  15598  Z= 0.390
  Chirality :  0.041   0.161   1941
  Planarity :  0.005   0.062   1969
  Dihedral  : 13.522  89.299   4010
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 10.32 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (0.18), residues: 1463
  helix: -1.82 (0.15), residues: 797
  sheet: -3.10 (0.35), residues: 134
  loop : -4.05 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 214 
 TYR   0.012   0.001   TYR D  96 
 PHE   0.007   0.001   PHE D 226 
 TRP   0.023   0.001   TRP J 231 
 HIS   0.004   0.001   HIS J 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11389)
  covalent geometry    : angle       0.69623 (15598)
  hydrogen bonds       : bond        0.14715 (  654)
  hydrogen bonds       : angle       6.56109 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 GLU cc_start: 0.8638 (tp30) cc_final: 0.8426 (tp30)
REVERT: E  110 GLU cc_start: 0.8405 (pp20) cc_final: 0.8090 (pp20)
REVERT: E  216 ASN cc_start: 0.8605 (m-40) cc_final: 0.8404 (m-40)
REVERT: E  232 MET cc_start: 0.8452 (ttp) cc_final: 0.8107 (ttt)
REVERT: E  288 GLN cc_start: 0.9225 (mp10) cc_final: 0.8462 (mp10)
REVERT: E  292 MET cc_start: 0.8723 (mmm) cc_final: 0.8312 (mmm)
REVERT: E  391 TYR cc_start: 0.8768 (t80) cc_final: 0.8548 (t80)
REVERT: E  407 TYR cc_start: 0.7966 (m-80) cc_final: 0.7576 (m-80)
REVERT: E  430 ASN cc_start: 0.7922 (t0) cc_final: 0.7648 (t0)
REVERT: E  445 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8427 (tpt-90)
REVERT: H  123 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8018 (mmt180)
REVERT: I   45 MET cc_start: 0.8739 (mmm) cc_final: 0.8006 (tpp)
REVERT: I   58 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7960 (mtt-85)
REVERT: I   59 MET cc_start: 0.8950 (mmm) cc_final: 0.8730 (tpp)
REVERT: I   62 ASP cc_start: 0.8557 (p0) cc_final: 0.8345 (p0)
REVERT: J  168 ASP cc_start: 0.8570 (p0) cc_final: 0.8189 (p0)
REVERT: J  376 GLN cc_start: 0.8720 (mp10) cc_final: 0.8426 (mp10)
REVERT: D   59 MET cc_start: 0.7481 (mmt) cc_final: 0.7255 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1175
  time to fit residues: 37.3165
Evaluate side-chains
  167 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
E  43 GLN
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 216 ASN
I  67 GLN
J 187 HIS
** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 136 GLN
D 162 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.080313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.065212 restraints weight = 37025.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.067167 restraints weight = 18820.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.068457 restraints weight = 12036.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.069374 restraints weight = 8846.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069953 restraints weight = 7113.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2997
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11389  Z= 0.249
  Angle     :  0.749   9.710  15598  Z= 0.376
  Chirality :  0.043   0.185   1941
  Planarity :  0.006   0.064   1969
  Dihedral  :  5.002  27.721   1614
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.59 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.19 %
    Favored  : 80.72 %
  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 are not related in a simple way.
  whole: -2.54 (0.21), residues: 1463
  helix: -0.33 (0.17), residues: 809
  sheet: -2.70 (0.36), residues: 135
  loop : -3.61 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG J 399 
 TYR   0.022   0.002   TYR D  96 
 PHE   0.007   0.001   PHE D 226 
 TRP   0.020   0.002   TRP J 231 
 HIS   0.005   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (11389)
  covalent geometry    : angle       0.74945 (15598)
  hydrogen bonds       : bond        0.04148 (  654)
  hydrogen bonds       : angle       4.88231 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 GLU cc_start: 0.8689 (tp30) cc_final: 0.8474 (tp30)
REVERT: E  124 ARG cc_start: 0.6355 (ptt-90) cc_final: 0.6046 (ptt90)
REVERT: E  232 MET cc_start: 0.8714 (ttp) cc_final: 0.8379 (ttt)
REVERT: E  288 GLN cc_start: 0.9053 (mp10) cc_final: 0.8346 (mp10)
REVERT: E  292 MET cc_start: 0.8694 (mmm) cc_final: 0.8326 (mmm)
REVERT: E  391 TYR cc_start: 0.8771 (t80) cc_final: 0.8508 (t80)
REVERT: E  407 TYR cc_start: 0.8023 (m-80) cc_final: 0.7731 (m-80)
REVERT: E  445 ARG cc_start: 0.8634 (mmp80) cc_final: 0.8356 (tpt-90)
REVERT: H   23 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8179 (ppt90)
REVERT: H  407 TYR cc_start: 0.8418 (m-80) cc_final: 0.7886 (m-80)
REVERT: I   45 MET cc_start: 0.8796 (mmm) cc_final: 0.8050 (tpp)
REVERT: I   58 ARG cc_start: 0.8615 (mtm180) cc_final: 0.7949 (mtt-85)
REVERT: I   59 MET cc_start: 0.8964 (mmm) cc_final: 0.8753 (tpp)
REVERT: I   62 ASP cc_start: 0.8574 (p0) cc_final: 0.8260 (p0)
REVERT: J  121 GLU cc_start: 0.8427 (tp30) cc_final: 0.7999 (tp30)
REVERT: J  168 ASP cc_start: 0.8524 (p0) cc_final: 0.8208 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 195
  average time/residue: 0.1058
  time to fit residues: 29.6005
Evaluate side-chains
  176 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   80 THR
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  237 THR
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  174 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 144 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 141 optimal weight:    8.9990
   chunk 143 optimal weight:    6.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 408 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 371 GLN
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.081561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.066533 restraints weight = 36912.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.068544 restraints weight = 18494.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069876 restraints weight = 11675.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.070752 restraints weight = 8516.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.071437 restraints weight = 6840.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11389  Z= 0.182
  Angle     :  0.697   9.603  15598  Z= 0.349
  Chirality :  0.042   0.173   1941
  Planarity :  0.005   0.064   1969
  Dihedral  :  4.908  27.504   1614
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.71 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.59 %
    Favored  : 75.83 %
  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 are not related in a simple way.
  whole: -1.77 (0.22), residues: 1463
  helix:  0.37 (0.18), residues: 805
  sheet: -2.32 (0.39), residues: 135
  loop : -3.38 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 399 
 TYR   0.014   0.002   TYR D  96 
 PHE   0.005   0.001   PHE D 226 
 TRP   0.019   0.001   TRP J 231 
 HIS   0.004   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (11389)
  covalent geometry    : angle       0.69719 (15598)
  hydrogen bonds       : bond        0.03867 (  654)
  hydrogen bonds       : angle       4.57777 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 GLU cc_start: 0.8674 (tp30) cc_final: 0.8453 (tp30)
REVERT: E  124 ARG cc_start: 0.6105 (ptt-90) cc_final: 0.5726 (ptt90)
REVERT: E  176 ILE cc_start: 0.8982 (mt) cc_final: 0.8780 (mm)
REVERT: E  292 MET cc_start: 0.8667 (mmm) cc_final: 0.8234 (mmm)
REVERT: E  391 TYR cc_start: 0.8714 (t80) cc_final: 0.8472 (t80)
REVERT: E  407 TYR cc_start: 0.8014 (m-80) cc_final: 0.7740 (m-80)
REVERT: E  445 ARG cc_start: 0.8602 (mmp80) cc_final: 0.8342 (ttt180)
REVERT: H   23 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8196 (ppt90)
REVERT: H  285 GLN cc_start: 0.8689 (tp40) cc_final: 0.7789 (tp40)
REVERT: H  288 GLN cc_start: 0.8478 (mp10) cc_final: 0.7884 (mp10)
REVERT: H  407 TYR cc_start: 0.8384 (m-80) cc_final: 0.7864 (m-80)
REVERT: I   45 MET cc_start: 0.8795 (mmm) cc_final: 0.8005 (tpp)
REVERT: I   58 ARG cc_start: 0.8562 (mtm180) cc_final: 0.7918 (mtt-85)
REVERT: I   59 MET cc_start: 0.8939 (mmm) cc_final: 0.8736 (tpp)
REVERT: I   62 ASP cc_start: 0.8553 (p0) cc_final: 0.8232 (p0)
REVERT: J  121 GLU cc_start: 0.8445 (tp30) cc_final: 0.8041 (tp30)
REVERT: J  172 LYS cc_start: 0.9396 (tmmt) cc_final: 0.8940 (tmmt)
REVERT: J  262 LYS cc_start: 0.8407 (mttm) cc_final: 0.7813 (tttt)
  outliers start: 41
  outliers final: 27
  residues processed: 195
  average time/residue: 0.0953
  time to fit residues: 27.4177
Evaluate side-chains
  186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  343 VAL
Chi-restraints excluded: chain E residue  449 PHE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  346 SER
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   80 THR
Chi-restraints excluded: chain J residue  237 THR
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  174 THR
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 116 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 114 optimal weight:    7.9990
   chunk 117 optimal weight:    0.4980
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 331 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 351 GLN
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.082145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.066771 restraints weight = 36825.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.068792 restraints weight = 18763.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.070133 restraints weight = 11976.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.071025 restraints weight = 8782.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.071663 restraints weight = 7076.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11389  Z= 0.166
  Angle     :  0.685  10.661  15598  Z= 0.338
  Chirality :  0.042   0.169   1941
  Planarity :  0.005   0.062   1969
  Dihedral  :  4.778  26.941   1614
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.77 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 21.47 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.22), residues: 1463
  helix:  0.66 (0.19), residues: 802
  sheet: -2.14 (0.39), residues: 138
  loop : -3.15 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 108 
 TYR   0.016   0.002   TYR E 361 
 PHE   0.005   0.001   PHE I  86 
 TRP   0.018   0.001   TRP J 231 
 HIS   0.004   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (11389)
  covalent geometry    : angle       0.68542 (15598)
  hydrogen bonds       : bond        0.03719 (  654)
  hydrogen bonds       : angle       4.42023 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 182
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 GLU cc_start: 0.8626 (tp30) cc_final: 0.8420 (tp30)
REVERT: E  124 ARG cc_start: 0.6081 (ptt-90) cc_final: 0.5713 (ptt90)
REVERT: E  216 ASN cc_start: 0.8777 (m-40) cc_final: 0.8023 (m-40)
REVERT: E  232 MET cc_start: 0.8704 (ttp) cc_final: 0.8401 (ttt)
REVERT: E  292 MET cc_start: 0.8655 (mmm) cc_final: 0.8249 (mmm)
REVERT: E  391 TYR cc_start: 0.8668 (t80) cc_final: 0.8458 (t80)
REVERT: E  407 TYR cc_start: 0.7994 (m-80) cc_final: 0.7752 (m-80)
REVERT: E  443 MET cc_start: 0.7430 (mtm) cc_final: 0.6979 (ptp)
REVERT: E  445 ARG cc_start: 0.8603 (mmp80) cc_final: 0.8306 (ttt180)
REVERT: E  462 MET cc_start: 0.7769 (mmm) cc_final: 0.7438 (mmm)
REVERT: H   23 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (ppt90)
REVERT: H  123 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8124 (mmt180)
REVERT: H  288 GLN cc_start: 0.8490 (mp10) cc_final: 0.8257 (mp10)
REVERT: H  361 TYR cc_start: 0.9395 (t80) cc_final: 0.9084 (t80)
REVERT: H  407 TYR cc_start: 0.8402 (m-80) cc_final: 0.7858 (m-80)
REVERT: I   45 MET cc_start: 0.8785 (mmm) cc_final: 0.7989 (tpp)
REVERT: I   58 ARG cc_start: 0.8475 (mtm180) cc_final: 0.7954 (mtt-85)
REVERT: I   62 ASP cc_start: 0.8536 (p0) cc_final: 0.8213 (p0)
REVERT: J  121 GLU cc_start: 0.8465 (tp30) cc_final: 0.8021 (tp30)
REVERT: J  172 LYS cc_start: 0.9386 (tmmt) cc_final: 0.8903 (tmmt)
REVERT: J  262 LYS cc_start: 0.8383 (mttm) cc_final: 0.7809 (tttt)
REVERT: J  288 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8063 (tm-30)
REVERT: J  397 LEU cc_start: 0.9466 (tp) cc_final: 0.9260 (tp)
  outliers start: 46
  outliers final: 38
  residues processed: 214
  average time/residue: 0.0830
  time to fit residues: 26.1938
Evaluate side-chains
  206 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   39 LEU
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  449 PHE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  346 SER
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   80 THR
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  297 LEU
Chi-restraints excluded: chain J residue  341 HIS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  174 THR
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 118 optimal weight:    0.6980
   chunk 119 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 39 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.082039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.066710 restraints weight = 36822.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.068748 restraints weight = 18784.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.070100 restraints weight = 11957.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.070952 restraints weight = 8754.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.071661 restraints weight = 7066.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11389  Z= 0.177
  Angle     :  0.694  10.316  15598  Z= 0.344
  Chirality :  0.042   0.177   1941
  Planarity :  0.005   0.062   1969
  Dihedral  :  4.746  30.062   1614
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.05 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.99 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.22), residues: 1463
  helix:  0.72 (0.18), residues: 812
  sheet: -1.85 (0.41), residues: 128
  loop : -3.04 (0.26), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J 399 
 TYR   0.012   0.002   TYR D  96 
 PHE   0.007   0.001   PHE I  86 
 TRP   0.018   0.001   TRP J 231 
 HIS   0.003   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (11389)
  covalent geometry    : angle       0.69386 (15598)
  hydrogen bonds       : bond        0.03650 (  654)
  hydrogen bonds       : angle       4.34505 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 175
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 GLU cc_start: 0.8640 (tp30) cc_final: 0.8431 (tp30)
REVERT: E  124 ARG cc_start: 0.6098 (ptt-90) cc_final: 0.5723 (ptt90)
REVERT: E  176 ILE cc_start: 0.8953 (mt) cc_final: 0.8748 (mm)
REVERT: E  216 ASN cc_start: 0.8789 (m-40) cc_final: 0.8121 (m-40)
REVERT: E  232 MET cc_start: 0.8685 (ttp) cc_final: 0.8389 (ttt)
REVERT: E  292 MET cc_start: 0.8620 (mmm) cc_final: 0.8220 (mmm)
REVERT: E  407 TYR cc_start: 0.8005 (m-80) cc_final: 0.7757 (m-80)
REVERT: E  443 MET cc_start: 0.7465 (mtm) cc_final: 0.6986 (ptp)
REVERT: E  445 ARG cc_start: 0.8599 (mmp80) cc_final: 0.8331 (ttt180)
REVERT: H   23 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8092 (ppt90)
REVERT: H  123 ARG cc_start: 0.8401 (mmt180) cc_final: 0.8126 (mmt180)
REVERT: H  361 TYR cc_start: 0.9379 (t80) cc_final: 0.9051 (t80)
REVERT: H  407 TYR cc_start: 0.8409 (m-80) cc_final: 0.7875 (m-80)
REVERT: I   45 MET cc_start: 0.8771 (mmm) cc_final: 0.8096 (tpp)
REVERT: I   58 ARG cc_start: 0.8438 (mtm180) cc_final: 0.7947 (mtt-85)
REVERT: I   62 ASP cc_start: 0.8532 (p0) cc_final: 0.8201 (p0)
REVERT: J  121 GLU cc_start: 0.8494 (tp30) cc_final: 0.8040 (tp30)
REVERT: J  145 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7834 (pp30)
REVERT: J  172 LYS cc_start: 0.9402 (tmmt) cc_final: 0.8912 (tmmt)
REVERT: J  262 LYS cc_start: 0.8430 (mttm) cc_final: 0.7744 (tttt)
REVERT: J  288 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7943 (tm-30)
  outliers start: 58
  outliers final: 40
  residues processed: 213
  average time/residue: 0.0910
  time to fit residues: 28.9304
Evaluate side-chains
  210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   27 MET
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  449 PHE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  346 SER
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain I residue   80 THR
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  341 HIS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  174 THR
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 147 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 128 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0060
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
E  43 GLN
E 354 ASN
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 331 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.068083 restraints weight = 36701.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.070147 restraints weight = 18358.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.071505 restraints weight = 11543.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.072488 restraints weight = 8345.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.073112 restraints weight = 6601.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11389  Z= 0.138
  Angle     :  0.675  10.278  15598  Z= 0.331
  Chirality :  0.042   0.224   1941
  Planarity :  0.005   0.059   1969
  Dihedral  :  4.615  28.154   1614
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.89 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 23.12 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.23), residues: 1463
  helix:  0.93 (0.19), residues: 806
  sheet: -1.67 (0.43), residues: 128
  loop : -2.95 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 108 
 TYR   0.013   0.002   TYR J 281 
 PHE   0.008   0.001   PHE I  86 
 TRP   0.019   0.001   TRP E 360 
 HIS   0.003   0.001   HIS J 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11389)
  covalent geometry    : angle       0.67543 (15598)
  hydrogen bonds       : bond        0.03569 (  654)
  hydrogen bonds       : angle       4.21728 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 190
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  124 ARG cc_start: 0.5945 (ptt-90) cc_final: 0.5668 (ptt90)
REVERT: E  216 ASN cc_start: 0.8753 (m-40) cc_final: 0.8124 (m-40)
REVERT: E  232 MET cc_start: 0.8668 (ttp) cc_final: 0.8315 (ttt)
REVERT: E  292 MET cc_start: 0.8613 (mmm) cc_final: 0.8192 (mmm)
REVERT: E  320 LEU cc_start: 0.9247 (tp) cc_final: 0.8971 (tp)
REVERT: E  407 TYR cc_start: 0.7982 (m-80) cc_final: 0.7689 (m-80)
REVERT: E  443 MET cc_start: 0.7530 (mtm) cc_final: 0.6971 (ptp)
REVERT: E  445 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8322 (ttt180)
REVERT: H   23 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8068 (ppt90)
REVERT: H  123 ARG cc_start: 0.8446 (mmt180) cc_final: 0.8188 (mmt180)
REVERT: H  361 TYR cc_start: 0.9345 (t80) cc_final: 0.9016 (t80)
REVERT: H  407 TYR cc_start: 0.8331 (m-80) cc_final: 0.7850 (m-80)
REVERT: H  444 ARG cc_start: 0.8108 (ptp-170) cc_final: 0.6302 (tpt170)
REVERT: I   45 MET cc_start: 0.8756 (mmm) cc_final: 0.8178 (tpp)
REVERT: I   58 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7926 (mtt-85)
REVERT: J  121 GLU cc_start: 0.8558 (tp30) cc_final: 0.8035 (tp30)
REVERT: J  145 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7743 (pp30)
REVERT: J  172 LYS cc_start: 0.9416 (tmmt) cc_final: 0.8932 (tmmt)
REVERT: J  262 LYS cc_start: 0.8430 (mttm) cc_final: 0.7735 (tttt)
REVERT: J  288 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7981 (tm-30)
REVERT: J  397 LEU cc_start: 0.9425 (tp) cc_final: 0.9124 (tp)
  outliers start: 51
  outliers final: 38
  residues processed: 227
  average time/residue: 0.0933
  time to fit residues: 30.9035
Evaluate side-chains
  218 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 177
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   39 LEU
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain H residue  426 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  185 VAL
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  341 HIS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0870
   chunk 110 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 132 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    2.1362

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

Flipped N/Q/H residues before XYZ refinement:
E  43 GLN
E 354 ASN
** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 331 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.082105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.067069 restraints weight = 36673.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.069108 restraints weight = 18561.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.070487 restraints weight = 11700.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.071402 restraints weight = 8483.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.072025 restraints weight = 6747.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11389  Z= 0.180
  Angle     :  0.702   9.700  15598  Z= 0.349
  Chirality :  0.042   0.191   1941
  Planarity :  0.005   0.058   1969
  Dihedral  :  4.617  28.628   1614
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.23 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 23.73 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.22), residues: 1463
  helix:  0.95 (0.19), residues: 807
  sheet: -1.54 (0.44), residues: 127
  loop : -2.91 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  52 
 TYR   0.012   0.002   TYR J 281 
 PHE   0.008   0.001   PHE D  48 
 TRP   0.024   0.001   TRP E 360 
 HIS   0.004   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11389)
  covalent geometry    : angle       0.70156 (15598)
  hydrogen bonds       : bond        0.03579 (  654)
  hydrogen bonds       : angle       4.27850 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 177
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 ASN cc_start: 0.8692 (m-40) cc_final: 0.8150 (m-40)
REVERT: E  232 MET cc_start: 0.8675 (ttp) cc_final: 0.8342 (ttt)
REVERT: E  292 MET cc_start: 0.8631 (mmm) cc_final: 0.8206 (mmm)
REVERT: E  407 TYR cc_start: 0.7980 (m-80) cc_final: 0.7705 (m-80)
REVERT: E  445 ARG cc_start: 0.8563 (mmp80) cc_final: 0.8306 (ttt180)
REVERT: H   23 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8130 (ppt90)
REVERT: H  121 GLU cc_start: 0.8936 (tp30) cc_final: 0.8547 (tm-30)
REVERT: H  123 ARG cc_start: 0.8441 (mmt180) cc_final: 0.7934 (mmt180)
REVERT: H  361 TYR cc_start: 0.9358 (t80) cc_final: 0.9037 (t80)
REVERT: H  407 TYR cc_start: 0.8389 (m-80) cc_final: 0.7869 (m-80)
REVERT: I   45 MET cc_start: 0.8831 (mmm) cc_final: 0.8130 (tpp)
REVERT: I   58 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7960 (mtt-85)
REVERT: I   59 MET cc_start: 0.8837 (mmm) cc_final: 0.8500 (tpp)
REVERT: J  121 GLU cc_start: 0.8567 (tp30) cc_final: 0.8084 (tp30)
REVERT: J  145 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7805 (pp30)
REVERT: J  172 LYS cc_start: 0.9458 (tmmt) cc_final: 0.8956 (tmmt)
REVERT: J  262 LYS cc_start: 0.8464 (mttm) cc_final: 0.7740 (tttt)
REVERT: J  288 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7931 (tm-30)
REVERT: J  291 GLU cc_start: 0.8456 (tp30) cc_final: 0.8175 (tm-30)
REVERT: J  397 LEU cc_start: 0.9442 (tp) cc_final: 0.9155 (tp)
REVERT: D  219 GLU cc_start: 0.7891 (tt0) cc_final: 0.7683 (tt0)
  outliers start: 50
  outliers final: 43
  residues processed: 211
  average time/residue: 0.0913
  time to fit residues: 28.5199
Evaluate side-chains
  218 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 172
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   39 LEU
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  362 ILE
Chi-restraints excluded: chain E residue  449 PHE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain H residue  426 VAL
Chi-restraints excluded: chain I residue   66 THR
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  258 TRP
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  312 LYS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  174 THR
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 142 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0770
   chunk 113 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 132 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
E  43 GLN
E 354 ASN
H 328 GLN
H 331 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.083824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.068946 restraints weight = 35784.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.071023 restraints weight = 17942.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.072425 restraints weight = 11240.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.073373 restraints weight = 8088.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.074022 restraints weight = 6374.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3077 r_free = 0.3077    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11389  Z= 0.132
  Angle     :  0.693  10.453  15598  Z= 0.336
  Chirality :  0.042   0.188   1941
  Planarity :  0.005   0.055   1969
  Dihedral  :  4.527  26.174   1614
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.75 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 24.35 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.23), residues: 1463
  helix:  1.05 (0.19), residues: 807
  sheet: -1.40 (0.45), residues: 128
  loop : -2.77 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 108 
 TYR   0.012   0.001   TYR J 352 
 PHE   0.011   0.001   PHE D  48 
 TRP   0.023   0.001   TRP D 164 
 HIS   0.003   0.001   HIS J 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (11389)
  covalent geometry    : angle       0.69285 (15598)
  hydrogen bonds       : bond        0.03478 (  654)
  hydrogen bonds       : angle       4.19565 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 ASN cc_start: 0.8633 (m-40) cc_final: 0.8097 (m-40)
REVERT: E  232 MET cc_start: 0.8654 (ttp) cc_final: 0.8358 (ttt)
REVERT: E  292 MET cc_start: 0.8642 (mmm) cc_final: 0.8163 (mmm)
REVERT: E  320 LEU cc_start: 0.9264 (tp) cc_final: 0.8978 (tp)
REVERT: E  407 TYR cc_start: 0.7934 (m-80) cc_final: 0.7617 (m-80)
REVERT: E  445 ARG cc_start: 0.8600 (mmp80) cc_final: 0.8364 (ttt-90)
REVERT: H   23 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8076 (ppt90)
REVERT: H  121 GLU cc_start: 0.8944 (tp30) cc_final: 0.8482 (tm-30)
REVERT: H  123 ARG cc_start: 0.8433 (mmt180) cc_final: 0.8158 (mmt180)
REVERT: H  361 TYR cc_start: 0.9308 (t80) cc_final: 0.8981 (t80)
REVERT: H  407 TYR cc_start: 0.8273 (m-80) cc_final: 0.7797 (m-80)
REVERT: H  444 ARG cc_start: 0.8140 (ptp-170) cc_final: 0.6310 (tpt90)
REVERT: I   45 MET cc_start: 0.8843 (mmm) cc_final: 0.8255 (tpp)
REVERT: I   58 ARG cc_start: 0.8369 (mtm180) cc_final: 0.7941 (mtt-85)
REVERT: I   59 MET cc_start: 0.8799 (mmm) cc_final: 0.8470 (tpp)
REVERT: J  121 GLU cc_start: 0.8566 (tp30) cc_final: 0.8090 (tp30)
REVERT: J  145 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7739 (pp30)
REVERT: J  172 LYS cc_start: 0.9448 (tmmt) cc_final: 0.8954 (tmmt)
REVERT: J  243 MET cc_start: 0.8868 (mmm) cc_final: 0.8494 (mmm)
REVERT: J  262 LYS cc_start: 0.8471 (mttm) cc_final: 0.7649 (tttt)
REVERT: J  288 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7990 (tm-30)
REVERT: J  291 GLU cc_start: 0.8426 (tp30) cc_final: 0.8173 (tm-30)
REVERT: J  376 GLN cc_start: 0.8065 (mp10) cc_final: 0.7799 (mp10)
REVERT: J  397 LEU cc_start: 0.9393 (tp) cc_final: 0.9093 (tp)
REVERT: D  219 GLU cc_start: 0.7993 (tt0) cc_final: 0.7772 (tt0)
  outliers start: 44
  outliers final: 35
  residues processed: 223
  average time/residue: 0.0901
  time to fit residues: 29.8042
Evaluate side-chains
  215 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  354 ASN
Chi-restraints excluded: chain E residue  362 ILE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain H residue  426 VAL
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  258 TRP
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  341 HIS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 89 optimal weight:    5.9990
   chunk 143 optimal weight:    8.9990
   chunk 126 optimal weight:    2.9990
   chunk 135 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
E 354 ASN
H 331 GLN
I  67 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.081965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.066594 restraints weight = 36574.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.068610 restraints weight = 18785.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069987 restraints weight = 12030.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.070857 restraints weight = 8774.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.071489 restraints weight = 7070.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11389  Z= 0.210
  Angle     :  0.734   9.685  15598  Z= 0.363
  Chirality :  0.043   0.196   1941
  Planarity :  0.005   0.060   1969
  Dihedral  :  4.642  27.281   1614
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.84 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.26 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.23), residues: 1463
  helix:  0.99 (0.19), residues: 810
  sheet: -1.37 (0.45), residues: 127
  loop : -2.82 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 108 
 TYR   0.015   0.002   TYR J 352 
 PHE   0.015   0.001   PHE E 165 
 TRP   0.033   0.002   TRP E 360 
 HIS   0.004   0.001   HIS J 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (11389)
  covalent geometry    : angle       0.73414 (15598)
  hydrogen bonds       : bond        0.03683 (  654)
  hydrogen bonds       : angle       4.31283 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 174
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 ASN cc_start: 0.8725 (m-40) cc_final: 0.8232 (m-40)
REVERT: E  232 MET cc_start: 0.8778 (ttp) cc_final: 0.8464 (ttt)
REVERT: E  292 MET cc_start: 0.8646 (mmm) cc_final: 0.8244 (mmm)
REVERT: E  407 TYR cc_start: 0.7949 (m-80) cc_final: 0.7609 (m-80)
REVERT: E  443 MET cc_start: 0.6949 (ptp) cc_final: 0.6388 (pmm)
REVERT: E  445 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8351 (ttt180)
REVERT: H   23 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8133 (ppt90)
REVERT: H  123 ARG cc_start: 0.8444 (mmt180) cc_final: 0.7962 (mmt180)
REVERT: H  391 TYR cc_start: 0.8490 (t80) cc_final: 0.8181 (t80)
REVERT: H  407 TYR cc_start: 0.8402 (m-80) cc_final: 0.7897 (m-80)
REVERT: I   45 MET cc_start: 0.8921 (mmm) cc_final: 0.8409 (tpp)
REVERT: I   58 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8035 (mtt-85)
REVERT: I   59 MET cc_start: 0.8835 (mmm) cc_final: 0.8518 (tpp)
REVERT: J  121 GLU cc_start: 0.8572 (tp30) cc_final: 0.8160 (tp30)
REVERT: J  145 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7819 (pp30)
REVERT: J  172 LYS cc_start: 0.9467 (tmmt) cc_final: 0.8990 (tmmt)
REVERT: J  243 MET cc_start: 0.8900 (mmm) cc_final: 0.8501 (mmm)
REVERT: J  262 LYS cc_start: 0.8376 (mttm) cc_final: 0.7674 (tttt)
REVERT: J  288 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7966 (tm-30)
REVERT: D  219 GLU cc_start: 0.8081 (tt0) cc_final: 0.7840 (tt0)
  outliers start: 47
  outliers final: 38
  residues processed: 209
  average time/residue: 0.0901
  time to fit residues: 27.9715
Evaluate side-chains
  212 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 171
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  244 PHE
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  362 ILE
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain H residue  426 VAL
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  258 TRP
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  297 LEU
Chi-restraints excluded: chain J residue  312 LYS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    0.3980
   chunk 109 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 116 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
H 331 GLN
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 131 ASN
D 136 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.083376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.067840 restraints weight = 36532.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069923 restraints weight = 18730.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.071311 restraints weight = 11936.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.072198 restraints weight = 8736.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.072863 restraints weight = 7041.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11389  Z= 0.149
  Angle     :  0.715   9.659  15598  Z= 0.350
  Chirality :  0.043   0.212   1941
  Planarity :  0.005   0.057   1969
  Dihedral  :  4.584  25.094   1614
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.02 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.04 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.23), residues: 1463
  helix:  1.05 (0.19), residues: 809
  sheet: -1.27 (0.46), residues: 128
  loop : -2.74 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 108 
 TYR   0.017   0.002   TYR J 352 
 PHE   0.017   0.001   PHE E 165 
 TRP   0.031   0.002   TRP D 164 
 HIS   0.005   0.001   HIS J 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11389)
  covalent geometry    : angle       0.71531 (15598)
  hydrogen bonds       : bond        0.03564 (  654)
  hydrogen bonds       : angle       4.23080 ( 1920)

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

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

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2926 Ramachandran restraints generated.
    1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 176
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  216 ASN cc_start: 0.8661 (m-40) cc_final: 0.8181 (m-40)
REVERT: E  232 MET cc_start: 0.8780 (ttp) cc_final: 0.8456 (ttt)
REVERT: E  292 MET cc_start: 0.8634 (mmm) cc_final: 0.8181 (mmm)
REVERT: E  320 LEU cc_start: 0.9277 (tp) cc_final: 0.9002 (tp)
REVERT: E  361 TYR cc_start: 0.8717 (t80) cc_final: 0.8364 (t80)
REVERT: E  407 TYR cc_start: 0.7940 (m-80) cc_final: 0.7590 (m-80)
REVERT: E  443 MET cc_start: 0.6954 (ptp) cc_final: 0.6401 (pmm)
REVERT: E  445 ARG cc_start: 0.8635 (mmp80) cc_final: 0.8419 (ttt180)
REVERT: H   23 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8127 (ppt90)
REVERT: H  121 GLU cc_start: 0.8929 (tp30) cc_final: 0.8558 (tm-30)
REVERT: H  123 ARG cc_start: 0.8467 (mmt180) cc_final: 0.8004 (mmt180)
REVERT: H  361 TYR cc_start: 0.9319 (t80) cc_final: 0.9014 (t80)
REVERT: H  407 TYR cc_start: 0.8339 (m-80) cc_final: 0.7903 (m-80)
REVERT: I   45 MET cc_start: 0.8937 (mmm) cc_final: 0.8578 (tpp)
REVERT: I   58 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8007 (mtt-85)
REVERT: I   59 MET cc_start: 0.8792 (mmm) cc_final: 0.8513 (tpt)
REVERT: J  121 GLU cc_start: 0.8570 (tp30) cc_final: 0.8100 (tp30)
REVERT: J  145 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7728 (pp30)
REVERT: J  172 LYS cc_start: 0.9473 (tmmt) cc_final: 0.9016 (tmmt)
REVERT: J  243 MET cc_start: 0.8884 (mmm) cc_final: 0.8497 (mmm)
REVERT: J  262 LYS cc_start: 0.8395 (mttm) cc_final: 0.7584 (tttt)
REVERT: J  288 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7970 (tm-30)
REVERT: J  376 GLN cc_start: 0.7957 (mp10) cc_final: 0.7683 (mp10)
REVERT: J  397 LEU cc_start: 0.9402 (tp) cc_final: 0.9103 (tp)
  outliers start: 43
  outliers final: 37
  residues processed: 207
  average time/residue: 0.0921
  time to fit residues: 28.0916
Evaluate side-chains
  212 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   99 VAL
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  229 LEU
Chi-restraints excluded: chain E residue  243 VAL
Chi-restraints excluded: chain E residue  244 PHE
Chi-restraints excluded: chain E residue  245 THR
Chi-restraints excluded: chain H residue   23 ARG
Chi-restraints excluded: chain H residue   88 VAL
Chi-restraints excluded: chain H residue  243 VAL
Chi-restraints excluded: chain H residue  245 THR
Chi-restraints excluded: chain H residue  249 VAL
Chi-restraints excluded: chain H residue  271 ILE
Chi-restraints excluded: chain H residue  315 SER
Chi-restraints excluded: chain H residue  331 GLN
Chi-restraints excluded: chain H residue  347 VAL
Chi-restraints excluded: chain H residue  395 VAL
Chi-restraints excluded: chain H residue  421 VAL
Chi-restraints excluded: chain H residue  426 VAL
Chi-restraints excluded: chain I residue   76 LEU
Chi-restraints excluded: chain J residue   13 THR
Chi-restraints excluded: chain J residue  145 GLN
Chi-restraints excluded: chain J residue  171 LEU
Chi-restraints excluded: chain J residue  212 LEU
Chi-restraints excluded: chain J residue  244 LEU
Chi-restraints excluded: chain J residue  258 TRP
Chi-restraints excluded: chain J residue  269 VAL
Chi-restraints excluded: chain J residue  286 THR
Chi-restraints excluded: chain J residue  288 GLU
Chi-restraints excluded: chain J residue  312 LYS
Chi-restraints excluded: chain J residue  381 VAL
Chi-restraints excluded: chain D residue    5 ILE
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain D residue  102 ILE
Chi-restraints excluded: chain D residue  124 LEU
Chi-restraints excluded: chain D residue  131 ASN
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  222 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 104 optimal weight:    0.3980
   chunk 141 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0870
   chunk 52 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 116 optimal weight:    6.9990
   chunk 128 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
H 331 GLN
** J 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.084661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.069190 restraints weight = 36313.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.071317 restraints weight = 18234.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.072725 restraints weight = 11487.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.073621 restraints weight = 8317.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.074336 restraints weight = 6634.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  11389  Z= 0.133
  Angle     :  0.711   9.673  15598  Z= 0.346
  Chirality :  0.043   0.258   1941
  Planarity :  0.005   0.054   1969
  Dihedral  :  4.457  23.429   1614
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.54 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.65 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.23), residues: 1463
  helix:  1.14 (0.19), residues: 809
  sheet: -1.07 (0.47), residues: 128
  loop : -2.64 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 108 
 TYR   0.018   0.002   TYR J 352 
 PHE   0.018   0.001   PHE E 165 
 TRP   0.028   0.002   TRP E 360 
 HIS   0.006   0.001   HIS H 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11389)
  covalent geometry    : angle       0.71149 (15598)
  hydrogen bonds       : bond        0.03459 (  654)
  hydrogen bonds       : angle       4.17919 ( 1920)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1821.99 seconds
wall clock time: 32 minutes 9.31 seconds (1929.31 seconds total)