Starting phenix.real_space_refine
on Tue Mar  3 14:30:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6z3y_11066/03_2026/6z3y_11066.cif"
  }
  resolution = 3.51
  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=  -0.000 sd=   0.003
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      46      5.16       5
     C    4137      2.51       5
     N     933      2.21       5
     O    1015      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.00s

  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: 6131
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 386, 3069
          Classifications: {'peptide': 386}
          Link IDs: {'PTRANS': 11, 'TRANS': 374}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3062
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 10, 'TRANS': 374}
          Chain breaks: 5
  Time building chain proxies: 1.28, per 1000 atoms: 0.21
  Number of scatterers: 6131
  At special positions: 0
  Unit cell: (76.775, 87.15, 106.862, 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      46     16.00
     O    1015      8.00
     N     933      7.00
     C    4137      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: 0.46
  Conformation dependent library (CDL) restraints added in 337.5 milliseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1438

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      83.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 4.148A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B  32 " --> pdb=" O   ASN B  28 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE B  41 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 56
      No H-bonds generated for 'chain 'B' and resid 54 through 56'
    Processing helix  chain 'B' and resid 57 through 66
      removed outlier: 4.473A  pdb=" N   ILE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE B  65 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.664A  pdb=" N   MET B 127 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 139
      removed outlier: 3.606A  pdb=" N   PHE B 135 " --> pdb=" O   PRO B 131 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN B 136 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 148
      removed outlier: 3.593A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 167
      removed outlier: 3.604A  pdb=" N   PHE B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 188
      removed outlier: 3.798A  pdb=" N   GLY B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B 185 " --> pdb=" O   MET B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 212
    Processing helix  chain 'B' and resid 216 through 227
      removed outlier: 3.730A  pdb=" N   HIS B 227 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 256
      removed outlier: 4.125A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   ALA B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 303
      removed outlier: 4.235A  pdb=" N   SER B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR B 292 " --> pdb=" O   MET B 288 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
      removed outlier: 3.882A  pdb=" N   GLU B 307 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 304 through 307'
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.910A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 341
    Processing helix  chain 'B' and resid 343 through 348
      removed outlier: 3.627A  pdb=" N   HIS B 347 " --> pdb=" O   VAL B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 370
      removed outlier: 4.041A  pdb=" N   ARG B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 386
      removed outlier: 4.162A  pdb=" N   VAL B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR B 379 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   MET B 380 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU B 384 " --> pdb=" O   MET B 380 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 410
      removed outlier: 3.508A  pdb=" N   ALA B 400 " --> pdb=" O   PHE B 396 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 405 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B 408 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 409 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
      removed outlier: 4.156A  pdb=" N   GLY B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 443 through 450
      removed outlier: 4.236A  pdb=" N   ALA B 447 " --> pdb=" O   ALA B 443 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B 450 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 479
      removed outlier: 3.859A  pdb=" N   MET B 461 " --> pdb=" O   PRO B 457 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   VAL B 475 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE B 476 " --> pdb=" O   THR B 472 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLY B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 487
      removed outlier: 4.410A  pdb=" N   LEU B 487 " --> pdb=" O   MET B 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.682A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU A  31 " --> pdb=" O   PHE A  27 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE A  32 " --> pdb=" O   ASN A  28 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE A  41 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 56
      No H-bonds generated for 'chain 'A' and resid 54 through 56'
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.616A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 129
      removed outlier: 3.664A  pdb=" N   MET A 127 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 129 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.805A  pdb=" N   ASN A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 158 through 165
    Processing helix  chain 'A' and resid 165 through 189
      removed outlier: 3.923A  pdb=" N   GLY A 169 " --> pdb=" O   TYR A 165 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   THR A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLY A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 3.713A  pdb=" N   CYS A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 229 through 254
      removed outlier: 3.618A  pdb=" N   LEU A 235 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLY A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 271 through 303
      removed outlier: 4.494A  pdb=" N   VAL A 275 " --> pdb=" O   PHE A 271 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   GLY A 276 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   THR A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 331
      removed outlier: 3.655A  pdb=" N   PHE A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 342 through 348
      removed outlier: 3.971A  pdb=" N   ALA A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 4.008A  pdb=" N   ARG A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 4.477A  pdb=" N   TYR A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   MET A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLY A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 382 " --> pdb=" O   CYS A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.532A  pdb=" N   ILE A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 3.893A  pdb=" N   PHE A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ASN A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 422
      removed outlier: 3.509A  pdb=" N   LEU A 415 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LEU A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.815A  pdb=" N   MET A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 3.854A  pdb=" N   ALA A 447 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.737A  pdb=" N   THR A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 468 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 475 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 488

    352 hydrogen bonds defined for protein.
    1050 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: 0.90

  Time building geometry restraints manager: 0.63 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: 1786
        1.34 -     1.46: 1696
        1.46 -     1.58: 2738
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 6300
  Sorted by residual:
  bond pdb=" N   ILE B 133 "
       pdb=" CA  ILE B 133 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.78e+00
  bond pdb=" N   VAL B 137 "
       pdb=" CA  VAL B 137 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.039 1.41e-02 5.03e+03 7.59e+00
  bond pdb=" N   ASN B 136 "
       pdb=" CA  ASN B 136 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.10e+00
  bond pdb=" N   GLU B 132 "
       pdb=" CA  GLU B 132 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.27e-02 6.20e+03 5.82e+00
  bond pdb=" N   PHE B 134 "
       pdb=" CA  PHE B 134 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.69e+00
  ... (remaining 6295 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 8285
        1.27 -     2.54: 182
        2.54 -     3.82: 50
        3.82 -     5.09: 13
        5.09 -     6.36: 6
  Bond angle restraints: 8536
  Sorted by residual:
  angle pdb=" CA  GLU A 239 "
        pdb=" C   GLU A 239 "
        pdb=" O   GLU A 239 "
      ideal   model   delta    sigma   weight residual
     120.55  117.31    3.24 1.06e+00 8.90e-01 9.33e+00
  angle pdb=" O   ILE B 133 "
        pdb=" C   ILE B 133 "
        pdb=" N   PHE B 134 "
      ideal   model   delta    sigma   weight residual
     121.87  124.67   -2.80 9.70e-01 1.06e+00 8.31e+00
  angle pdb=" CA  GLU B 239 "
        pdb=" C   GLU B 239 "
        pdb=" O   GLU B 239 "
      ideal   model   delta    sigma   weight residual
     120.42  117.44    2.98 1.06e+00 8.90e-01 7.92e+00
  angle pdb=" C   ARG A 451 "
        pdb=" N   ASP A 452 "
        pdb=" CA  ASP A 452 "
      ideal   model   delta    sigma   weight residual
     121.54  126.33   -4.79 1.91e+00 2.74e-01 6.28e+00
  angle pdb=" CA  ASN B 136 "
        pdb=" C   ASN B 136 "
        pdb=" O   ASN B 136 "
      ideal   model   delta    sigma   weight residual
     120.55  117.92    2.63 1.06e+00 8.90e-01 6.17e+00
  ... (remaining 8531 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 3335
       17.41 -    34.82: 179
       34.82 -    52.23: 37
       52.23 -    69.64: 3
       69.64 -    87.05: 6
  Dihedral angle restraints: 3560
    sinusoidal: 1337
      harmonic: 2223
  Sorted by residual:
  dihedral pdb=" CA  PHE B 129 "
           pdb=" C   PHE B 129 "
           pdb=" N   ASP B 130 "
           pdb=" CA  ASP B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  PHE A 129 "
           pdb=" C   PHE A 129 "
           pdb=" N   ASP A 130 "
           pdb=" CA  ASP A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ASP B 452 "
           pdb=" C   ASP B 452 "
           pdb=" N   THR B 453 "
           pdb=" CA  THR B 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.95   16.05     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 3557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 596
       0.031 -    0.062: 307
       0.062 -    0.093: 71
       0.093 -    0.124: 15
       0.124 -    0.155: 2
  Chirality restraints: 991
  Sorted by residual:
  chirality pdb=" CA  GLU A 239 "
            pdb=" N   GLU A 239 "
            pdb=" C   GLU A 239 "
            pdb=" CB  GLU A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE B 133 "
            pdb=" N   ILE B 133 "
            pdb=" C   ILE B 133 "
            pdb=" CB  ILE B 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  ASP A 229 "
            pdb=" N   ASP A 229 "
            pdb=" C   ASP A 229 "
            pdb=" CB  ASP A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.33e-01
  ... (remaining 988 not shown)

  Planarity restraints: 1030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 139 "    0.036 5.00e-02 4.00e+02   5.41e-02 4.69e+00
        pdb=" N   PRO B 140 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 140 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 139 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 140 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 140 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 140 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 131 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   PRO B 131 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PRO B 131 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU B 132 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1027 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1681
        2.80 -     3.32: 6544
        3.32 -     3.85: 9741
        3.85 -     4.37: 11818
        4.37 -     4.90: 18863
  Nonbonded interactions: 48647
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 382 "
            pdb=" OG1 THR B 386 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   GLY A 477 "
            pdb=" OG1 THR A 480 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER A 455 "
            pdb=" OE1 GLN A 459 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   TYR A 350 "
            pdb=" NZ  LYS A 358 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   TYR B 350 "
            pdb=" NZ  LYS B 358 "
     model   vdw
     2.293 3.120
  ... (remaining 48642 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 23 through 258 or resid 269 through 489))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.050
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6300  Z= 0.140
  Angle     :  0.523   6.361   8536  Z= 0.292
  Chirality :  0.037   0.155    991
  Planarity :  0.003   0.054   1030
  Dihedral  : 11.752  87.051   2122
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  9.65 %
    Favored  : 88.67 %
  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:  0.09 (0.32), residues: 747
  helix:  0.77 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.47 (0.45), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  45 
 TYR   0.009   0.001   TYR A 379 
 PHE   0.007   0.001   PHE B 184 
 TRP   0.003   0.001   TRP B  39 
 HIS   0.002   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6300)
  covalent geometry    : angle       0.52278 ( 8536)
  hydrogen bonds       : bond        0.28356 (  352)
  hydrogen bonds       : angle       7.63136 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 TYR cc_start: 0.8044 (t80) cc_final: 0.7758 (t80)
REVERT: B  458 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7474 (tttt)
REVERT: A   33 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8266 (pp)
REVERT: A   60 LEU cc_start: 0.8577 (mt) cc_final: 0.8360 (mp)
REVERT: A  206 PHE cc_start: 0.8670 (t80) cc_final: 0.8327 (t80)
  outliers start: 11
  outliers final: 1
  residues processed: 186
  average time/residue: 0.0740
  time to fit residues: 18.4533
Evaluate side-chains
  129 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   33 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  43 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.092470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.083736 restraints weight = 30613.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.085165 restraints weight = 19148.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.086335 restraints weight = 13970.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.086947 restraints weight = 10602.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.087678 restraints weight = 8721.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6300  Z= 0.192
  Angle     :  0.794  10.467   8536  Z= 0.395
  Chirality :  0.045   0.195    991
  Planarity :  0.005   0.054   1030
  Dihedral  :  4.943  36.831    804
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.47 %
    Favored  : 82.08 %
  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: -0.49 (0.31), residues: 747
  helix:  0.31 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -2.00 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 451 
 TYR   0.028   0.002   TYR A 165 
 PHE   0.025   0.002   PHE B 324 
 TRP   0.012   0.001   TRP A  39 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6300)
  covalent geometry    : angle       0.79376 ( 8536)
  hydrogen bonds       : bond        0.07284 (  352)
  hydrogen bonds       : angle       5.60286 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  211 MET cc_start: 0.8856 (tpp) cc_final: 0.8651 (tpp)
REVERT: B  368 MET cc_start: 0.8581 (mpp) cc_final: 0.7775 (mpp)
REVERT: B  458 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7341 (ttpt)
REVERT: A   33 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8474 (pp)
REVERT: A   60 LEU cc_start: 0.8494 (mt) cc_final: 0.8256 (mp)
REVERT: A  451 ARG cc_start: 0.7566 (mmm160) cc_final: 0.6907 (mmm160)
  outliers start: 16
  outliers final: 9
  residues processed: 146
  average time/residue: 0.0646
  time to fit residues: 13.0795
Evaluate side-chains
  131 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0870
   chunk 30 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    0.7162

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
B 390 HIS
A  43 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 432 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.094114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.085436 restraints weight = 30340.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.086847 restraints weight = 19415.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.088000 restraints weight = 14326.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.088570 restraints weight = 10856.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.089242 restraints weight = 9074.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6300  Z= 0.152
  Angle     :  0.711  10.318   8536  Z= 0.357
  Chirality :  0.042   0.170    991
  Planarity :  0.004   0.054   1030
  Dihedral  :  4.985  35.986    804
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.30 %
    Favored  : 77.79 %
  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: -0.61 (0.32), residues: 747
  helix:  0.16 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.76 (0.50), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 451 
 TYR   0.018   0.001   TYR A 379 
 PHE   0.033   0.001   PHE B 470 
 TRP   0.024   0.001   TRP A  39 
 HIS   0.004   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6300)
  covalent geometry    : angle       0.71142 ( 8536)
  hydrogen bonds       : bond        0.06072 (  352)
  hydrogen bonds       : angle       5.30046 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  220 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8538 (mm)
REVERT: B  310 MET cc_start: 0.8116 (tpp) cc_final: 0.7900 (tpp)
REVERT: B  368 MET cc_start: 0.8205 (mpp) cc_final: 0.7802 (mpp)
REVERT: B  458 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7283 (ttpt)
REVERT: A   33 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8395 (pp)
REVERT: A  369 ASN cc_start: 0.8414 (t160) cc_final: 0.8181 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 151
  average time/residue: 0.0671
  time to fit residues: 14.0214
Evaluate side-chains
  138 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 363 GLN
B 369 ASN
B 390 HIS
** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 389 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.091515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.082824 restraints weight = 30087.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.084226 restraints weight = 19003.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.085254 restraints weight = 13999.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.086211 restraints weight = 10655.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.086605 restraints weight = 8271.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6300  Z= 0.174
  Angle     :  0.717  10.507   8536  Z= 0.361
  Chirality :  0.043   0.152    991
  Planarity :  0.004   0.055   1030
  Dihedral  :  5.122  37.297    804
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.91 %
    Favored  : 76.11 %
  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 (0.32), residues: 747
  helix:  0.09 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -1.93 (0.52), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 451 
 TYR   0.024   0.002   TYR A 379 
 PHE   0.047   0.002   PHE B 470 
 TRP   0.027   0.002   TRP A  39 
 HIS   0.005   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6300)
  covalent geometry    : angle       0.71704 ( 8536)
  hydrogen bonds       : bond        0.05495 (  352)
  hydrogen bonds       : angle       5.26660 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 MET cc_start: 0.8318 (mpp) cc_final: 0.7574 (mpp)
REVERT: B  458 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7341 (ttpt)
REVERT: A   33 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8484 (pp)
REVERT: A   60 LEU cc_start: 0.8231 (mp) cc_final: 0.7915 (mt)
  outliers start: 26
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0677
  time to fit residues: 13.6714
Evaluate side-chains
  137 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  390 HIS
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 70 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
B 390 HIS
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.092697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.084031 restraints weight = 30889.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.085408 restraints weight = 19740.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.086419 restraints weight = 14657.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.087366 restraints weight = 11289.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.087712 restraints weight = 9034.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6300  Z= 0.149
  Angle     :  0.718  11.475   8536  Z= 0.358
  Chirality :  0.044   0.302    991
  Planarity :  0.004   0.055   1030
  Dihedral  :  5.116  36.164    804
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.44 %
    Favored  : 75.04 %
  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: -0.77 (0.32), residues: 747
  helix:  0.09 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -2.07 (0.52), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 451 
 TYR   0.023   0.001   TYR A 379 
 PHE   0.050   0.001   PHE B 470 
 TRP   0.026   0.001   TRP A  39 
 HIS   0.008   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6300)
  covalent geometry    : angle       0.71767 ( 8536)
  hydrogen bonds       : bond        0.05231 (  352)
  hydrogen bonds       : angle       5.21600 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 MET cc_start: 0.8253 (mpp) cc_final: 0.7642 (mpp)
REVERT: B  458 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7241 (ttpt)
REVERT: A   33 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8475 (pp)
REVERT: A   60 LEU cc_start: 0.8076 (mp) cc_final: 0.7773 (mt)
REVERT: A  229 ASP cc_start: 0.6820 (p0) cc_final: 0.6608 (p0)
REVERT: A  369 ASN cc_start: 0.8423 (t0) cc_final: 0.8218 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 148
  average time/residue: 0.0637
  time to fit residues: 13.0915
Evaluate side-chains
  136 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.0070
   chunk 16 optimal weight:    0.0470
   chunk 40 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.6100

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.092528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.084203 restraints weight = 30318.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.085434 restraints weight = 19183.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.086755 restraints weight = 14090.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.087405 restraints weight = 10490.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.087795 restraints weight = 8522.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6300  Z= 0.153
  Angle     :  0.736  13.044   8536  Z= 0.364
  Chirality :  0.044   0.309    991
  Planarity :  0.004   0.053   1030
  Dihedral  :  5.083  35.371    804
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.90 %
    Favored  : 74.27 %
  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: -0.82 (0.32), residues: 747
  helix:  0.07 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.16 (0.52), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 451 
 TYR   0.022   0.001   TYR A 379 
 PHE   0.044   0.001   PHE B 470 
 TRP   0.023   0.001   TRP A  39 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6300)
  covalent geometry    : angle       0.73599 ( 8536)
  hydrogen bonds       : bond        0.05017 (  352)
  hydrogen bonds       : angle       5.20588 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  368 MET cc_start: 0.8261 (mpp) cc_final: 0.7627 (mpp)
REVERT: B  458 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7208 (ttpt)
REVERT: A   33 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8488 (pp)
REVERT: A   60 LEU cc_start: 0.8055 (mp) cc_final: 0.7659 (mt)
REVERT: A  363 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7562 (mm-40)
  outliers start: 25
  outliers final: 17
  residues processed: 141
  average time/residue: 0.0633
  time to fit residues: 12.5013
Evaluate side-chains
  135 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.093346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.085084 restraints weight = 30167.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.086469 restraints weight = 19157.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.087539 restraints weight = 13943.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.088253 restraints weight = 10538.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.088632 restraints weight = 8361.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6300  Z= 0.145
  Angle     :  0.742  12.873   8536  Z= 0.366
  Chirality :  0.044   0.323    991
  Planarity :  0.004   0.056   1030
  Dihedral  :  5.098  35.074    804
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.90 %
    Favored  : 74.12 %
  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: -0.73 (0.32), residues: 747
  helix:  0.07 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.85 (0.53), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 451 
 TYR   0.023   0.001   TYR A 379 
 PHE   0.040   0.001   PHE B 470 
 TRP   0.027   0.002   TRP A 429 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6300)
  covalent geometry    : angle       0.74178 ( 8536)
  hydrogen bonds       : bond        0.04889 (  352)
  hydrogen bonds       : angle       5.14713 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  458 LYS cc_start: 0.7693 (mtmt) cc_final: 0.7142 (ttpt)
REVERT: A   33 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8465 (pp)
REVERT: A   60 LEU cc_start: 0.8060 (mp) cc_final: 0.7674 (mt)
  outliers start: 26
  outliers final: 18
  residues processed: 141
  average time/residue: 0.0632
  time to fit residues: 12.4452
Evaluate side-chains
  133 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.092921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.084665 restraints weight = 30252.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.085867 restraints weight = 19064.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.086990 restraints weight = 14161.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.087785 restraints weight = 10756.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.088419 restraints weight = 8568.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6300  Z= 0.149
  Angle     :  0.769  11.364   8536  Z= 0.374
  Chirality :  0.047   0.360    991
  Planarity :  0.004   0.052   1030
  Dihedral  :  5.087  35.276    804
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.82 %
    Favored  : 73.51 %
  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 (0.32), residues: 747
  helix:  0.06 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.86 (0.53), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 451 
 TYR   0.023   0.001   TYR A 379 
 PHE   0.037   0.002   PHE B 470 
 TRP   0.026   0.002   TRP A 429 
 HIS   0.007   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6300)
  covalent geometry    : angle       0.76913 ( 8536)
  hydrogen bonds       : bond        0.04779 (  352)
  hydrogen bonds       : angle       5.17883 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LEU cc_start: 0.8323 (mp) cc_final: 0.8111 (mp)
REVERT: B  458 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7192 (ttpp)
REVERT: A   33 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8413 (pp)
REVERT: A   60 LEU cc_start: 0.8070 (mp) cc_final: 0.7690 (mt)
REVERT: A  363 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7302 (mm-40)
REVERT: A  402 LEU cc_start: 0.9095 (pp) cc_final: 0.8760 (mm)
  outliers start: 24
  outliers final: 20
  residues processed: 133
  average time/residue: 0.0660
  time to fit residues: 12.0807
Evaluate side-chains
  133 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  359 MET
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0370
   chunk 73 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
B 369 ASN
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.093451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.085238 restraints weight = 30147.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.086602 restraints weight = 19055.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.087654 restraints weight = 13931.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.088484 restraints weight = 10538.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.089097 restraints weight = 8315.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6300  Z= 0.143
  Angle     :  0.780  11.863   8536  Z= 0.377
  Chirality :  0.047   0.388    991
  Planarity :  0.004   0.055   1030
  Dihedral  :  5.119  34.773    804
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.28 %
    Favored  : 73.51 %
  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: -0.74 (0.32), residues: 747
  helix:  0.08 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.94 (0.53), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 451 
 TYR   0.022   0.001   TYR A 379 
 PHE   0.037   0.001   PHE B 470 
 TRP   0.022   0.001   TRP A 429 
 HIS   0.007   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6300)
  covalent geometry    : angle       0.77963 ( 8536)
  hydrogen bonds       : bond        0.04711 (  352)
  hydrogen bonds       : angle       5.15461 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   31 LEU cc_start: 0.8306 (mp) cc_final: 0.8105 (mp)
REVERT: B  458 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7188 (ttpt)
REVERT: A   33 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8392 (pp)
REVERT: A   60 LEU cc_start: 0.8080 (mp) cc_final: 0.7807 (mt)
REVERT: A  402 LEU cc_start: 0.9061 (pp) cc_final: 0.8711 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 133
  average time/residue: 0.0637
  time to fit residues: 11.8810
Evaluate side-chains
  130 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 145 HIS
** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.090771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.082356 restraints weight = 30938.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.083584 restraints weight = 19298.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.084799 restraints weight = 14281.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.085641 restraints weight = 10516.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.085946 restraints weight = 8256.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6300  Z= 0.200
  Angle     :  0.814  11.564   8536  Z= 0.401
  Chirality :  0.048   0.361    991
  Planarity :  0.004   0.052   1030
  Dihedral  :  5.333  35.706    804
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.58 %
    Favored  : 73.20 %
  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: -0.82 (0.32), residues: 747
  helix:  0.08 (0.22), residues: 557
  sheet:  None (None), residues: 0
  loop : -2.21 (0.51), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 451 
 TYR   0.026   0.002   TYR A 379 
 PHE   0.035   0.002   PHE B 470 
 TRP   0.027   0.002   TRP A 429 
 HIS   0.006   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6300)
  covalent geometry    : angle       0.81440 ( 8536)
  hydrogen bonds       : bond        0.04839 (  352)
  hydrogen bonds       : angle       5.31041 ( 1050)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.6290 (ptt) cc_final: 0.5918 (ptt)
REVERT: B  368 MET cc_start: 0.8278 (mpp) cc_final: 0.7569 (mpp)
REVERT: B  458 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7240 (ttpp)
REVERT: A   33 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8441 (pp)
REVERT: A   60 LEU cc_start: 0.8144 (mp) cc_final: 0.7778 (mt)
REVERT: A  402 LEU cc_start: 0.9125 (pp) cc_final: 0.8802 (mm)
  outliers start: 21
  outliers final: 19
  residues processed: 130
  average time/residue: 0.0691
  time to fit residues: 12.2887
Evaluate side-chains
  129 residues out of total 653 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  170 THR
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  228 VAL
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  369 ASN
Chi-restraints excluded: chain B residue  379 TYR
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  481 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  453 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 73 optimal weight:    0.3980
   chunk 55 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6100

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 GLN
A 369 ASN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.093180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.084873 restraints weight = 30016.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.086261 restraints weight = 18960.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.087247 restraints weight = 13887.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.088115 restraints weight = 10644.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.088441 restraints weight = 8290.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6300  Z= 0.144
  Angle     :  0.816  13.568   8536  Z= 0.390
  Chirality :  0.047   0.377    991
  Planarity :  0.004   0.056   1030
  Dihedral  :  5.206  35.691    804
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 23.43 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.32), residues: 747
  helix:  0.08 (0.22), residues: 562
  sheet:  None (None), residues: 0
  loop : -2.24 (0.53), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 451 
 TYR   0.025   0.002   TYR B 252 
 PHE   0.034   0.001   PHE B 470 
 TRP   0.018   0.001   TRP A  39 
 HIS   0.005   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6300)
  covalent geometry    : angle       0.81565 ( 8536)
  hydrogen bonds       : bond        0.04635 (  352)
  hydrogen bonds       : angle       5.12563 ( 1050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1034.62 seconds
wall clock time: 18 minutes 34.66 seconds (1114.66 seconds total)