Starting phenix.real_space_refine
on Sat Aug 23 14:41:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ems_28263/08_2025/8ems_28263.map"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      56      5.16       5
     C    8154      2.51       5
     N    2152      2.21       5
     O    2324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12688
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 6329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 780, 6329
          Classifications: {'peptide': 780}
          Link IDs: {'PTRANS': 29, 'TRANS': 750}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Restraints were copied for chains:
    A
  Time building chain proxies: 5.66, per 1000 atoms: 0.45
  Number of scatterers: 12688
  At special positions: 0
  Unit cell: (130.68, 102.6, 79.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P       2     15.00
     O    2324      8.00
     N    2152      7.00
     C    8154      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 530.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2956

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 10 sheets defined
      59.6% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 24 through 37
    Processing helix  chain 'B' and resid 47 through 72
      removed outlier: 4.555A  pdb=" N   GLY B  65 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ARG B  66 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 103
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 118 through 126
      removed outlier: 4.023A  pdb=" N   LEU B 122 " --> pdb=" O   ASP B 118 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 150
    Processing helix  chain 'B' and resid 193 through 197
      removed outlier: 3.600A  pdb=" N   MET B 197 " --> pdb=" O   PRO B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 268 through 274
      removed outlier: 4.316A  pdb=" N   ALA B 272 " --> pdb=" O   ASP B 268 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU B 273 " --> pdb=" O   ARG B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 313
    Processing helix  chain 'B' and resid 325 through 329
    Processing helix  chain 'B' and resid 340 through 343
      removed outlier: 3.542A  pdb=" N   ALA B 343 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 340 through 343'
    Processing helix  chain 'B' and resid 344 through 355
    Processing helix  chain 'B' and resid 360 through 371
    Processing helix  chain 'B' and resid 380 through 384
      removed outlier: 3.729A  pdb=" N   LEU B 384 " --> pdb=" O   PRO B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 396
    Processing helix  chain 'B' and resid 396 through 418
      removed outlier: 3.645A  pdb=" N   LEU B 417 " --> pdb=" O   ARG B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 428
      removed outlier: 3.591A  pdb=" N   ARG B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 448
    Processing helix  chain 'B' and resid 456 through 466
    Processing helix  chain 'B' and resid 468 through 475
      removed outlier: 3.678A  pdb=" N   LEU B 474 " --> pdb=" O   ASP B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 492
    Processing helix  chain 'B' and resid 496 through 508
      removed outlier: 3.520A  pdb=" N   LYS B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 513
    Processing helix  chain 'B' and resid 514 through 525
      removed outlier: 3.591A  pdb=" N   SER B 523 " --> pdb=" O   LYS B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 554
      removed outlier: 4.136A  pdb=" N   LEU B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR B 551 " --> pdb=" O   GLN B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 593
      removed outlier: 4.025A  pdb=" N   ASN B 579 " --> pdb=" O   ARG B 575 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASP B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 632
      removed outlier: 3.550A  pdb=" N   LYS B 617 " --> pdb=" O   TYR B 613 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN B 632 " --> pdb=" O   ASP B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 657
      removed outlier: 3.639A  pdb=" N   LYS B 655 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 660
      No H-bonds generated for 'chain 'B' and resid 658 through 660'
    Processing helix  chain 'B' and resid 676 through 684
    Processing helix  chain 'B' and resid 694 through 704
      removed outlier: 4.465A  pdb=" N   GLU B 698 " --> pdb=" O   GLY B 694 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 708
    Processing helix  chain 'B' and resid 714 through 725
    Processing helix  chain 'B' and resid 727 through 734
      removed outlier: 4.065A  pdb=" N   TYR B 731 " --> pdb=" O   GLU B 727 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 735 through 747
    Processing helix  chain 'B' and resid 758 through 767
    Processing helix  chain 'B' and resid 773 through 775
      No H-bonds generated for 'chain 'B' and resid 773 through 775'
    Processing helix  chain 'B' and resid 776 through 792
    Processing helix  chain 'B' and resid 793 through 807
    Processing helix  chain 'B' and resid 808 through 811
    Processing helix  chain 'B' and resid 812 through 824
      removed outlier: 3.678A  pdb=" N   THR B 816 " --> pdb=" O   SER B 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 47 through 72
      removed outlier: 4.555A  pdb=" N   GLY A  65 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ARG A  66 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 103
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 4.023A  pdb=" N   LEU A 122 " --> pdb=" O   ASP A 118 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 150
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.600A  pdb=" N   MET A 197 " --> pdb=" O   PRO A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 268 through 274
      removed outlier: 4.316A  pdb=" N   ALA A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 313
    Processing helix  chain 'A' and resid 325 through 329
    Processing helix  chain 'A' and resid 340 through 343
      removed outlier: 3.542A  pdb=" N   ALA A 343 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 340 through 343'
    Processing helix  chain 'A' and resid 344 through 355
    Processing helix  chain 'A' and resid 360 through 371
    Processing helix  chain 'A' and resid 380 through 384
      removed outlier: 3.730A  pdb=" N   LEU A 384 " --> pdb=" O   PRO A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 396
    Processing helix  chain 'A' and resid 396 through 418
      removed outlier: 3.644A  pdb=" N   LEU A 417 " --> pdb=" O   ARG A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 428
      removed outlier: 3.591A  pdb=" N   ARG A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 448
    Processing helix  chain 'A' and resid 456 through 466
    Processing helix  chain 'A' and resid 468 through 475
      removed outlier: 3.678A  pdb=" N   LEU A 474 " --> pdb=" O   ASP A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 492
    Processing helix  chain 'A' and resid 496 through 508
      removed outlier: 3.520A  pdb=" N   LYS A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 513
    Processing helix  chain 'A' and resid 514 through 525
      removed outlier: 3.591A  pdb=" N   SER A 523 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 554
      removed outlier: 4.136A  pdb=" N   LEU A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 593
      removed outlier: 4.025A  pdb=" N   ASN A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASP A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 632
      removed outlier: 3.550A  pdb=" N   LYS A 617 " --> pdb=" O   TYR A 613 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN A 632 " --> pdb=" O   ASP A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 657
      removed outlier: 3.640A  pdb=" N   LYS A 655 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 660
      No H-bonds generated for 'chain 'A' and resid 658 through 660'
    Processing helix  chain 'A' and resid 676 through 684
    Processing helix  chain 'A' and resid 694 through 704
      removed outlier: 4.466A  pdb=" N   GLU A 698 " --> pdb=" O   GLY A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 708
    Processing helix  chain 'A' and resid 714 through 725
    Processing helix  chain 'A' and resid 727 through 734
      removed outlier: 4.065A  pdb=" N   TYR A 731 " --> pdb=" O   GLU A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 735 through 747
    Processing helix  chain 'A' and resid 758 through 767
    Processing helix  chain 'A' and resid 773 through 775
      No H-bonds generated for 'chain 'A' and resid 773 through 775'
    Processing helix  chain 'A' and resid 776 through 792
    Processing helix  chain 'A' and resid 793 through 807
    Processing helix  chain 'A' and resid 808 through 811
    Processing helix  chain 'A' and resid 812 through 824
      removed outlier: 3.677A  pdb=" N   THR A 816 " --> pdb=" O   SER A 812 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 202
      removed outlier: 7.135A  pdb=" N   ALA B 154 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   ARG B 242 " --> pdb=" O   ALA B 154 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLY B 156 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   TRP B 244 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   GLY B 158 " --> pdb=" O   TRP B 244 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   ALA B 246 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
      removed outlier: 9.390A  pdb=" N   ASN B 453 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   TYR B 374 " --> pdb=" O   ASN B 453 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 171
    Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 208
    Processing sheet with id=AA4, first strand: chain 'B' and resid 386 through 388
    Processing sheet with id=AA5, first strand: chain 'B' and resid 640 through 643
      removed outlier: 3.771A  pdb=" N   LYS B 641 " --> pdb=" O   ARG B 601 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   MET B 562 " --> pdb=" O   THR B 602 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ILE B 604 " --> pdb=" O   MET B 562 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP B 564 " --> pdb=" O   ILE B 604 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLY B 606 " --> pdb=" O   ASP B 564 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLN B 566 " --> pdb=" O   GLY B 606 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   VAL B 567 " --> pdb=" O   GLU B 664 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 202
      removed outlier: 7.135A  pdb=" N   ALA A 154 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   ARG A 242 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLY A 156 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   TRP A 244 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   GLY A 158 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   ALA A 246 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
      removed outlier: 9.391A  pdb=" N   ASN A 453 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   TYR A 374 " --> pdb=" O   ASN A 453 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 171
    Processing sheet with id=AA8, first strand: chain 'A' and resid 205 through 208
    Processing sheet with id=AA9, first strand: chain 'A' and resid 386 through 388
    Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 643
      removed outlier: 3.771A  pdb=" N   LYS A 641 " --> pdb=" O   ARG A 601 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   MET A 562 " --> pdb=" O   THR A 602 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ILE A 604 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP A 564 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   GLY A 606 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   GLN A 566 " --> pdb=" O   GLY A 606 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   VAL A 567 " --> pdb=" O   GLU A 664 " (cutoff:3.500A)

    663 hydrogen bonds defined for protein.
    1845 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: 2.43

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4110
        1.34 -     1.46: 2483
        1.46 -     1.58: 6269
        1.58 -     1.69: 2
        1.69 -     1.81: 100
  Bond restraints: 12964
  Sorted by residual:
  bond pdb=" CA  VAL B  59 "
       pdb=" C   VAL B  59 "
    ideal  model  delta    sigma   weight residual
    1.524  1.535 -0.012 1.30e-02 5.92e+03 8.18e-01
  bond pdb=" CA  VAL A  59 "
       pdb=" C   VAL A  59 "
    ideal  model  delta    sigma   weight residual
    1.524  1.535 -0.012 1.30e-02 5.92e+03 8.18e-01
  bond pdb=" N   GLN B 480 "
       pdb=" CA  GLN B 480 "
    ideal  model  delta    sigma   weight residual
    1.456  1.469 -0.013 1.44e-02 4.82e+03 8.05e-01
  bond pdb=" CA  LYS B 482 "
       pdb=" C   LYS B 482 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 1.14e-02 7.69e+03 8.00e-01
  bond pdb=" N   GLN A 480 "
       pdb=" CA  GLN A 480 "
    ideal  model  delta    sigma   weight residual
    1.456  1.468 -0.012 1.44e-02 4.82e+03 7.05e-01
  ... (remaining 12959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 16889
        1.18 -     2.37: 492
        2.37 -     3.55: 107
        3.55 -     4.74: 27
        4.74 -     5.92: 13
  Bond angle restraints: 17528
  Sorted by residual:
  angle pdb=" C   ILE A 165 "
        pdb=" N   PHE A 166 "
        pdb=" CA  PHE A 166 "
      ideal   model   delta    sigma   weight residual
     121.54  127.46   -5.92 1.91e+00 2.74e-01 9.61e+00
  angle pdb=" C   ILE B 165 "
        pdb=" N   PHE B 166 "
        pdb=" CA  PHE B 166 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.55e+00
  angle pdb=" N   ARG B 292 "
        pdb=" CA  ARG B 292 "
        pdb=" CB  ARG B 292 "
      ideal   model   delta    sigma   weight residual
     114.17  110.71    3.46 1.14e+00 7.69e-01 9.22e+00
  angle pdb=" N   ARG A 292 "
        pdb=" CA  ARG A 292 "
        pdb=" CB  ARG A 292 "
      ideal   model   delta    sigma   weight residual
     114.17  110.73    3.44 1.14e+00 7.69e-01 9.09e+00
  angle pdb=" N   GLN A 480 "
        pdb=" CA  GLN A 480 "
        pdb=" C   GLN A 480 "
      ideal   model   delta    sigma   weight residual
     109.18  113.23   -4.05 1.42e+00 4.96e-01 8.12e+00
  ... (remaining 17523 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 7027
       16.62 -    33.24: 617
       33.24 -    49.86: 132
       49.86 -    66.48: 12
       66.48 -    83.10: 10
  Dihedral angle restraints: 7798
    sinusoidal: 3224
      harmonic: 4574
  Sorted by residual:
  dihedral pdb=" CA  ILE B 165 "
           pdb=" C   ILE B 165 "
           pdb=" N   PHE B 166 "
           pdb=" CA  PHE B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.09   19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  ILE A 165 "
           pdb=" C   ILE A 165 "
           pdb=" N   PHE A 166 "
           pdb=" CA  PHE A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.12   19.88     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ARG B 292 "
           pdb=" C   ARG B 292 "
           pdb=" N   LEU B 293 "
           pdb=" CA  LEU B 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.21   17.79     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 7795 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1771
       0.072 -    0.144: 147
       0.144 -    0.216: 2
       0.216 -    0.288: 0
       0.288 -    0.360: 2
  Chirality restraints: 1922
  Sorted by residual:
  chirality pdb=" CB  ILE B 165 "
            pdb=" CA  ILE B 165 "
            pdb=" CG1 ILE B 165 "
            pdb=" CG2 ILE B 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CB  ILE A 165 "
            pdb=" CA  ILE A 165 "
            pdb=" CG1 ILE A 165 "
            pdb=" CG2 ILE A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  LYS B 482 "
            pdb=" N   LYS B 482 "
            pdb=" C   LYS B 482 "
            pdb=" CB  LYS B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.04e-01
  ... (remaining 1919 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 292 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.42e+00
        pdb=" C   ARG B 292 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ARG B 292 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU B 293 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 292 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   ARG A 292 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ARG A 292 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 293 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  90 "    0.013 2.00e-02 2.50e+03   1.01e-02 2.05e+00
        pdb=" CG  TYR A  90 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  90 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  90 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  90 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  90 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  90 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A  90 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1560
        2.75 -     3.29: 12239
        3.29 -     3.83: 21711
        3.83 -     4.36: 26772
        4.36 -     4.90: 45066
  Nonbonded interactions: 107348
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 311 "
            pdb=" OG  SER B 314 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   PHE A 311 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE1 GLN A  71 "
            pdb=" OG1 THR A 240 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OE1 GLN B  71 "
            pdb=" OG1 THR B 240 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE1 GLU A 664 "
            pdb=" OH  TYR A 780 "
     model   vdw
     2.278 3.040
  ... (remaining 107343 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.300
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
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      :  0.005   0.373  12966  Z= 0.479
  Angle     :  0.530   5.922  17528  Z= 0.294
  Chirality :  0.042   0.360   1922
  Planarity :  0.003   0.040   2240
  Dihedral  : 13.281  83.104   4842
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.21), residues: 1544
  helix:  0.99 (0.18), residues: 828
  sheet: -0.70 (0.38), residues: 166
  loop : -1.33 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 309 
 TYR   0.025   0.002   TYR A  90 
 PHE   0.015   0.001   PHE A 298 
 TRP   0.007   0.001   TRP A 491 
 HIS   0.002   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12964)
  covalent geometry    : angle       0.53047 (17528)
  hydrogen bonds       : bond        0.16679 (  663)
  hydrogen bonds       : angle       6.31272 ( 1845)
  Misc. bond           : bond        0.37233 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 214
  time to evaluate  : 0.388 
Fit side-chains
REVERT: B  764 MET cc_start: 0.7291 (tmm) cc_final: 0.7063 (tmt)
REVERT: B  827 VAL cc_start: 0.7493 (t) cc_final: 0.7105 (m)
REVERT: A  547 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6782 (mm-40)
REVERT: A  827 VAL cc_start: 0.7492 (t) cc_final: 0.7111 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 216
  average time/residue: 0.6452
  time to fit residues: 150.5369
Evaluate side-chains
  176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.194868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.177946 restraints weight = 12950.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.4096 rms_B_bonded: 1.17
r_work: 0.4001 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3904 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12966  Z= 0.130
  Angle     :  0.533   5.455  17528  Z= 0.282
  Chirality :  0.041   0.231   1922
  Planarity :  0.004   0.032   2240
  Dihedral  :  4.842  40.586   1702
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.38 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.21), residues: 1544
  helix:  1.13 (0.18), residues: 820
  sheet: -0.31 (0.36), residues: 190
  loop : -0.92 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 489 
 TYR   0.029   0.002   TYR A 297 
 PHE   0.016   0.002   PHE B 166 
 TRP   0.014   0.001   TRP A 365 
 HIS   0.007   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12964)
  covalent geometry    : angle       0.53285 (17528)
  hydrogen bonds       : bond        0.04523 (  663)
  hydrogen bonds       : angle       5.00237 ( 1845)
  Misc. bond           : bond        0.00038 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.562 
Fit side-chains
REVERT: B   90 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6628 (t80)
REVERT: B  126 GLU cc_start: 0.6230 (tt0) cc_final: 0.5894 (tt0)
REVERT: B  764 MET cc_start: 0.7370 (tmm) cc_final: 0.7060 (tmt)
REVERT: B  827 VAL cc_start: 0.7514 (t) cc_final: 0.7051 (m)
REVERT: A   90 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6640 (t80)
REVERT: A  126 GLU cc_start: 0.6207 (tt0) cc_final: 0.5868 (tt0)
REVERT: A  827 VAL cc_start: 0.7527 (t) cc_final: 0.7065 (m)
  outliers start: 18
  outliers final: 9
  residues processed: 179
  average time/residue: 0.6806
  time to fit residues: 132.0532
Evaluate side-chains
  165 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  599 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 146 optimal weight:    5.9990
   chunk 148 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 121 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.189680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.172493 restraints weight = 13129.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 1.17
r_work: 0.3934 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3831 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12966  Z= 0.215
  Angle     :  0.655   7.386  17528  Z= 0.342
  Chirality :  0.046   0.186   1922
  Planarity :  0.005   0.042   2240
  Dihedral  :  5.311  44.420   1702
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.95 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.21), residues: 1544
  helix:  0.71 (0.18), residues: 810
  sheet: -0.51 (0.34), residues: 190
  loop : -1.07 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.025   0.003   TYR B  90 
 PHE   0.020   0.002   PHE B 285 
 TRP   0.011   0.002   TRP B 174 
 HIS   0.007   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (12964)
  covalent geometry    : angle       0.65507 (17528)
  hydrogen bonds       : bond        0.05335 (  663)
  hydrogen bonds       : angle       5.18578 ( 1845)
  Misc. bond           : bond        0.00123 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.599 
Fit side-chains
REVERT: B   90 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6574 (t80)
REVERT: B  385 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7265 (mt-10)
REVERT: B  506 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6391 (mptt)
REVERT: B  689 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7271 (pp)
REVERT: B  706 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6381 (pp20)
REVERT: B  764 MET cc_start: 0.7490 (tmm) cc_final: 0.7171 (tmt)
REVERT: B  827 VAL cc_start: 0.7696 (t) cc_final: 0.7220 (m)
REVERT: A   90 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6578 (t80)
REVERT: A  126 GLU cc_start: 0.6266 (tt0) cc_final: 0.5911 (tt0)
REVERT: A  385 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: A  506 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6389 (mptt)
REVERT: A  689 ILE cc_start: 0.7729 (tt) cc_final: 0.7286 (pp)
REVERT: A  827 VAL cc_start: 0.7696 (t) cc_final: 0.7223 (m)
  outliers start: 35
  outliers final: 13
  residues processed: 180
  average time/residue: 0.6639
  time to fit residues: 130.1543
Evaluate side-chains
  175 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  477 ASP
Chi-restraints excluded: chain B residue  506 LYS
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  689 ILE
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 150 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 148 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 ASN
** A 133 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 = 0.4218 r_free = 0.4218 target = 0.189697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.172556 restraints weight = 13020.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 1.15
r_work: 0.3938 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12966  Z= 0.196
  Angle     :  0.633   6.602  17528  Z= 0.332
  Chirality :  0.044   0.167   1922
  Planarity :  0.004   0.039   2240
  Dihedral  :  5.365  47.261   1702
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.86 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.21), residues: 1544
  helix:  0.65 (0.18), residues: 810
  sheet: -0.53 (0.35), residues: 190
  loop : -1.15 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.023   0.002   TYR B  90 
 PHE   0.018   0.002   PHE A 285 
 TRP   0.010   0.002   TRP A 365 
 HIS   0.005   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (12964)
  covalent geometry    : angle       0.63342 (17528)
  hydrogen bonds       : bond        0.05079 (  663)
  hydrogen bonds       : angle       5.09111 ( 1845)
  Misc. bond           : bond        0.00110 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.500 
Fit side-chains
REVERT: B   84 TYR cc_start: 0.7366 (t80) cc_final: 0.7088 (t80)
REVERT: B   90 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6514 (t80)
REVERT: B  234 MET cc_start: 0.6940 (mmm) cc_final: 0.6647 (mmm)
REVERT: B  385 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7271 (mt-10)
REVERT: B  506 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6441 (mptt)
REVERT: B  689 ILE cc_start: 0.7743 (tt) cc_final: 0.7301 (pp)
REVERT: B  706 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6330 (pp20)
REVERT: B  764 MET cc_start: 0.7507 (tmm) cc_final: 0.7261 (tmt)
REVERT: B  789 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6942 (mp-120)
REVERT: A   84 TYR cc_start: 0.7359 (t80) cc_final: 0.7086 (t80)
REVERT: A   90 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6512 (t80)
REVERT: A  385 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7257 (mt-10)
REVERT: A  506 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6339 (mptt)
REVERT: A  706 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6335 (pp20)
REVERT: A  789 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6905 (mp-120)
  outliers start: 33
  outliers final: 15
  residues processed: 173
  average time/residue: 0.6199
  time to fit residues: 116.9951
Evaluate side-chains
  175 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  506 LYS
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  722 ASP
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  722 ASP
Chi-restraints excluded: chain A residue  789 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 70 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0470
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 133 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 = 0.4263 r_free = 0.4263 target = 0.194190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.176979 restraints weight = 12975.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 1.18
r_work: 0.3984 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3884 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12966  Z= 0.119
  Angle     :  0.513   5.358  17528  Z= 0.273
  Chirality :  0.040   0.141   1922
  Planarity :  0.003   0.033   2240
  Dihedral  :  4.972  45.472   1702
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.10 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.21), residues: 1544
  helix:  1.13 (0.18), residues: 820
  sheet: -0.18 (0.37), residues: 190
  loop : -0.94 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 601 
 TYR   0.015   0.001   TYR B  90 
 PHE   0.015   0.001   PHE A 298 
 TRP   0.012   0.001   TRP B 365 
 HIS   0.003   0.001   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (12964)
  covalent geometry    : angle       0.51256 (17528)
  hydrogen bonds       : bond        0.03924 (  663)
  hydrogen bonds       : angle       4.75320 ( 1845)
  Misc. bond           : bond        0.00049 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.585 
Fit side-chains
REVERT: B   90 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6465 (t80)
REVERT: B  385 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7250 (mt-10)
REVERT: B  405 GLU cc_start: 0.7178 (tp30) cc_final: 0.6329 (mt-10)
REVERT: B  706 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6419 (pp20)
REVERT: B  759 LYS cc_start: 0.7685 (mptt) cc_final: 0.7225 (ttpp)
REVERT: B  764 MET cc_start: 0.7442 (tmm) cc_final: 0.7086 (tmt)
REVERT: B  827 VAL cc_start: 0.7639 (t) cc_final: 0.7157 (m)
REVERT: A   29 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6798 (mtmp)
REVERT: A   90 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6466 (t80)
REVERT: A  385 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7247 (mt-10)
REVERT: A  706 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6405 (pp20)
REVERT: A  759 LYS cc_start: 0.7669 (mptt) cc_final: 0.7221 (ttpp)
REVERT: A  827 VAL cc_start: 0.7647 (t) cc_final: 0.7163 (m)
  outliers start: 29
  outliers final: 12
  residues processed: 171
  average time/residue: 0.6814
  time to fit residues: 126.6137
Evaluate side-chains
  167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  706 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 126 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 124 optimal weight:    0.8980
   chunk 155 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.193784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.176553 restraints weight = 12822.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 1.16
r_work: 0.3980 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3879 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12966  Z= 0.129
  Angle     :  0.530   5.386  17528  Z= 0.280
  Chirality :  0.041   0.152   1922
  Planarity :  0.003   0.032   2240
  Dihedral  :  4.975  45.832   1702
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.98 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.21), residues: 1544
  helix:  1.15 (0.18), residues: 824
  sheet: -0.10 (0.37), residues: 190
  loop : -0.92 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.016   0.002   TYR B  90 
 PHE   0.016   0.001   PHE A 298 
 TRP   0.011   0.001   TRP B 365 
 HIS   0.005   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12964)
  covalent geometry    : angle       0.52972 (17528)
  hydrogen bonds       : bond        0.04059 (  663)
  hydrogen bonds       : angle       4.74445 ( 1845)
  Misc. bond           : bond        0.00059 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.511 
Fit side-chains
REVERT: B   84 TYR cc_start: 0.7274 (t80) cc_final: 0.6968 (t80)
REVERT: B  165 ILE cc_start: 0.5625 (OUTLIER) cc_final: 0.4942 (tp)
REVERT: B  171 ARG cc_start: 0.6908 (mpt-90) cc_final: 0.6683 (mpt-90)
REVERT: B  197 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6505 (tmt)
REVERT: B  205 LYS cc_start: 0.6414 (mmmt) cc_final: 0.6074 (mmmm)
REVERT: B  385 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: B  689 ILE cc_start: 0.7865 (tt) cc_final: 0.7464 (pp)
REVERT: B  706 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6396 (pp20)
REVERT: B  764 MET cc_start: 0.7445 (tmm) cc_final: 0.7082 (tmt)
REVERT: B  789 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6886 (mp-120)
REVERT: B  827 VAL cc_start: 0.7645 (t) cc_final: 0.7173 (m)
REVERT: A   29 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6792 (mtmp)
REVERT: A   84 TYR cc_start: 0.7281 (t80) cc_final: 0.6979 (t80)
REVERT: A  165 ILE cc_start: 0.5613 (OUTLIER) cc_final: 0.4926 (tp)
REVERT: A  171 ARG cc_start: 0.6914 (mpt-90) cc_final: 0.6691 (mpt-90)
REVERT: A  197 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6650 (tmt)
REVERT: A  205 LYS cc_start: 0.6688 (mmmt) cc_final: 0.6323 (mmmm)
REVERT: A  385 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7270 (mt-10)
REVERT: A  689 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7200 (pp)
REVERT: A  706 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6408 (pp20)
REVERT: A  789 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6844 (mp-120)
REVERT: A  827 VAL cc_start: 0.7654 (t) cc_final: 0.7180 (m)
  outliers start: 27
  outliers final: 13
  residues processed: 164
  average time/residue: 0.6623
  time to fit residues: 118.3061
Evaluate side-chains
  168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  133 ASN
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  789 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 124 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
A 133 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.193302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.176126 restraints weight = 12926.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.18
r_work: 0.3975 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3873 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12966  Z= 0.135
  Angle     :  0.539   5.395  17528  Z= 0.285
  Chirality :  0.041   0.153   1922
  Planarity :  0.003   0.032   2240
  Dihedral  :  4.997  46.837   1702
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.13 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.21), residues: 1544
  helix:  1.13 (0.18), residues: 824
  sheet: -0.11 (0.36), residues: 190
  loop : -0.93 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.016   0.002   TYR B  90 
 PHE   0.016   0.001   PHE B 166 
 TRP   0.012   0.001   TRP B 361 
 HIS   0.004   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12964)
  covalent geometry    : angle       0.53881 (17528)
  hydrogen bonds       : bond        0.04119 (  663)
  hydrogen bonds       : angle       4.74958 ( 1845)
  Misc. bond           : bond        0.00067 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.506 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6776 (mttp)
REVERT: B   84 TYR cc_start: 0.7282 (t80) cc_final: 0.6999 (t80)
REVERT: B  165 ILE cc_start: 0.5610 (OUTLIER) cc_final: 0.4918 (tp)
REVERT: B  205 LYS cc_start: 0.6456 (mmmt) cc_final: 0.6120 (mmmm)
REVERT: B  385 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7277 (mt-10)
REVERT: B  706 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6398 (pp20)
REVERT: B  764 MET cc_start: 0.7459 (tmm) cc_final: 0.7219 (tmt)
REVERT: B  789 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6886 (mp-120)
REVERT: B  827 VAL cc_start: 0.7661 (t) cc_final: 0.7184 (m)
REVERT: A   29 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6797 (mtmp)
REVERT: A   84 TYR cc_start: 0.7292 (t80) cc_final: 0.7011 (t80)
REVERT: A  165 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.4918 (tp)
REVERT: A  197 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6637 (tmt)
REVERT: A  205 LYS cc_start: 0.6477 (mmmt) cc_final: 0.6158 (mmmm)
REVERT: A  385 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7280 (mt-10)
REVERT: A  706 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6428 (pp20)
REVERT: A  789 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6852 (mp-120)
REVERT: A  827 VAL cc_start: 0.7671 (t) cc_final: 0.7199 (m)
  outliers start: 30
  outliers final: 14
  residues processed: 161
  average time/residue: 0.6721
  time to fit residues: 117.9103
Evaluate side-chains
  167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 142
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  789 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 52 optimal weight:    0.4980
   chunk 134 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 137 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
** A 133 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 = 0.4259 r_free = 0.4259 target = 0.193512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.176412 restraints weight = 12823.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 1.17
r_work: 0.3979 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3878 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12966  Z= 0.136
  Angle     :  0.549   6.573  17528  Z= 0.290
  Chirality :  0.041   0.151   1922
  Planarity :  0.003   0.032   2240
  Dihedral  :  5.008  47.671   1702
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.98 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.21), residues: 1544
  helix:  1.12 (0.18), residues: 824
  sheet: -0.12 (0.36), residues: 190
  loop : -0.94 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.016   0.002   TYR A  90 
 PHE   0.015   0.001   PHE B 166 
 TRP   0.010   0.001   TRP B 365 
 HIS   0.004   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (12964)
  covalent geometry    : angle       0.54923 (17528)
  hydrogen bonds       : bond        0.04132 (  663)
  hydrogen bonds       : angle       4.77117 ( 1845)
  Misc. bond           : bond        0.00064 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.500 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6780 (mttp)
REVERT: B   84 TYR cc_start: 0.7175 (t80) cc_final: 0.6888 (t80)
REVERT: B  165 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.4927 (tp)
REVERT: B  205 LYS cc_start: 0.6440 (mmmt) cc_final: 0.6119 (mmmm)
REVERT: B  385 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7266 (mt-10)
REVERT: B  689 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7429 (pp)
REVERT: B  706 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6395 (pp20)
REVERT: B  764 MET cc_start: 0.7470 (tmm) cc_final: 0.7230 (tmt)
REVERT: B  789 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6867 (mp-120)
REVERT: B  827 VAL cc_start: 0.7664 (t) cc_final: 0.7186 (m)
REVERT: A   29 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6800 (mtmp)
REVERT: A   84 TYR cc_start: 0.7116 (t80) cc_final: 0.6835 (t80)
REVERT: A  165 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.4910 (tp)
REVERT: A  197 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6581 (tmt)
REVERT: A  205 LYS cc_start: 0.6469 (mmmt) cc_final: 0.6163 (mmmm)
REVERT: A  385 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7273 (mt-10)
REVERT: A  706 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6385 (pp20)
REVERT: A  759 LYS cc_start: 0.7646 (mptt) cc_final: 0.6779 (pmtt)
REVERT: A  789 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6843 (mp-120)
REVERT: A  827 VAL cc_start: 0.7667 (t) cc_final: 0.7191 (m)
  outliers start: 32
  outliers final: 17
  residues processed: 163
  average time/residue: 0.6661
  time to fit residues: 118.1370
Evaluate side-chains
  169 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  421 ASP
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  689 ILE
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  133 ASN
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  789 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 130 optimal weight:    1.9990
   chunk 153 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 134 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
** A 133 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 = 0.4258 r_free = 0.4258 target = 0.193572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.176504 restraints weight = 12948.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 1.18
r_work: 0.3981 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3880 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12966  Z= 0.132
  Angle     :  0.552   9.964  17528  Z= 0.290
  Chirality :  0.041   0.147   1922
  Planarity :  0.003   0.031   2240
  Dihedral  :  5.002  48.081   1702
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.69 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.21), residues: 1544
  helix:  1.15 (0.18), residues: 824
  sheet: -0.09 (0.36), residues: 190
  loop : -0.94 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.015   0.002   TYR B  90 
 PHE   0.015   0.001   PHE B 166 
 TRP   0.013   0.001   TRP B 365 
 HIS   0.003   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12964)
  covalent geometry    : angle       0.55153 (17528)
  hydrogen bonds       : bond        0.04056 (  663)
  hydrogen bonds       : angle       4.76520 ( 1845)
  Misc. bond           : bond        0.00059 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 149
  time to evaluate  : 0.507 
Fit side-chains
REVERT: B   29 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6772 (mttp)
REVERT: B  165 ILE cc_start: 0.5590 (OUTLIER) cc_final: 0.4909 (tp)
REVERT: B  205 LYS cc_start: 0.6482 (mmmt) cc_final: 0.6165 (mmmm)
REVERT: B  385 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7259 (mt-10)
REVERT: B  689 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7433 (pp)
REVERT: B  706 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6396 (pp20)
REVERT: B  759 LYS cc_start: 0.7648 (mptt) cc_final: 0.6771 (pmtt)
REVERT: B  764 MET cc_start: 0.7470 (tmm) cc_final: 0.7227 (tmt)
REVERT: B  789 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6855 (mp-120)
REVERT: B  827 VAL cc_start: 0.7658 (t) cc_final: 0.7165 (m)
REVERT: A   29 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6795 (mtmp)
REVERT: A  165 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.4898 (tp)
REVERT: A  197 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6609 (tmt)
REVERT: A  205 LYS cc_start: 0.6486 (mmmt) cc_final: 0.6138 (mmmm)
REVERT: A  385 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7277 (mt-10)
REVERT: A  706 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6396 (pp20)
REVERT: A  789 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6850 (mp-120)
REVERT: A  827 VAL cc_start: 0.7664 (t) cc_final: 0.7176 (m)
  outliers start: 35
  outliers final: 15
  residues processed: 169
  average time/residue: 0.6830
  time to fit residues: 125.2867
Evaluate side-chains
  176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  689 ILE
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  706 GLU
Chi-restraints excluded: chain A residue  789 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 45 optimal weight:    0.0980
   chunk 108 optimal weight:    0.0870
   chunk 39 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0670
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.196717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.179848 restraints weight = 12972.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.4120 rms_B_bonded: 1.17
r_work: 0.4020 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060  12966  Z= 0.107
  Angle     :  0.514   9.415  17528  Z= 0.272
  Chirality :  0.040   0.139   1922
  Planarity :  0.003   0.030   2240
  Dihedral  :  4.835  46.706   1702
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.42 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.21), residues: 1544
  helix:  1.36 (0.18), residues: 824
  sheet:  0.03 (0.37), residues: 190
  loop : -0.86 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 171 
 TYR   0.011   0.001   TYR A  90 
 PHE   0.017   0.001   PHE B 298 
 TRP   0.013   0.001   TRP B 365 
 HIS   0.002   0.001   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (12964)
  covalent geometry    : angle       0.51423 (17528)
  hydrogen bonds       : bond        0.03574 (  663)
  hydrogen bonds       : angle       4.66799 ( 1845)
  Misc. bond           : bond        0.00033 (    2)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.534 
Fit side-chains
REVERT: B  205 LYS cc_start: 0.6382 (mmmt) cc_final: 0.6075 (mmmm)
REVERT: B  385 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7323 (mt-10)
REVERT: B  533 GLU cc_start: 0.5040 (tp30) cc_final: 0.4733 (tm-30)
REVERT: B  689 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7500 (pp)
REVERT: B  706 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6442 (pp20)
REVERT: B  759 LYS cc_start: 0.7650 (mptt) cc_final: 0.6788 (pmtt)
REVERT: B  764 MET cc_start: 0.7435 (tmm) cc_final: 0.7080 (tmt)
REVERT: B  789 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6840 (mp-120)
REVERT: B  827 VAL cc_start: 0.7647 (t) cc_final: 0.7131 (m)
REVERT: A   29 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6756 (mtmp)
REVERT: A  205 LYS cc_start: 0.6417 (mmmt) cc_final: 0.6114 (mmmm)
REVERT: A  385 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7327 (mt-10)
REVERT: A  533 GLU cc_start: 0.4940 (tp30) cc_final: 0.4681 (tm-30)
REVERT: A  706 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6428 (pp20)
REVERT: A  759 LYS cc_start: 0.7698 (mptt) cc_final: 0.6793 (pmtt)
REVERT: A  827 VAL cc_start: 0.7648 (t) cc_final: 0.7132 (m)
  outliers start: 26
  outliers final: 16
  residues processed: 158
  average time/residue: 0.7150
  time to fit residues: 122.7665
Evaluate side-chains
  163 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  206 VAL
Chi-restraints excluded: chain B residue  385 GLU
Chi-restraints excluded: chain B residue  599 VAL
Chi-restraints excluded: chain B residue  615 MET
Chi-restraints excluded: chain B residue  635 MET
Chi-restraints excluded: chain B residue  689 ILE
Chi-restraints excluded: chain B residue  706 GLU
Chi-restraints excluded: chain B residue  789 GLN
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  421 ASP
Chi-restraints excluded: chain A residue  599 VAL
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  689 ILE
Chi-restraints excluded: chain A residue  706 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 123 optimal weight:    0.0980
   chunk 77 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.194727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.177532 restraints weight = 12852.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 1.18
r_work: 0.3987 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.3886 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  12966  Z= 0.135
  Angle     :  0.570  11.004  17528  Z= 0.298
  Chirality :  0.042   0.178   1922
  Planarity :  0.003   0.031   2240
  Dihedral  :  4.989  48.579   1702
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.42 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.21), residues: 1544
  helix:  1.23 (0.18), residues: 826
  sheet: -0.11 (0.36), residues: 190
  loop : -0.87 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  49 
 TYR   0.014   0.002   TYR B  90 
 PHE   0.016   0.002   PHE A 166 
 TRP   0.013   0.001   TRP B 365 
 HIS   0.003   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12964)
  covalent geometry    : angle       0.56968 (17528)
  hydrogen bonds       : bond        0.04057 (  663)
  hydrogen bonds       : angle       4.74536 ( 1845)
  Misc. bond           : bond        0.00065 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4241.85 seconds
wall clock time: 73 minutes 22.99 seconds (4402.99 seconds total)