Starting phenix.real_space_refine
on Sat Aug 23 01:00:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsp_41597/08_2025/8tsp_41597.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.043
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      54      5.16       5
     C    5630      2.51       5
     N    1548      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8888
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4444
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 13, 'TRANS': 559}
    Chain: "B"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4444
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 13, 'TRANS': 559}
  Time building chain proxies: 2.40, per 1000 atoms: 0.27
  Number of scatterers: 8888
  At special positions: 0
  Unit cell: (67.095, 122.475, 136.32, 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      54     16.00
     O    1656      8.00
     N    1548      7.00
     C    5630      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: 0.66
  Conformation dependent library (CDL) restraints added in 344.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      69.5% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 9
      No H-bonds generated for 'chain 'A' and resid 7 through 9'
    Processing helix  chain 'A' and resid 10 through 21
      removed outlier: 4.044A  pdb=" N   ARG A  14 " --> pdb=" O   TRP A  10 " (cutoff:3.500A)
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.678A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ALA A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.685A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 109
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 4.286A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN A 119 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 163
      removed outlier: 3.899A  pdb=" N   LEU A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   SER A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU A 133 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 3.774A  pdb=" N   SER A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 224 through 272
      Proline residue:  A 253  - end of helix
      removed outlier: 3.681A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 294
      removed outlier: 3.594A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   THR A 285 " --> pdb=" O   ALA A 281 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER A 289 " --> pdb=" O   THR A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 323
      removed outlier: 3.526A  pdb=" N   LEU A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
    Processing helix  chain 'A' and resid 408 through 410
      No H-bonds generated for 'chain 'A' and resid 408 through 410'
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 433 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 460 through 465
      removed outlier: 3.634A  pdb=" N   LYS A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 471
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 512 through 526
    Processing helix  chain 'A' and resid 538 through 544
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'B' and resid 7 through 9
      No H-bonds generated for 'chain 'B' and resid 7 through 9'
    Processing helix  chain 'B' and resid 10 through 21
      removed outlier: 4.048A  pdb=" N   ARG B  14 " --> pdb=" O   TRP B  10 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 3.674A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA B  30 " --> pdb=" O   GLY B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 53
      removed outlier: 3.702A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 4.153A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 163
      removed outlier: 3.587A  pdb=" N   LEU B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU B 133 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      removed outlier: 3.632A  pdb=" N   SER B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 170 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 213 through 218
    Processing helix  chain 'B' and resid 224 through 272
      Proline residue:  B 253  - end of helix
      removed outlier: 3.661A  pdb=" N   PHE B 272 " --> pdb=" O   TYR B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 294
      removed outlier: 4.012A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 282 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL B 287 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 323
      removed outlier: 3.538A  pdb=" N   LEU B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 391
    Processing helix  chain 'B' and resid 408 through 410
      No H-bonds generated for 'chain 'B' and resid 408 through 410'
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 468 through 471
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 512 through 526
    Processing helix  chain 'B' and resid 538 through 544
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 6.390A  pdb=" N   ARG A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 346 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 342 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 3.788A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 422 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLU A 558 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   GLU A 552 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   ILE A 556 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 432
    Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 366
      removed outlier: 5.082A  pdb=" N   ARG B 360 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   PHE B 349 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   LEU B 364 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   ARG B 345 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ILE B 366 " --> pdb=" O   GLU B 343 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   GLU B 343 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   VAL B 347 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   GLU B 397 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET B 402 " --> pdb=" O   HIS B 405 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   HIS B 405 " --> pdb=" O   MET B 402 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.726A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   ASP B 505 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 505 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU B 547 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   GLU B 558 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   GLU B 552 " --> pdb=" O   ILE B 556 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ILE B 556 " --> pdb=" O   GLU B 552 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 431 through 432

    581 hydrogen bonds defined for protein.
    1722 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2781
        1.34 -     1.46: 1587
        1.46 -     1.58: 4546
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 9018
  Sorted by residual:
  bond pdb=" N   VAL B 555 "
       pdb=" CA  VAL B 555 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.15e+01
  bond pdb=" N   ILE B 250 "
       pdb=" CA  ILE B 250 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.09e-02 8.42e+03 9.88e+00
  bond pdb=" N   ASP B 252 "
       pdb=" CA  ASP B 252 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.20e-03 1.18e+04 9.67e+00
  bond pdb=" N   VAL A 551 "
       pdb=" CA  VAL A 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.67e+00
  bond pdb=" N   ILE B 177 "
       pdb=" CA  ILE B 177 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.19e-02 7.06e+03 8.42e+00
  ... (remaining 9013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 12027
        2.59 -     5.19: 142
        5.19 -     7.78: 15
        7.78 -    10.38: 2
       10.38 -    12.97: 2
  Bond angle restraints: 12188
  Sorted by residual:
  angle pdb=" N   ILE B 250 "
        pdb=" CA  ILE B 250 "
        pdb=" C   ILE B 250 "
      ideal   model   delta    sigma   weight residual
     113.43  108.13    5.30 1.09e+00 8.42e-01 2.37e+01
  angle pdb=" CB  MET A 295 "
        pdb=" CG  MET A 295 "
        pdb=" SD  MET A 295 "
      ideal   model   delta    sigma   weight residual
     112.70  125.67  -12.97 3.00e+00 1.11e-01 1.87e+01
  angle pdb=" N   ASN A 477 "
        pdb=" CA  ASN A 477 "
        pdb=" C   ASN A 477 "
      ideal   model   delta    sigma   weight residual
     111.81  106.25    5.56 1.54e+00 4.22e-01 1.30e+01
  angle pdb=" CA  ASP A 553 "
        pdb=" C   ASP A 553 "
        pdb=" O   ASP A 553 "
      ideal   model   delta    sigma   weight residual
     121.84  117.67    4.17 1.16e+00 7.43e-01 1.29e+01
  angle pdb=" N   ASN B 477 "
        pdb=" CA  ASN B 477 "
        pdb=" C   ASN B 477 "
      ideal   model   delta    sigma   weight residual
     111.81  106.32    5.49 1.54e+00 4.22e-01 1.27e+01
  ... (remaining 12183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4718
       17.83 -    35.65: 594
       35.65 -    53.48: 143
       53.48 -    71.31: 29
       71.31 -    89.14: 8
  Dihedral angle restraints: 5492
    sinusoidal: 2178
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  ARG B 391 "
           pdb=" C   ARG B 391 "
           pdb=" N   PHE B 392 "
           pdb=" CA  PHE B 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  SER A 249 "
           pdb=" C   SER A 249 "
           pdb=" N   ILE A 250 "
           pdb=" CA  ILE A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  ASP A 471 "
           pdb=" CB  ASP A 471 "
           pdb=" CG  ASP A 471 "
           pdb=" OD1 ASP A 471 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.41   57.41     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 5489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1016
       0.042 -    0.085: 313
       0.085 -    0.127: 86
       0.127 -    0.170: 27
       0.170 -    0.212: 10
  Chirality restraints: 1452
  Sorted by residual:
  chirality pdb=" CA  ILE A 556 "
            pdb=" N   ILE A 556 "
            pdb=" C   ILE A 556 "
            pdb=" CB  ILE A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE B 255 "
            pdb=" N   ILE B 255 "
            pdb=" C   ILE B 255 "
            pdb=" CB  ILE B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  ILE B 180 "
            pdb=" N   ILE B 180 "
            pdb=" C   ILE B 180 "
            pdb=" CB  ILE B 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.43e-01
  ... (remaining 1449 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 186 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.23e+00
        pdb=" C   SER A 186 "    0.036 2.00e-02 2.50e+03
        pdb=" O   SER A 186 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 187 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 184 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" C   VAL A 184 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A 184 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 185 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 184 "   -0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   VAL B 184 "    0.035 2.00e-02 2.50e+03
        pdb=" O   VAL B 184 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL B 185 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 788
        2.74 -     3.28: 9452
        3.28 -     3.82: 14911
        3.82 -     4.36: 16760
        4.36 -     4.90: 28594
  Nonbonded interactions: 70505
  Sorted by model distance:
  nonbonded pdb=" O   THR B   9 "
            pdb=" OG1 THR B  12 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   THR A   9 "
            pdb=" OG1 THR A  12 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" ND2 ASN A 430 "
            pdb=" OE1 GLN B 209 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NH1 ARG A 102 "
            pdb=" OD1 ASP B 231 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   GLU A 224 "
            pdb=" OG1 THR A 227 "
     model   vdw
     2.299 3.040
  ... (remaining 70500 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.080
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.970
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9018  Z= 0.297
  Angle     :  0.752  12.969  12188  Z= 0.470
  Chirality :  0.048   0.212   1452
  Planarity :  0.005   0.066   1542
  Dihedral  : 16.525  89.137   3348
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 23.26 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1142
  helix:  1.08 (0.20), residues: 714
  sheet:  0.37 (0.61), residues: 78
  loop : -1.15 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 559 
 TYR   0.015   0.001   TYR A 445 
 PHE   0.019   0.002   PHE A 115 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9018)
  covalent geometry    : angle       0.75211 (12188)
  hydrogen bonds       : bond        0.17929 (  581)
  hydrogen bonds       : angle       6.94766 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  295 MET cc_start: 0.5770 (mmm) cc_final: 0.5148 (mtt)
REVERT: B  111 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.5796 (mpp)
REVERT: B  117 ASP cc_start: 0.5455 (m-30) cc_final: 0.5115 (m-30)
REVERT: B  283 THR cc_start: 0.8056 (p) cc_final: 0.7597 (t)
REVERT: B  312 MET cc_start: 0.8902 (mmt) cc_final: 0.8416 (mmt)
REVERT: B  363 ASN cc_start: 0.5549 (m-40) cc_final: 0.5337 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 155
  average time/residue: 0.0879
  time to fit residues: 18.1816
Evaluate side-chains
  136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ASP
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  356 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0170
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0070
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
B 107 HIS
B 316 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.192080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.174489 restraints weight = 10017.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.169764 restraints weight = 13989.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 76)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.167250 restraints weight = 16249.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.166885 restraints weight = 15347.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.166196 restraints weight = 14384.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9018  Z= 0.141
  Angle     :  0.546   7.375  12188  Z= 0.292
  Chirality :  0.041   0.166   1452
  Planarity :  0.004   0.035   1542
  Dihedral  :  4.327  45.637   1253
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 22.03 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.25), residues: 1142
  helix:  1.87 (0.20), residues: 720
  sheet:  0.40 (0.59), residues: 66
  loop : -0.82 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 559 
 TYR   0.011   0.001   TYR A 162 
 PHE   0.020   0.002   PHE B  56 
 TRP   0.017   0.001   TRP A  66 
 HIS   0.004   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9018)
  covalent geometry    : angle       0.54560 (12188)
  hydrogen bonds       : bond        0.06219 (  581)
  hydrogen bonds       : angle       4.51086 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 160
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7644 (tpp) cc_final: 0.7175 (ttm)
REVERT: A  127 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7393 (tpp-160)
REVERT: B  260 SER cc_start: 0.8788 (m) cc_final: 0.8339 (m)
REVERT: B  283 THR cc_start: 0.8292 (p) cc_final: 0.7888 (t)
  outliers start: 33
  outliers final: 16
  residues processed: 186
  average time/residue: 0.0813
  time to fit residues: 20.7145
Evaluate side-chains
  161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  119 GLN
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 80 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
** B 107 HIS ** 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 = 0.4063 r_free = 0.4063 target = 0.186586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.169112 restraints weight = 10048.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.165649 restraints weight = 15468.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.164272 restraints weight = 16047.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.162354 restraints weight = 16142.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.162129 restraints weight = 16700.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9018  Z= 0.148
  Angle     :  0.550   6.333  12188  Z= 0.291
  Chirality :  0.041   0.150   1452
  Planarity :  0.004   0.034   1542
  Dihedral  :  4.021  20.505   1248
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.41 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1142
  helix:  2.14 (0.20), residues: 716
  sheet:  0.63 (0.56), residues: 78
  loop : -0.69 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 559 
 TYR   0.015   0.001   TYR B 130 
 PHE   0.015   0.002   PHE B 230 
 TRP   0.026   0.002   TRP A  66 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9018)
  covalent geometry    : angle       0.55027 (12188)
  hydrogen bonds       : bond        0.06017 (  581)
  hydrogen bonds       : angle       4.39040 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7936 (tpp) cc_final: 0.7355 (ttm)
REVERT: A  127 ARG cc_start: 0.7600 (tpp-160) cc_final: 0.7393 (tpp-160)
REVERT: B  283 THR cc_start: 0.8321 (p) cc_final: 0.8033 (t)
REVERT: B  301 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7270 (mp)
  outliers start: 50
  outliers final: 31
  residues processed: 179
  average time/residue: 0.0801
  time to fit residues: 19.9741
Evaluate side-chains
  161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 PHE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  363 ASN
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0770
   chunk 87 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
B 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.186997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 128)---------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.165277 restraints weight = 10125.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 93)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.150392 restraints weight = 16481.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.149540 restraints weight = 17942.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.149815 restraints weight = 17899.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150074 restraints weight = 16075.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9018  Z= 0.134
  Angle     :  0.517   5.169  12188  Z= 0.277
  Chirality :  0.040   0.148   1452
  Planarity :  0.003   0.033   1542
  Dihedral  :  3.958  20.674   1248
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.62 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.26), residues: 1142
  helix:  2.26 (0.20), residues: 718
  sheet:  0.65 (0.55), residues: 78
  loop : -0.50 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 559 
 TYR   0.012   0.001   TYR B 130 
 PHE   0.016   0.001   PHE B 189 
 TRP   0.021   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9018)
  covalent geometry    : angle       0.51663 (12188)
  hydrogen bonds       : bond        0.05679 (  581)
  hydrogen bonds       : angle       4.21267 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8051 (tpp) cc_final: 0.7481 (ttm)
REVERT: B  200 MET cc_start: 0.5511 (tpt) cc_final: 0.5020 (tpt)
REVERT: B  301 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7033 (mp)
  outliers start: 45
  outliers final: 29
  residues processed: 167
  average time/residue: 0.1035
  time to fit residues: 23.6234
Evaluate side-chains
  153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 PHE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  157 PHE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 85 optimal weight:    0.5980
   chunk 103 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0050
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.0398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.184460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165307 restraints weight = 10150.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.159384 restraints weight = 14229.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158076 restraints weight = 16547.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157647 restraints weight = 16198.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.157324 restraints weight = 15181.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9018  Z= 0.161
  Angle     :  0.572  10.317  12188  Z= 0.297
  Chirality :  0.041   0.143   1452
  Planarity :  0.003   0.033   1542
  Dihedral  :  4.042  21.196   1248
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 22.85 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1142
  helix:  2.06 (0.20), residues: 730
  sheet:  0.67 (0.55), residues: 78
  loop : -0.48 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 517 
 TYR   0.010   0.001   TYR B 130 
 PHE   0.016   0.002   PHE B 189 
 TRP   0.023   0.002   TRP B  66 
 HIS   0.004   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9018)
  covalent geometry    : angle       0.57237 (12188)
  hydrogen bonds       : bond        0.05927 (  581)
  hydrogen bonds       : angle       4.27462 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 130
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8052 (tpp) cc_final: 0.7548 (ttm)
REVERT: B  200 MET cc_start: 0.5573 (tpt) cc_final: 0.5062 (tpt)
REVERT: B  301 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7229 (mp)
REVERT: B  451 GLU cc_start: 0.6617 (tp30) cc_final: 0.5824 (tp30)
REVERT: B  474 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6630 (mt)
  outliers start: 42
  outliers final: 34
  residues processed: 157
  average time/residue: 0.1089
  time to fit residues: 23.1465
Evaluate side-chains
  160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  363 ASN
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  491 ILE
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 113 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
B 107 HIS
B 326 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.178769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.154639 restraints weight = 10518.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.151106 restraints weight = 15062.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.147677 restraints weight = 14675.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.147007 restraints weight = 14850.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145887 restraints weight = 14107.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9018  Z= 0.224
  Angle     :  0.659   8.124  12188  Z= 0.342
  Chirality :  0.044   0.142   1452
  Planarity :  0.004   0.033   1542
  Dihedral  :  4.327  22.425   1248
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 23.98 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1142
  helix:  1.74 (0.20), residues: 728
  sheet:  0.21 (0.60), residues: 70
  loop : -0.50 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.013   0.002   TYR B  83 
 PHE   0.018   0.002   PHE B 189 
 TRP   0.029   0.002   TRP A  66 
 HIS   0.006   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 9018)
  covalent geometry    : angle       0.65897 (12188)
  hydrogen bonds       : bond        0.06660 (  581)
  hydrogen bonds       : angle       4.55545 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 129
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8276 (tpp) cc_final: 0.7523 (tmm)
REVERT: B  301 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7798 (mp)
  outliers start: 54
  outliers final: 39
  residues processed: 174
  average time/residue: 0.1058
  time to fit residues: 24.9050
Evaluate side-chains
  158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 118
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   54 ASP
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  307 GLN
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  363 ASN
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  491 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0060
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
B 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.193000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.178343 restraints weight = 10277.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.174432 restraints weight = 14368.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 105)---------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.173072 restraints weight = 14652.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.172247 restraints weight = 14012.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.171653 restraints weight = 14074.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9018  Z= 0.138
  Angle     :  0.559  10.479  12188  Z= 0.289
  Chirality :  0.041   0.154   1452
  Planarity :  0.004   0.032   1542
  Dihedral  :  4.079  21.532   1248
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 25.92 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.26), residues: 1142
  helix:  1.98 (0.20), residues: 730
  sheet:  0.24 (0.56), residues: 80
  loop : -0.46 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 455 
 TYR   0.016   0.001   TYR B 445 
 PHE   0.020   0.001   PHE B 189 
 TRP   0.027   0.002   TRP B  66 
 HIS   0.004   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9018)
  covalent geometry    : angle       0.55948 (12188)
  hydrogen bonds       : bond        0.05788 (  581)
  hydrogen bonds       : angle       4.24425 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8094 (tpp) cc_final: 0.7586 (tmm)
REVERT: B  200 MET cc_start: 0.5894 (tpt) cc_final: 0.5455 (tpt)
REVERT: B  301 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7304 (mp)
REVERT: B  456 MET cc_start: 0.7963 (tpp) cc_final: 0.7544 (tpp)
  outliers start: 37
  outliers final: 26
  residues processed: 156
  average time/residue: 0.0940
  time to fit residues: 20.3244
Evaluate side-chains
  147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.183484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.160872 restraints weight = 10339.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 83)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.155666 restraints weight = 13380.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 93)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.151843 restraints weight = 15256.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.151610 restraints weight = 14259.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.150599 restraints weight = 13029.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9018  Z= 0.151
  Angle     :  0.593  10.915  12188  Z= 0.301
  Chirality :  0.042   0.178   1452
  Planarity :  0.004   0.034   1542
  Dihedral  :  4.127  21.245   1248
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 25.51 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.26), residues: 1142
  helix:  1.95 (0.20), residues: 730
  sheet:  0.28 (0.56), residues: 80
  loop : -0.40 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 559 
 TYR   0.012   0.001   TYR B 445 
 PHE   0.019   0.002   PHE B 189 
 TRP   0.028   0.002   TRP B  66 
 HIS   0.005   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9018)
  covalent geometry    : angle       0.59285 (12188)
  hydrogen bonds       : bond        0.05737 (  581)
  hydrogen bonds       : angle       4.22207 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 117
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8196 (tpp) cc_final: 0.7640 (tmm)
REVERT: B  200 MET cc_start: 0.5783 (tpt) cc_final: 0.5322 (tpt)
REVERT: B  301 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7268 (mp)
  outliers start: 38
  outliers final: 34
  residues processed: 146
  average time/residue: 0.0957
  time to fit residues: 19.4935
Evaluate side-chains
  149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue   66 TRP
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  544 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0050
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 537 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.191140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.172437 restraints weight = 10116.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.168212 restraints weight = 12724.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.165430 restraints weight = 14407.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.164593 restraints weight = 14794.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 79)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.163632 restraints weight = 13305.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9018  Z= 0.136
  Angle     :  0.587  11.131  12188  Z= 0.296
  Chirality :  0.041   0.174   1452
  Planarity :  0.004   0.037   1542
  Dihedral  :  4.085  21.924   1248
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 25.61 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.26), residues: 1142
  helix:  2.00 (0.20), residues: 734
  sheet:  0.30 (0.61), residues: 70
  loop : -0.31 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 559 
 TYR   0.012   0.001   TYR B 445 
 PHE   0.020   0.001   PHE B 189 
 TRP   0.035   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9018)
  covalent geometry    : angle       0.58704 (12188)
  hydrogen bonds       : bond        0.05437 (  581)
  hydrogen bonds       : angle       4.13547 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.8616 (mm) cc_final: 0.8196 (mm)
REVERT: A   44 MET cc_start: 0.8093 (tpp) cc_final: 0.7606 (tmm)
REVERT: A  301 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7664 (mp)
REVERT: B  200 MET cc_start: 0.5834 (tpt) cc_final: 0.5475 (tpt)
REVERT: B  301 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7132 (mp)
REVERT: B  451 GLU cc_start: 0.7019 (tp30) cc_final: 0.6778 (tp30)
  outliers start: 39
  outliers final: 33
  residues processed: 152
  average time/residue: 0.0876
  time to fit residues: 19.0100
Evaluate side-chains
  152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 117
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  544 LYS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 61 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.193585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.174736 restraints weight = 10112.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.171184 restraints weight = 13911.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 78)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.169266 restraints weight = 14850.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.168734 restraints weight = 14270.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.167687 restraints weight = 14504.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9018  Z= 0.143
  Angle     :  0.601  10.630  12188  Z= 0.300
  Chirality :  0.041   0.142   1452
  Planarity :  0.004   0.049   1542
  Dihedral  :  4.104  22.562   1248
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.23 %
    Favored  : 70.08 %
  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 aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1142
  helix:  1.95 (0.20), residues: 734
  sheet:  0.23 (0.61), residues: 70
  loop : -0.27 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 559 
 TYR   0.011   0.001   TYR B 445 
 PHE   0.020   0.002   PHE B 189 
 TRP   0.030   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9018)
  covalent geometry    : angle       0.60141 (12188)
  hydrogen bonds       : bond        0.05462 (  581)
  hydrogen bonds       : angle       4.15429 ( 1722)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.8569 (mm) cc_final: 0.8138 (mm)
REVERT: A   44 MET cc_start: 0.8141 (tpp) cc_final: 0.7587 (tmm)
REVERT: A  301 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7646 (mp)
REVERT: B  200 MET cc_start: 0.5853 (tpt) cc_final: 0.5515 (tpt)
REVERT: B  301 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7231 (mp)
  outliers start: 36
  outliers final: 34
  residues processed: 148
  average time/residue: 0.0921
  time to fit residues: 19.4575
Evaluate side-chains
  151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASP
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  286 VAL
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  544 LYS
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
A 537 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.185530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.167048 restraints weight = 10098.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 82)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.162624 restraints weight = 13831.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 79)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.161009 restraints weight = 15145.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.160111 restraints weight = 14329.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 79)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.158719 restraints weight = 15273.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
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Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9018  Z= 0.155
  Angle     :  0.617  10.503  12188  Z= 0.310
  Chirality :  0.041   0.159   1452
  Planarity :  0.004   0.045   1542
  Dihedral  :  4.146  22.501   1248
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.51 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.26), residues: 1142
  helix:  1.96 (0.19), residues: 730
  sheet:  0.23 (0.57), residues: 80
  loop : -0.30 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 559 
 TYR   0.011   0.001   TYR B 445 
 PHE   0.020   0.002   PHE B 189 
 TRP   0.030   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 9018)
  covalent geometry    : angle       0.61715 (12188)
  hydrogen bonds       : bond        0.05607 (  581)
  hydrogen bonds       : angle       4.20749 ( 1722)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1532.81 seconds
wall clock time: 27 minutes 7.49 seconds (1627.49 seconds total)