Starting phenix.real_space_refine
on Mon May 12 09:00:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsp_41597/05_2025/8tsp_41597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsp_41597/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tsp_41597/05_2025/8tsp_41597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsp_41597/05_2025/8tsp_41597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsp_41597/05_2025/8tsp_41597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsp_41597/05_2025/8tsp_41597.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.32, per 1000 atoms: 0.60
  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: 2.22
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.86
  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: 2.52

  Time building geometry restraints manager: 2.58 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: 0.04
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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.940
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (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
 TRP   0.010   0.001   TRP A  66 
 HIS   0.008   0.001   HIS A 214 
 PHE   0.019   0.002   PHE A 115 
 TYR   0.015   0.001   TYR A 445 
 ARG   0.011   0.001   ARG B 559 

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

*********************** 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  : 0.962 
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: 0.2367
  time to fit residues: 49.2150
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  : 1.004 
-------------------------------------------------------------------------------
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 96 optimal weight:   20.0000
   chunk 86 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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
B 316 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.183183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165476 restraints weight = 10050.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.161756 restraints weight = 14978.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.159864 restraints weight = 16448.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9018  Z= 0.193
  Angle     :  0.627   7.546  12188  Z= 0.331
  Chirality :  0.043   0.158   1452
  Planarity :  0.004   0.037   1542
  Dihedral  :  4.515  44.255   1253
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 22.44 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1142
  helix:  1.54 (0.19), residues: 728
  sheet:  0.41 (0.57), residues: 78
  loop : -0.96 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.005   0.001   HIS B 107 
 PHE   0.025   0.002   PHE B  56 
 TYR   0.010   0.002   TYR A  87 
 ARG   0.005   0.001   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06977 (  581)
  hydrogen bonds       : angle       4.75390 ( 1722)
  covalent geometry    : bond        0.00427 ( 9018)
  covalent geometry    : angle       0.62675 (12188)

*********************** 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
  184 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 141
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7710 (tpp) cc_final: 0.7438 (ttm)
REVERT: A  291 MET cc_start: 0.7916 (mmm) cc_final: 0.7574 (tmm)
REVERT: B  301 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7466 (mp)
  outliers start: 43
  outliers final: 22
  residues processed: 176
  average time/residue: 0.2067
  time to fit residues: 49.9756
Evaluate side-chains
  158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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  153 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   36 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  153 ILE
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  301 LEU
Chi-restraints excluded: chain B residue  307 GLN
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  389 ILE
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 44 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0060
   chunk 43 optimal weight:    0.4980
   chunk 109 optimal weight:    0.2980
   chunk 0 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 97 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
B 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.194606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 155)---------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.164393 restraints weight = 10051.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.159490 restraints weight = 10459.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.159938 restraints weight = 9747.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9018  Z= 0.130
  Angle     :  0.521   6.455  12188  Z= 0.278
  Chirality :  0.040   0.151   1452
  Planarity :  0.004   0.033   1542
  Dihedral  :  3.984  21.031   1248
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.67 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.26), residues: 1142
  helix:  2.13 (0.20), residues: 716
  sheet:  0.59 (0.55), residues: 78
  loop : -0.72 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  66 
 HIS   0.007   0.001   HIS A 214 
 PHE   0.015   0.001   PHE A  56 
 TYR   0.009   0.001   TYR B 130 
 ARG   0.005   0.000   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05847 (  581)
  hydrogen bonds       : angle       4.31880 ( 1722)
  covalent geometry    : bond        0.00243 ( 9018)
  covalent geometry    : angle       0.52084 (12188)

*********************** 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
  181 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.7973 (tpp) cc_final: 0.7371 (ttm)
REVERT: B   67 MET cc_start: 0.8004 (tpp) cc_final: 0.7718 (mmm)
REVERT: B  200 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.5071 (tpt)
  outliers start: 38
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2055
  time to fit residues: 47.6333
Evaluate side-chains
  150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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   63 VAL
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  119 GLN
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  284 ILE
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  371 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 89 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0470
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.9684

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.185198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 182)---------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.162991 restraints weight = 10075.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.161936 restraints weight = 16911.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.157640 restraints weight = 14977.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9018  Z= 0.157
  Angle     :  0.560   5.634  12188  Z= 0.294
  Chirality :  0.041   0.146   1452
  Planarity :  0.004   0.034   1542
  Dihedral  :  4.038  21.997   1248
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 23.46 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.26), residues: 1142
  helix:  2.10 (0.20), residues: 718
  sheet:  0.66 (0.56), residues: 78
  loop : -0.52 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.018   0.002   PHE A  56 
 TYR   0.016   0.001   TYR B 130 
 ARG   0.003   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06004 (  581)
  hydrogen bonds       : angle       4.33724 ( 1722)
  covalent geometry    : bond        0.00336 ( 9018)
  covalent geometry    : angle       0.55961 (12188)

*********************** 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
  181 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 134
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   44 MET cc_start: 0.8081 (tpp) cc_final: 0.7416 (ttm)
REVERT: A  127 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7390 (ttm-80)
REVERT: B  200 MET cc_start: 0.5605 (tpt) cc_final: 0.5049 (tpt)
REVERT: B  231 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6994 (t70)
REVERT: B  301 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7356 (mp)
  outliers start: 47
  outliers final: 32
  residues processed: 172
  average time/residue: 0.2168
  time to fit residues: 50.9767
Evaluate side-chains
  158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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   89 ILE
Chi-restraints excluded: chain A residue  127 ARG
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  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  335 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   64 LEU
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  231 ASP
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  335 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  389 ILE
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 0 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   chunk 96 optimal weight:    0.3980
   chunk 39 optimal weight:    8.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS
B 107 HIS
B 326 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.184888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.167057 restraints weight = 9961.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.162980 restraints weight = 14193.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.159930 restraints weight = 17898.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7086
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9018  Z= 0.144
  Angle     :  0.554   9.971  12188  Z= 0.290
  Chirality :  0.041   0.146   1452
  Planarity :  0.004   0.033   1542
  Dihedral  :  4.009  21.669   1248
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 24.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.26), residues: 1142
  helix:  2.17 (0.20), residues: 718
  sheet:  0.70 (0.55), residues: 78
  loop : -0.47 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  66 
 HIS   0.005   0.001   HIS A 405 
 PHE   0.017   0.001   PHE B 189 
 TYR   0.013   0.001   TYR B 130 
 ARG   0.003   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05802 (  581)
  hydrogen bonds       : angle       4.26241 ( 1722)
  covalent geometry    : bond        0.00301 ( 9018)
  covalent geometry    : angle       0.55433 (12188)

*********************** 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
  178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 130
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   44 MET cc_start: 0.8047 (tpp) cc_final: 0.7342 (ttm)
REVERT: B  200 MET cc_start: 0.5581 (tpt) cc_final: 0.5156 (tpt)
REVERT: B  301 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7196 (mp)
REVERT: B  451 GLU cc_start: 0.6505 (tp30) cc_final: 0.6293 (tp30)
  outliers start: 48
  outliers final: 33
  residues processed: 166
  average time/residue: 0.2006
  time to fit residues: 45.9158
Evaluate side-chains
  155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  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  335 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   64 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  275 VAL
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  371 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
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 16 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 326 GLN
B 405 HIS
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.185292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.159572 restraints weight = 10380.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 100)---------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.148292 restraints weight = 13783.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.145423 restraints weight = 15818.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9018  Z= 0.147
  Angle     :  0.553   6.412  12188  Z= 0.289
  Chirality :  0.041   0.143   1452
  Planarity :  0.004   0.033   1542
  Dihedral  :  4.034  21.768   1248
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 24.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.26), residues: 1142
  helix:  2.06 (0.20), residues: 730
  sheet:  0.49 (0.56), residues: 80
  loop : -0.47 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  66 
 HIS   0.009   0.001   HIS B 405 
 PHE   0.017   0.002   PHE B 189 
 TYR   0.012   0.001   TYR B 130 
 ARG   0.003   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05776 (  581)
  hydrogen bonds       : angle       4.24876 ( 1722)
  covalent geometry    : bond        0.00311 ( 9018)
  covalent geometry    : angle       0.55303 (12188)

*********************** 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
  169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 123
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8150 (tpp) cc_final: 0.7346 (ttm)
REVERT: A  301 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (mp)
REVERT: B  200 MET cc_start: 0.5644 (tpt) cc_final: 0.5096 (tpt)
REVERT: B  301 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7245 (mp)
  outliers start: 46
  outliers final: 39
  residues processed: 161
  average time/residue: 0.2078
  time to fit residues: 45.7610
Evaluate side-chains
  157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 116
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   54 ASP
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  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  301 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  356 VAL
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   56 PHE
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  231 ASP
Chi-restraints excluded: chain B residue  275 VAL
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  371 THR
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 107 optimal weight:   20.0000
   chunk 109 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.189468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152957 restraints weight = 10418.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.151879 restraints weight = 10173.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.152456 restraints weight = 9073.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9018  Z= 0.139
  Angle     :  0.557  10.832  12188  Z= 0.286
  Chirality :  0.040   0.149   1452
  Planarity :  0.003   0.032   1542
  Dihedral  :  4.004  21.448   1248
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 25.00 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.26), residues: 1142
  helix:  2.04 (0.19), residues: 734
  sheet:  0.43 (0.60), residues: 70
  loop : -0.39 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 562 
 PHE   0.018   0.001   PHE B 189 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.003   0.000   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05589 (  581)
  hydrogen bonds       : angle       4.21098 ( 1722)
  covalent geometry    : bond        0.00290 ( 9018)
  covalent geometry    : angle       0.55686 (12188)

*********************** 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
  166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 119
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8218 (tpp) cc_final: 0.6772 (ttm)
REVERT: A   75 MET cc_start: 0.7589 (tpp) cc_final: 0.7337 (mmm)
REVERT: A  301 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: B  200 MET cc_start: 0.5801 (tpt) cc_final: 0.5333 (tpt)
REVERT: B  301 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7171 (mp)
  outliers start: 47
  outliers final: 33
  residues processed: 162
  average time/residue: 0.2219
  time to fit residues: 49.4816
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  : 0.925 
-------------------------------------------------------------------------------
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  153 ILE
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  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 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  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   66 TRP
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  231 ASP
Chi-restraints excluded: chain B residue  275 VAL
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  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  531 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0050
   chunk 0 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0770
   chunk 10 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.4752

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

Flipped N/Q/H residues before XYZ refinement:
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.163472 restraints weight = 10455.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161036 restraints weight = 13757.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.162976 restraints weight = 13196.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9018  Z= 0.125
  Angle     :  0.552  10.683  12188  Z= 0.281
  Chirality :  0.040   0.146   1452
  Planarity :  0.004   0.033   1542
  Dihedral  :  3.932  21.048   1248
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 26.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.26), residues: 1142
  helix:  2.18 (0.20), residues: 734
  sheet:  0.53 (0.61), residues: 70
  loop : -0.32 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  66 
 HIS   0.003   0.001   HIS B 576 
 PHE   0.018   0.001   PHE B 189 
 TYR   0.015   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05239 (  581)
  hydrogen bonds       : angle       4.10464 ( 1722)
  covalent geometry    : bond        0.00247 ( 9018)
  covalent geometry    : angle       0.55221 (12188)

*********************** 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
  159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8222 (tpp) cc_final: 0.7402 (tmm)
REVERT: A  301 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7519 (mp)
REVERT: A  578 MET cc_start: 0.3130 (tmm) cc_final: 0.2142 (tpp)
REVERT: B  200 MET cc_start: 0.5821 (tpt) cc_final: 0.5406 (tpt)
REVERT: B  301 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.6975 (mp)
  outliers start: 32
  outliers final: 27
  residues processed: 151
  average time/residue: 0.2126
  time to fit residues: 44.5730
Evaluate side-chains
  147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  153 ILE
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  301 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  356 VAL
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   66 TRP
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  164 SER
Chi-restraints excluded: chain B residue  231 ASP
Chi-restraints excluded: chain B residue  275 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  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  526 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 92 optimal weight:    3.9990
   chunk 80 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.187742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.168979 restraints weight = 10396.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.164476 restraints weight = 14778.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.161820 restraints weight = 16661.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.3420

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= 0.151
  Angle     :  0.598  10.268  12188  Z= 0.300
  Chirality :  0.041   0.143   1452
  Planarity :  0.004   0.048   1542
  Dihedral  :  4.045  21.455   1248
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.00 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.26), residues: 1142
  helix:  2.02 (0.19), residues: 734
  sheet:  0.56 (0.61), residues: 70
  loop : -0.33 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.018   0.002   PHE B 189 
 TYR   0.010   0.001   TYR B 445 
 ARG   0.006   0.000   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05578 (  581)
  hydrogen bonds       : angle       4.20464 ( 1722)
  covalent geometry    : bond        0.00328 ( 9018)
  covalent geometry    : angle       0.59771 (12188)

*********************** 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: 41
    poor density    : 119
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8160 (tpp) cc_final: 0.7514 (tmm)
REVERT: A  301 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7658 (mp)
REVERT: B  200 MET cc_start: 0.5866 (tpt) cc_final: 0.5370 (tpt)
REVERT: B  301 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7027 (mp)
  outliers start: 41
  outliers final: 35
  residues processed: 153
  average time/residue: 0.2024
  time to fit residues: 43.1819
Evaluate side-chains
  154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
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   69 LEU
Chi-restraints excluded: chain A residue  153 ILE
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  301 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  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  526 LEU
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   66 TRP
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  231 ASP
Chi-restraints excluded: chain B residue  275 VAL
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  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  531 THR
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 107 optimal weight:   20.0000
   chunk 23 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 110 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0970
   chunk 64 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.186593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172015 restraints weight = 10614.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.168655 restraints weight = 19419.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.167938 restraints weight = 21477.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9018  Z= 0.190
  Angle     :  0.657  11.347  12188  Z= 0.330
  Chirality :  0.043   0.140   1452
  Planarity :  0.004   0.047   1542
  Dihedral  :  4.243  22.607   1248
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 25.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1142
  helix:  1.87 (0.19), residues: 732
  sheet:  0.39 (0.57), residues: 80
  loop : -0.37 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B  66 
 HIS   0.005   0.001   HIS A 405 
 PHE   0.019   0.002   PHE B 189 
 TYR   0.010   0.002   TYR A 410 
 ARG   0.006   0.000   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06092 (  581)
  hydrogen bonds       : angle       4.38742 ( 1722)
  covalent geometry    : bond        0.00433 ( 9018)
  covalent geometry    : angle       0.65676 (12188)

********************** 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
  159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 116
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.8139 (tpp) cc_final: 0.7589 (tmm)
REVERT: A  301 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7764 (mp)
REVERT: A  321 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6804 (mt)
REVERT: A  474 ILE cc_start: 0.7811 (pt) cc_final: 0.7173 (mt)
REVERT: B  301 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7291 (mp)
  outliers start: 43
  outliers final: 36
  residues processed: 153
  average time/residue: 0.1949
  time to fit residues: 41.9137
Evaluate side-chains
  153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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  153 ILE
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  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  321 ILE
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  436 ASN
Chi-restraints excluded: chain A residue  531 THR
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   66 TRP
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  231 ASP
Chi-restraints excluded: chain B residue  275 VAL
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  372 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  531 THR
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 45 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0980
   chunk 113 optimal weight:   10.0000
   chunk 81 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 537 HIS
** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 537 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.186520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.164775 restraints weight = 10437.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.160582 restraints weight = 14283.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 77)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.156655 restraints weight = 15837.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9018  Z= 0.140
  Angle     :  0.597  11.743  12188  Z= 0.299
  Chirality :  0.041   0.159   1452
  Planarity :  0.004   0.037   1542
  Dihedral  :  4.106  22.271   1248
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 26.54 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.26), residues: 1142
  helix:  2.02 (0.19), residues: 734
  sheet:  0.34 (0.63), residues: 70
  loop : -0.28 (0.37), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B  66 
 HIS   0.003   0.001   HIS A 405 
 PHE   0.019   0.001   PHE B 189 
 TYR   0.009   0.001   TYR B 445 
 ARG   0.005   0.000   ARG B 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05590 (  581)
  hydrogen bonds       : angle       4.19897 ( 1722)
  covalent geometry    : bond        0.00292 ( 9018)
  covalent geometry    : angle       0.59672 (12188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2854.61 seconds
wall clock time: 50 minutes 41.23 seconds (3041.23 seconds total)