Starting phenix.real_space_refine
on Wed Mar  4 02:03:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dra_27675/03_2026/8dra_27675.map"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    6369      2.51       5
     N    1713      2.21       5
     O    1785      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9899
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "F"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3257
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 17, 'TRANS': 386}
  Time building chain proxies: 2.34, per 1000 atoms: 0.24
  Number of scatterers: 9899
  At special positions: 0
  Unit cell: (119.472, 114.232, 92.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1785      8.00
     N    1713      7.00
     C    6369      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 468.5 milliseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      33.2% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.637A  pdb=" N   PHE A 443 " --> pdb=" O   PRO A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 467
      removed outlier: 3.527A  pdb=" N   ILE A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
    Processing helix  chain 'A' and resid 536 through 542
      removed outlier: 3.889A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
      removed outlier: 3.694A  pdb=" N   THR A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 3.911A  pdb=" N   LYS A 588 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS A 589 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 613
    Processing helix  chain 'A' and resid 629 through 638
      removed outlier: 3.954A  pdb=" N   ILE A 633 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.606A  pdb=" N   CYS A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 706
    Processing helix  chain 'A' and resid 724 through 730
      removed outlier: 3.644A  pdb=" N   CYS A 730 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 753
      removed outlier: 3.549A  pdb=" N   VAL A 750 " --> pdb=" O   PRO A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
      removed outlier: 3.655A  pdb=" N   CYS A 776 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 793
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'B' and resid 403 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 440 through 445
    Processing helix  chain 'B' and resid 462 through 468
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.647A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.878A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 508 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 586 through 590
      removed outlier: 4.011A  pdb=" N   LYS B 589 " --> pdb=" O   SER B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
      removed outlier: 3.512A  pdb=" N   LEU B 613 " --> pdb=" O   ILE B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 638
      removed outlier: 3.756A  pdb=" N   HIS B 637 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.718A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B 661 " --> pdb=" O   ILE B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.866A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 705
      removed outlier: 3.619A  pdb=" N   ILE B 704 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 729
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.638A  pdb=" N   VAL B 750 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 776
      removed outlier: 3.510A  pdb=" N   CYS B 776 " --> pdb=" O   LEU B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'F' and resid 401 through 409
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 460 through 466
      removed outlier: 3.649A  pdb=" N   ILE F 463 " --> pdb=" O   PRO F 460 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 482 through 493
    Processing helix  chain 'F' and resid 502 through 506
    Processing helix  chain 'F' and resid 508 through 513
      removed outlier: 3.710A  pdb=" N   TYR F 511 " --> pdb=" O   PRO F 508 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU F 513 " --> pdb=" O   MET F 510 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 534 through 540
      removed outlier: 4.042A  pdb=" N   ARG F 539 " --> pdb=" O   GLU F 536 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 557 through 563
      removed outlier: 3.573A  pdb=" N   VAL F 561 " --> pdb=" O   PRO F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 582 through 587
    Processing helix  chain 'F' and resid 605 through 610
    Processing helix  chain 'F' and resid 629 through 636
      removed outlier: 4.564A  pdb=" N   GLN F 634 " --> pdb=" O   VAL F 631 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 653 through 659
      removed outlier: 3.797A  pdb=" N   ILE F 656 " --> pdb=" O   PRO F 653 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU F 659 " --> pdb=" O   ILE F 656 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 676 through 682
      removed outlier: 3.938A  pdb=" N   PHE F 680 " --> pdb=" O   PRO F 676 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   CYS F 682 " --> pdb=" O   HIS F 678 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 699 through 705
      removed outlier: 3.537A  pdb=" N   ILE F 702 " --> pdb=" O   PRO F 699 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLY F 703 " --> pdb=" O   PRO F 700 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 724 through 728
    Processing helix  chain 'F' and resid 768 through 774
      removed outlier: 3.696A  pdb=" N   CYS F 774 " --> pdb=" O   LEU F 771 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 785 through 791
    Processing helix  chain 'F' and resid 793 through 802
      removed outlier: 3.839A  pdb=" N   MET F 800 " --> pdb=" O   VAL F 796 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.379A  pdb=" N   LEU A 428 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LYS A 452 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   LEU A 430 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   GLU A 454 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   LEU A 432 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU A 451 " --> pdb=" O   TRP A 475 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   LEU A 453 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU A 572 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ILE A 574 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU A 596 " --> pdb=" O   ASP A 620 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ILE A 619 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 461
      removed outlier: 6.351A  pdb=" N   VAL A 459 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668
      removed outlier: 3.660A  pdb=" N   ASP A 691 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760
      removed outlier: 6.341A  pdb=" N   ILE A 759 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.518A  pdb=" N   LEU B 428 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LYS B 452 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   LEU B 430 " --> pdb=" O   LYS B 452 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   GLU B 454 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 432 " --> pdb=" O   GLU B 454 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU B 498 " --> pdb=" O   HIS B 522 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   THR B 524 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B 500 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU B 667 " --> pdb=" O   ASP B 691 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461
    Processing sheet with id=AA7, first strand: chain 'B' and resid 712 through 714
      removed outlier: 7.029A  pdb=" N   LEU B 713 " --> pdb=" O   HIS B 737 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 419 through 420
      removed outlier: 6.080A  pdb=" N   LEU F 426 " --> pdb=" O   SER F 448 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   LYS F 450 " --> pdb=" O   LEU F 426 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LEU F 428 " --> pdb=" O   LYS F 450 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU F 449 " --> pdb=" O   CYS F 473 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   HIS F 475 " --> pdb=" O   LEU F 449 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU F 451 " --> pdb=" O   HIS F 475 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU F 472 " --> pdb=" O   SER F 497 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU F 474 " --> pdb=" O   LYS F 499 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   MET F 570 " --> pdb=" O   GLU F 595 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL F 597 " --> pdb=" O   MET F 570 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL F 572 " --> pdb=" O   VAL F 597 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU F 617 " --> pdb=" O   LYS F 643 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS F 735 " --> pdb=" O   PHE F 711 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP F 758 " --> pdb=" O   LEU F 734 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU F 757 " --> pdb=" O   VAL F 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 457 through 459
      removed outlier: 5.735A  pdb=" N   VAL F 457 " --> pdb=" O   LYS F 480 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    238 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3172
        1.34 -     1.46: 1052
        1.46 -     1.57: 5803
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 10071
  Sorted by residual:
  bond pdb=" N   ASP F 540 "
       pdb=" CA  ASP F 540 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.56e+00
  bond pdb=" N   ASN F 456 "
       pdb=" CA  ASN F 456 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.022 1.29e-02 6.01e+03 3.03e+00
  bond pdb=" CB  TRP B 411 "
       pdb=" CG  TRP B 411 "
    ideal  model  delta    sigma   weight residual
    1.498  1.538 -0.040 3.10e-02 1.04e+03 1.70e+00
  bond pdb=" CB  PRO F 507 "
       pdb=" CG  PRO F 507 "
    ideal  model  delta    sigma   weight residual
    1.492  1.556 -0.064 5.00e-02 4.00e+02 1.65e+00
  bond pdb=" C   PRO A 607 "
       pdb=" O   PRO A 607 "
    ideal  model  delta    sigma   weight residual
    1.235  1.219  0.016 1.30e-02 5.92e+03 1.52e+00
  ... (remaining 10066 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 13252
        1.96 -     3.91: 310
        3.91 -     5.87: 55
        5.87 -     7.82: 18
        7.82 -     9.78: 7
  Bond angle restraints: 13642
  Sorted by residual:
  angle pdb=" CA  LYS F 555 "
        pdb=" CB  LYS F 555 "
        pdb=" CG  LYS F 555 "
      ideal   model   delta    sigma   weight residual
     114.10  122.88   -8.78 2.00e+00 2.50e-01 1.93e+01
  angle pdb=" N   ILE F 713 "
        pdb=" CA  ILE F 713 "
        pdb=" C   ILE F 713 "
      ideal   model   delta    sigma   weight residual
     112.17  108.09    4.08 9.50e-01 1.11e+00 1.85e+01
  angle pdb=" CA  VAL B 715 "
        pdb=" CB  VAL B 715 "
        pdb=" CG1 VAL B 715 "
      ideal   model   delta    sigma   weight residual
     110.40  116.85   -6.45 1.70e+00 3.46e-01 1.44e+01
  angle pdb=" C   SER B 553 "
        pdb=" N   ASN B 554 "
        pdb=" CA  ASN B 554 "
      ideal   model   delta    sigma   weight residual
     121.54  128.42   -6.88 1.91e+00 2.74e-01 1.30e+01
  angle pdb=" CA  MET F 581 "
        pdb=" CB  MET F 581 "
        pdb=" CG  MET F 581 "
      ideal   model   delta    sigma   weight residual
     114.10  121.28   -7.18 2.00e+00 2.50e-01 1.29e+01
  ... (remaining 13637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5469
       17.83 -    35.65: 595
       35.65 -    53.48: 157
       53.48 -    71.30: 24
       71.30 -    89.13: 5
  Dihedral angle restraints: 6250
    sinusoidal: 2646
      harmonic: 3604
  Sorted by residual:
  dihedral pdb=" CA  ASP B 703 "
           pdb=" C   ASP B 703 "
           pdb=" N   ILE B 704 "
           pdb=" CA  ILE B 704 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.66   20.34     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  PRO B 747 "
           pdb=" C   PRO B 747 "
           pdb=" N   SER B 748 "
           pdb=" CA  SER B 748 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.82  -19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  GLN B 758 "
           pdb=" C   GLN B 758 "
           pdb=" N   ILE B 759 "
           pdb=" CA  ILE B 759 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.93   18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 6247 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1325
       0.056 -    0.111: 267
       0.111 -    0.167: 34
       0.167 -    0.222: 5
       0.222 -    0.278: 2
  Chirality restraints: 1633
  Sorted by residual:
  chirality pdb=" CB  ILE B 677 "
            pdb=" CA  ILE B 677 "
            pdb=" CG1 ILE B 677 "
            pdb=" CG2 ILE B 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CB  ILE B 456 "
            pdb=" CA  ILE B 456 "
            pdb=" CG1 ILE B 456 "
            pdb=" CG2 ILE B 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ASN F 456 "
            pdb=" N   ASN F 456 "
            pdb=" C   ASN F 456 "
            pdb=" CB  ASN F 456 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.98e-01
  ... (remaining 1630 not shown)

  Planarity restraints: 1715
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 795 "    0.047 5.00e-02 4.00e+02   7.16e-02 8.20e+00
        pdb=" N   PRO A 796 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 796 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 796 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 438 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO B 439 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 439 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 439 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 475 "   -0.009 2.00e-02 2.50e+03   1.45e-02 5.27e+00
        pdb=" CG  TRP A 475 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 475 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 475 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 475 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 475 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 475 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 475 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 475 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 475 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1712 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2095
        2.79 -     3.31: 9310
        3.31 -     3.84: 17119
        3.84 -     4.37: 21342
        4.37 -     4.90: 33726
  Nonbonded interactions: 83592
  Sorted by model distance:
  nonbonded pdb=" O   ILE F 556 "
            pdb=" ND2 ASN F 584 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   TRP A 411 "
            pdb=" OG1 THR A 441 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   GLN A 560 "
            pdb=" OG1 THR A 563 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   GLU F 790 "
            pdb=" NH2 ARG F 797 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" NH1 ARG B 749 "
            pdb=" OE1 GLU B 752 "
     model   vdw
     2.313 3.120
  ... (remaining 83587 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.870
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.190
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10071  Z= 0.157
  Angle     :  0.766   9.779  13642  Z= 0.399
  Chirality :  0.046   0.278   1633
  Planarity :  0.006   0.072   1715
  Dihedral  : 15.743  89.126   3886
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 21.09 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.23), residues: 1212
  helix: -2.86 (0.22), residues: 369
  sheet: -2.58 (0.37), residues: 182
  loop : -1.18 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 749 
 TYR   0.016   0.001   TYR F 756 
 PHE   0.029   0.002   PHE F 609 
 TRP   0.033   0.003   TRP A 475 
 HIS   0.009   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10071)
  covalent geometry    : angle       0.76596 (13642)
  hydrogen bonds       : bond        0.22086 (  238)
  hydrogen bonds       : angle       8.77381 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 377
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 GLU cc_start: 0.8048 (pm20) cc_final: 0.7523 (pm20)
REVERT: A  534 TYR cc_start: 0.7233 (m-80) cc_final: 0.6984 (m-10)
REVERT: A  540 LEU cc_start: 0.9316 (mt) cc_final: 0.9112 (mt)
REVERT: A  616 LEU cc_start: 0.7902 (mt) cc_final: 0.7360 (mt)
REVERT: A  624 ASN cc_start: 0.8522 (m-40) cc_final: 0.8190 (m-40)
REVERT: A  626 LEU cc_start: 0.8220 (mt) cc_final: 0.7558 (mp)
REVERT: A  682 PHE cc_start: 0.8523 (m-10) cc_final: 0.8263 (m-80)
REVERT: B  503 THR cc_start: 0.8813 (m) cc_final: 0.8599 (p)
REVERT: B  570 GLN cc_start: 0.7773 (mt0) cc_final: 0.7380 (mm110)
REVERT: B  623 ASP cc_start: 0.7996 (t0) cc_final: 0.7507 (t0)
REVERT: B  637 HIS cc_start: 0.7817 (m90) cc_final: 0.6765 (t-90)
REVERT: B  644 LEU cc_start: 0.8857 (pt) cc_final: 0.8576 (tp)
REVERT: B  648 TYR cc_start: 0.8373 (m-80) cc_final: 0.8084 (m-10)
REVERT: B  664 LEU cc_start: 0.9077 (tp) cc_final: 0.8836 (tp)
REVERT: B  682 PHE cc_start: 0.8600 (m-80) cc_final: 0.8219 (m-80)
REVERT: F  428 LEU cc_start: 0.9160 (mt) cc_final: 0.8958 (mt)
REVERT: F  476 GLN cc_start: 0.7831 (mp-120) cc_final: 0.6511 (mm-40)
REVERT: F  490 LYS cc_start: 0.9409 (tttt) cc_final: 0.9146 (ttpp)
REVERT: F  504 ARG cc_start: 0.8292 (tpt170) cc_final: 0.8074 (tpt90)
REVERT: F  545 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8508 (mmmt)
REVERT: F  567 LEU cc_start: 0.7844 (tp) cc_final: 0.7429 (tp)
REVERT: F  637 ARG cc_start: 0.7585 (ptp90) cc_final: 0.7343 (ptp90)
REVERT: F  777 LEU cc_start: 0.7998 (tp) cc_final: 0.7533 (tp)
  outliers start: 4
  outliers final: 0
  residues processed: 378
  average time/residue: 0.1080
  time to fit residues: 54.6089
Evaluate side-chains
  218 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 478 HIS
** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 558 GLN
F 635 HIS
F 693 ASN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.114278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.093054 restraints weight = 33277.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.094105 restraints weight = 21141.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.094596 restraints weight = 15544.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.095319 restraints weight = 14027.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.095475 restraints weight = 13542.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10071  Z= 0.182
  Angle     :  0.736   8.702  13642  Z= 0.361
  Chirality :  0.047   0.352   1633
  Planarity :  0.005   0.062   1715
  Dihedral  :  5.044  23.428   1303
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.48 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.24), residues: 1212
  helix: -2.51 (0.24), residues: 355
  sheet: -2.71 (0.35), residues: 191
  loop : -0.94 (0.25), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 749 
 TYR   0.020   0.002   TYR A 513 
 PHE   0.022   0.002   PHE F 609 
 TRP   0.013   0.002   TRP B 647 
 HIS   0.003   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10071)
  covalent geometry    : angle       0.73634 (13642)
  hydrogen bonds       : bond        0.04867 (  238)
  hydrogen bonds       : angle       7.08536 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 216
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  451 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7784 (pt)
REVERT: A  512 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8320 (pt)
REVERT: A  534 TYR cc_start: 0.5980 (m-80) cc_final: 0.5517 (m-10)
REVERT: A  629 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8240 (mt)
REVERT: A  646 LEU cc_start: 0.8870 (mt) cc_final: 0.8420 (mt)
REVERT: B  614 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.6423 (t70)
REVERT: F  446 LEU cc_start: 0.8936 (tp) cc_final: 0.8710 (tp)
REVERT: F  452 GLU cc_start: 0.7693 (tt0) cc_final: 0.7386 (tt0)
REVERT: F  567 LEU cc_start: 0.7790 (tp) cc_final: 0.7199 (tp)
REVERT: F  570 MET cc_start: 0.8479 (tmm) cc_final: 0.8216 (tmm)
REVERT: F  584 ASN cc_start: 0.5708 (m-40) cc_final: 0.4642 (m110)
REVERT: F  599 CYS cc_start: 0.8462 (m) cc_final: 0.8236 (m)
REVERT: F  616 GLU cc_start: 0.8090 (pt0) cc_final: 0.7853 (pt0)
REVERT: F  638 LYS cc_start: 0.7060 (mttt) cc_final: 0.6639 (ptmt)
REVERT: F  686 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7030 (ptp-170)
  outliers start: 42
  outliers final: 21
  residues processed: 244
  average time/residue: 0.0901
  time to fit residues: 31.0340
Evaluate side-chains
  213 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  757 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 101 optimal weight:    9.9990
   chunk 77 optimal weight:    0.1980
   chunk 56 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 50 optimal weight:    0.3980
   chunk 107 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 711 GLN
B 650 HIS
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 402 GLN
** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 532 ASN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.114079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.091313 restraints weight = 33344.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.092601 restraints weight = 21521.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.094169 restraints weight = 14591.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.094362 restraints weight = 11233.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.094701 restraints weight = 11258.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10071  Z= 0.137
  Angle     :  0.691  10.591  13642  Z= 0.333
  Chirality :  0.045   0.299   1633
  Planarity :  0.005   0.058   1715
  Dihedral  :  4.956  21.892   1303
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 24.78 %
    Favored  : 70.74 %
  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 are not related in a simple way.
  whole: -2.52 (0.24), residues: 1212
  helix: -2.32 (0.25), residues: 345
  sheet: -2.50 (0.37), residues: 193
  loop : -0.93 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 504 
 TYR   0.012   0.002   TYR F 756 
 PHE   0.021   0.002   PHE F 609 
 TRP   0.011   0.002   TRP B 647 
 HIS   0.004   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10071)
  covalent geometry    : angle       0.69078 (13642)
  hydrogen bonds       : bond        0.03889 (  238)
  hydrogen bonds       : angle       6.56101 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 198
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: A  451 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (pt)
REVERT: A  615 ASN cc_start: 0.7393 (m110) cc_final: 0.6682 (t0)
REVERT: A  784 LEU cc_start: 0.8857 (tp) cc_final: 0.8475 (tt)
REVERT: B  438 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (mp)
REVERT: B  550 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7815 (mtt-85)
REVERT: B  700 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6993 (tt)
REVERT: B  711 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8079 (tm-30)
REVERT: F  446 LEU cc_start: 0.8811 (tp) cc_final: 0.8567 (tp)
REVERT: F  567 LEU cc_start: 0.7704 (tp) cc_final: 0.7295 (tp)
REVERT: F  570 MET cc_start: 0.8578 (tmm) cc_final: 0.8293 (tmm)
REVERT: F  599 CYS cc_start: 0.8404 (m) cc_final: 0.8049 (m)
REVERT: F  617 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8072 (mt)
REVERT: F  638 LYS cc_start: 0.7136 (mttt) cc_final: 0.6741 (ptmt)
REVERT: F  643 LYS cc_start: 0.8061 (mttt) cc_final: 0.7636 (mttm)
REVERT: F  686 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6997 (ptp-170)
REVERT: F  711 PHE cc_start: 0.8164 (t80) cc_final: 0.7897 (t80)
  outliers start: 51
  outliers final: 27
  residues processed: 224
  average time/residue: 0.0734
  time to fit residues: 24.7526
Evaluate side-chains
  201 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  711 GLN
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain F residue  472 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  757 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 92 optimal weight:    0.2980
   chunk 69 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 598 HIS
** F 716 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 = 0.4104 r_free = 0.4104 target = 0.113397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.090374 restraints weight = 33861.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.091440 restraints weight = 22140.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.093136 restraints weight = 15290.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.093209 restraints weight = 12011.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.093572 restraints weight = 11735.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10071  Z= 0.132
  Angle     :  0.677  17.727  13642  Z= 0.322
  Chirality :  0.045   0.268   1633
  Planarity :  0.004   0.044   1715
  Dihedral  :  4.830  20.567   1303
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.31 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.24), residues: 1212
  helix: -2.55 (0.24), residues: 374
  sheet: -2.49 (0.37), residues: 199
  loop : -0.99 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 749 
 TYR   0.030   0.002   TYR F 756 
 PHE   0.020   0.002   PHE F 609 
 TRP   0.011   0.001   TRP F 645 
 HIS   0.004   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10071)
  covalent geometry    : angle       0.67692 (13642)
  hydrogen bonds       : bond        0.03519 (  238)
  hydrogen bonds       : angle       6.33336 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 179
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8410 (mp)
REVERT: A  519 GLU cc_start: 0.7944 (mp0) cc_final: 0.7676 (mp0)
REVERT: A  615 ASN cc_start: 0.7424 (m110) cc_final: 0.6710 (t0)
REVERT: A  626 LEU cc_start: 0.8490 (mt) cc_final: 0.8281 (mt)
REVERT: B  438 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8568 (mp)
REVERT: B  550 ARG cc_start: 0.8469 (mtt90) cc_final: 0.7904 (mtt-85)
REVERT: B  590 MET cc_start: 0.7995 (mpp) cc_final: 0.7782 (mpp)
REVERT: B  700 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6830 (tt)
REVERT: B  754 THR cc_start: 0.5411 (OUTLIER) cc_final: 0.5021 (p)
REVERT: F  446 LEU cc_start: 0.8837 (tp) cc_final: 0.8356 (tp)
REVERT: F  545 LYS cc_start: 0.8677 (ptpt) cc_final: 0.8349 (mmmt)
REVERT: F  567 LEU cc_start: 0.7723 (tp) cc_final: 0.7392 (tp)
REVERT: F  570 MET cc_start: 0.8622 (tmm) cc_final: 0.8253 (tmm)
REVERT: F  588 MET cc_start: 0.7435 (mmm) cc_final: 0.7139 (mmm)
REVERT: F  599 CYS cc_start: 0.8294 (m) cc_final: 0.8066 (m)
REVERT: F  617 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (mt)
REVERT: F  638 LYS cc_start: 0.7218 (mttt) cc_final: 0.6801 (ptmt)
REVERT: F  643 LYS cc_start: 0.8021 (mttt) cc_final: 0.7572 (mttm)
REVERT: F  686 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7034 (ptp-170)
REVERT: F  693 ASN cc_start: 0.7297 (m-40) cc_final: 0.6966 (m-40)
REVERT: F  711 PHE cc_start: 0.8195 (t80) cc_final: 0.7903 (t80)
REVERT: F  727 PHE cc_start: 0.8466 (t80) cc_final: 0.8239 (m-80)
  outliers start: 53
  outliers final: 30
  residues processed: 212
  average time/residue: 0.0805
  time to fit residues: 25.0730
Evaluate side-chains
  197 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  687 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0770
   chunk 117 optimal weight:    0.0870
   chunk 68 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.2322

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 ASN
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 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 = 0.4131 r_free = 0.4131 target = 0.114003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.094758 restraints weight = 35327.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.095120 restraints weight = 22412.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.095868 restraints weight = 18289.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.096225 restraints weight = 14878.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.096509 restraints weight = 14378.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10071  Z= 0.143
  Angle     :  0.681  14.923  13642  Z= 0.324
  Chirality :  0.045   0.242   1633
  Planarity :  0.005   0.054   1715
  Dihedral  :  4.824  23.199   1303
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 26.36 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.24), residues: 1212
  helix: -2.53 (0.24), residues: 367
  sheet: -2.60 (0.35), residues: 210
  loop : -0.83 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 797 
 TYR   0.017   0.002   TYR B 689 
 PHE   0.016   0.002   PHE F 609 
 TRP   0.013   0.001   TRP B 647 
 HIS   0.004   0.001   HIS F 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10071)
  covalent geometry    : angle       0.68055 (13642)
  hydrogen bonds       : bond        0.03354 (  238)
  hydrogen bonds       : angle       6.15014 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 166
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8381 (mp)
REVERT: A  615 ASN cc_start: 0.7207 (m110) cc_final: 0.6550 (t0)
REVERT: B  438 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8548 (mp)
REVERT: B  550 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7629 (mtt-85)
REVERT: B  590 MET cc_start: 0.7935 (mpp) cc_final: 0.7686 (mpp)
REVERT: B  723 LEU cc_start: 0.8229 (tp) cc_final: 0.7830 (tp)
REVERT: B  727 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6913 (pp)
REVERT: B  754 THR cc_start: 0.5133 (OUTLIER) cc_final: 0.4773 (p)
REVERT: F  545 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8158 (mmmt)
REVERT: F  567 LEU cc_start: 0.7414 (tp) cc_final: 0.7207 (tp)
REVERT: F  588 MET cc_start: 0.7280 (mmm) cc_final: 0.6886 (mmm)
REVERT: F  611 LEU cc_start: 0.8632 (mm) cc_final: 0.8381 (mm)
REVERT: F  617 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7984 (mt)
REVERT: F  638 LYS cc_start: 0.7218 (mttt) cc_final: 0.6909 (ptmt)
REVERT: F  643 LYS cc_start: 0.8007 (mttt) cc_final: 0.7183 (mttm)
REVERT: F  645 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.4991 (p90)
REVERT: F  686 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6926 (ptp-170)
  outliers start: 54
  outliers final: 31
  residues processed: 204
  average time/residue: 0.0762
  time to fit residues: 23.1107
Evaluate side-chains
  192 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 154
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 111 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 115 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 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 = 0.4088 r_free = 0.4088 target = 0.113006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.090942 restraints weight = 33939.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.091413 restraints weight = 23523.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.092803 restraints weight = 16359.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.092789 restraints weight = 13770.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.093047 restraints weight = 12830.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10071  Z= 0.118
  Angle     :  0.651  12.178  13642  Z= 0.308
  Chirality :  0.044   0.233   1633
  Planarity :  0.004   0.046   1715
  Dihedral  :  4.676  20.292   1303
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 27.59 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.24), residues: 1212
  helix: -2.55 (0.24), residues: 371
  sheet: -2.40 (0.39), residues: 190
  loop : -0.87 (0.25), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 419 
 TYR   0.017   0.002   TYR F 646 
 PHE   0.016   0.001   PHE F 609 
 TRP   0.011   0.001   TRP F 645 
 HIS   0.004   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10071)
  covalent geometry    : angle       0.65058 (13642)
  hydrogen bonds       : bond        0.03120 (  238)
  hydrogen bonds       : angle       5.94953 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 166
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  615 ASN cc_start: 0.7410 (m110) cc_final: 0.6701 (t0)
REVERT: A  626 LEU cc_start: 0.8959 (mt) cc_final: 0.8334 (mp)
REVERT: B  438 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8603 (mp)
REVERT: B  545 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7665 (ttm-80)
REVERT: B  550 ARG cc_start: 0.8402 (mtt90) cc_final: 0.7899 (mtt-85)
REVERT: B  754 THR cc_start: 0.5310 (OUTLIER) cc_final: 0.4962 (p)
REVERT: F  499 LYS cc_start: 0.8089 (tptt) cc_final: 0.7788 (tptp)
REVERT: F  545 LYS cc_start: 0.8689 (ptpt) cc_final: 0.8349 (mmmt)
REVERT: F  588 MET cc_start: 0.7228 (mmm) cc_final: 0.7009 (mmm)
REVERT: F  598 HIS cc_start: 0.8778 (t-170) cc_final: 0.8456 (t70)
REVERT: F  611 LEU cc_start: 0.8643 (mm) cc_final: 0.8303 (mm)
REVERT: F  617 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: F  633 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7444 (t80)
REVERT: F  643 LYS cc_start: 0.8017 (mttt) cc_final: 0.7228 (mttm)
REVERT: F  645 TRP cc_start: 0.6356 (OUTLIER) cc_final: 0.5248 (p90)
REVERT: F  711 PHE cc_start: 0.8234 (t80) cc_final: 0.7907 (t80)
REVERT: F  756 TYR cc_start: 0.6700 (t80) cc_final: 0.6418 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 194
  average time/residue: 0.0766
  time to fit residues: 22.1468
Evaluate side-chains
  178 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 81 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 90 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 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 = 0.4089 r_free = 0.4089 target = 0.113044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.090772 restraints weight = 33756.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.091121 restraints weight = 26456.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.092354 restraints weight = 17844.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.092893 restraints weight = 13685.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.093066 restraints weight = 12690.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10071  Z= 0.119
  Angle     :  0.669  16.425  13642  Z= 0.311
  Chirality :  0.044   0.221   1633
  Planarity :  0.004   0.046   1715
  Dihedral  :  4.625  20.092   1303
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 28.38 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.24), residues: 1212
  helix: -2.56 (0.23), residues: 384
  sheet: -2.54 (0.36), residues: 210
  loop : -0.79 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 749 
 TYR   0.015   0.001   TYR A 534 
 PHE   0.015   0.002   PHE B 433 
 TRP   0.011   0.001   TRP B 647 
 HIS   0.008   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10071)
  covalent geometry    : angle       0.66879 (13642)
  hydrogen bonds       : bond        0.03012 (  238)
  hydrogen bonds       : angle       5.82022 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  615 ASN cc_start: 0.7340 (m110) cc_final: 0.6642 (t0)
REVERT: B  438 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: B  545 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7663 (ttm-80)
REVERT: B  550 ARG cc_start: 0.8375 (mtt90) cc_final: 0.7884 (mtt-85)
REVERT: B  673 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7450 (tptp)
REVERT: B  754 THR cc_start: 0.5303 (OUTLIER) cc_final: 0.4991 (p)
REVERT: F  476 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6282 (mm110)
REVERT: F  496 LEU cc_start: 0.8359 (tt) cc_final: 0.7930 (tp)
REVERT: F  545 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8360 (mmmt)
REVERT: F  598 HIS cc_start: 0.8783 (t-170) cc_final: 0.8488 (t70)
REVERT: F  617 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8185 (mt)
REVERT: F  633 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7156 (t80)
REVERT: F  711 PHE cc_start: 0.8266 (t80) cc_final: 0.7903 (t80)
  outliers start: 43
  outliers final: 29
  residues processed: 192
  average time/residue: 0.0734
  time to fit residues: 21.3245
Evaluate side-chains
  188 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 111 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 103 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 758 GLN
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 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 = 0.4017 r_free = 0.4017 target = 0.108557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.088656 restraints weight = 34812.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.088438 restraints weight = 23324.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.089113 restraints weight = 19698.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.089400 restraints weight = 16044.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.089573 restraints weight = 15441.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10071  Z= 0.248
  Angle     :  0.808  16.766  13642  Z= 0.388
  Chirality :  0.048   0.227   1633
  Planarity :  0.005   0.051   1715
  Dihedral  :  5.093  20.775   1303
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 23.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 28.30 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.23), residues: 1212
  helix: -2.65 (0.23), residues: 370
  sheet: -2.27 (0.39), residues: 186
  loop : -1.18 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 749 
 TYR   0.019   0.002   TYR B 653 
 PHE   0.025   0.002   PHE B 728 
 TRP   0.018   0.002   TRP B 647 
 HIS   0.007   0.001   HIS F 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (10071)
  covalent geometry    : angle       0.80808 (13642)
  hydrogen bonds       : bond        0.03801 (  238)
  hydrogen bonds       : angle       6.23556 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 142
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  615 ASN cc_start: 0.7606 (m110) cc_final: 0.6890 (t0)
REVERT: A  626 LEU cc_start: 0.8596 (mt) cc_final: 0.8291 (mt)
REVERT: B  426 ASP cc_start: 0.8296 (m-30) cc_final: 0.7882 (t70)
REVERT: B  438 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8777 (mp)
REVERT: B  454 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: B  550 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7838 (mtt-85)
REVERT: B  590 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7400 (pmm)
REVERT: B  668 TYR cc_start: 0.8029 (m-10) cc_final: 0.7333 (m-10)
REVERT: B  673 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7781 (tmtt)
REVERT: B  754 THR cc_start: 0.5466 (OUTLIER) cc_final: 0.5142 (p)
REVERT: F  541 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8161 (mp)
REVERT: F  545 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8225 (mmmt)
REVERT: F  588 MET cc_start: 0.7113 (mmm) cc_final: 0.6511 (mmm)
REVERT: F  598 HIS cc_start: 0.8815 (t-170) cc_final: 0.8278 (t70)
REVERT: F  617 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8184 (mt)
REVERT: F  633 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7154 (t80)
REVERT: F  638 LYS cc_start: 0.7572 (mttt) cc_final: 0.7118 (ptmt)
REVERT: F  645 TRP cc_start: 0.6794 (OUTLIER) cc_final: 0.5989 (p90)
REVERT: F  711 PHE cc_start: 0.8191 (t80) cc_final: 0.7927 (t80)
  outliers start: 54
  outliers final: 31
  residues processed: 179
  average time/residue: 0.0748
  time to fit residues: 20.2619
Evaluate side-chains
  172 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 113 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 HIS
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 750 ASN
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.111244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089048 restraints weight = 33901.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.089682 restraints weight = 23945.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.090355 restraints weight = 16481.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.090850 restraints weight = 15171.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.091187 restraints weight = 13556.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.5432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10071  Z= 0.126
  Angle     :  0.717  17.352  13642  Z= 0.335
  Chirality :  0.046   0.212   1633
  Planarity :  0.004   0.047   1715
  Dihedral  :  4.831  19.786   1303
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 30.67 %
    Favored  : 66.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.23), residues: 1212
  helix: -2.65 (0.23), residues: 386
  sheet: -2.33 (0.37), residues: 201
  loop : -1.08 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 749 
 TYR   0.015   0.002   TYR A 534 
 PHE   0.022   0.002   PHE F 727 
 TRP   0.018   0.001   TRP B 411 
 HIS   0.008   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10071)
  covalent geometry    : angle       0.71728 (13642)
  hydrogen bonds       : bond        0.03125 (  238)
  hydrogen bonds       : angle       5.84110 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  615 ASN cc_start: 0.7355 (m110) cc_final: 0.6715 (t0)
REVERT: A  626 LEU cc_start: 0.8554 (mt) cc_final: 0.8186 (mt)
REVERT: B  426 ASP cc_start: 0.8195 (m-30) cc_final: 0.7892 (t70)
REVERT: B  438 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8795 (mp)
REVERT: B  454 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7382 (mt-10)
REVERT: B  507 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6775 (tp30)
REVERT: B  545 ARG cc_start: 0.7928 (mtt180) cc_final: 0.7676 (ttm-80)
REVERT: B  550 ARG cc_start: 0.8423 (mtt90) cc_final: 0.7896 (mtt-85)
REVERT: B  590 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7415 (pmm)
REVERT: B  668 TYR cc_start: 0.7885 (m-10) cc_final: 0.7391 (m-10)
REVERT: B  673 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7418 (tptp)
REVERT: B  754 THR cc_start: 0.5469 (OUTLIER) cc_final: 0.5180 (p)
REVERT: F  541 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8142 (mp)
REVERT: F  545 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8320 (mmmt)
REVERT: F  588 MET cc_start: 0.7093 (mmm) cc_final: 0.6507 (mmm)
REVERT: F  598 HIS cc_start: 0.8880 (t-170) cc_final: 0.8446 (t70)
REVERT: F  617 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: F  633 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7118 (t80)
REVERT: F  638 LYS cc_start: 0.7498 (mttt) cc_final: 0.7158 (ptmt)
REVERT: F  646 TYR cc_start: 0.6956 (m-10) cc_final: 0.6695 (m-10)
  outliers start: 29
  outliers final: 21
  residues processed: 175
  average time/residue: 0.0918
  time to fit residues: 22.9533
Evaluate side-chains
  178 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9990
   chunk 117 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 115 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 558 GLN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 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 = 0.4056 r_free = 0.4056 target = 0.110905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.089636 restraints weight = 33684.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.090158 restraints weight = 24806.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.091315 restraints weight = 17151.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.091481 restraints weight = 15162.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.091892 restraints weight = 13983.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.5607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10071  Z= 0.143
  Angle     :  0.736  15.051  13642  Z= 0.347
  Chirality :  0.046   0.207   1633
  Planarity :  0.005   0.061   1715
  Dihedral  :  4.825  20.742   1303
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 31.20 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.80 (0.23), residues: 1212
  helix: -2.55 (0.24), residues: 381
  sheet: -2.32 (0.36), residues: 201
  loop : -1.09 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 637 
 TYR   0.016   0.002   TYR A 534 
 PHE   0.012   0.002   PHE F 609 
 TRP   0.017   0.002   TRP B 411 
 HIS   0.007   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10071)
  covalent geometry    : angle       0.73619 (13642)
  hydrogen bonds       : bond        0.03203 (  238)
  hydrogen bonds       : angle       5.90017 (  504)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  553 SER cc_start: 0.8386 (p) cc_final: 0.7949 (p)
REVERT: A  615 ASN cc_start: 0.7415 (m110) cc_final: 0.6743 (t0)
REVERT: A  666 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8177 (mtp85)
REVERT: B  426 ASP cc_start: 0.8213 (m-30) cc_final: 0.7823 (t70)
REVERT: B  438 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8813 (mp)
REVERT: B  506 LYS cc_start: 0.8614 (tptt) cc_final: 0.8043 (tppt)
REVERT: B  507 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6954 (tp30)
REVERT: B  545 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7522 (ttm-80)
REVERT: B  550 ARG cc_start: 0.8410 (mtt90) cc_final: 0.7884 (mtt-85)
REVERT: B  590 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7450 (pmm)
REVERT: B  668 TYR cc_start: 0.7918 (m-10) cc_final: 0.7495 (m-10)
REVERT: B  673 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7435 (tptp)
REVERT: B  754 THR cc_start: 0.5332 (OUTLIER) cc_final: 0.5053 (p)
REVERT: F  541 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8232 (mp)
REVERT: F  581 MET cc_start: 0.7266 (ppp) cc_final: 0.6539 (ppp)
REVERT: F  588 MET cc_start: 0.7208 (mmm) cc_final: 0.6562 (mmm)
REVERT: F  598 HIS cc_start: 0.8880 (t-170) cc_final: 0.8440 (t70)
REVERT: F  633 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.6987 (t80)
REVERT: F  638 LYS cc_start: 0.7506 (mttt) cc_final: 0.7187 (ptmt)
REVERT: F  646 TYR cc_start: 0.6855 (m-10) cc_final: 0.6589 (m-10)
REVERT: F  711 PHE cc_start: 0.8198 (t80) cc_final: 0.7896 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 174
  average time/residue: 0.0815
  time to fit residues: 20.8744
Evaluate side-chains
  182 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 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 = 0.4038 r_free = 0.4038 target = 0.109950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.089028 restraints weight = 33903.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.089954 restraints weight = 23976.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.090394 restraints weight = 16855.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.090812 restraints weight = 15424.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.091095 restraints weight = 13703.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10071  Z= 0.168
  Angle     :  0.740  13.822  13642  Z= 0.352
  Chirality :  0.047   0.210   1633
  Planarity :  0.005   0.059   1715
  Dihedral  :  4.876  21.511   1303
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 30.32 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.23), residues: 1212
  helix: -2.54 (0.24), residues: 386
  sheet: -2.31 (0.36), residues: 203
  loop : -1.13 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 749 
 TYR   0.015   0.002   TYR A 534 
 PHE   0.029   0.002   PHE B 728 
 TRP   0.018   0.002   TRP B 411 
 HIS   0.006   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10071)
  covalent geometry    : angle       0.74040 (13642)
  hydrogen bonds       : bond        0.03248 (  238)
  hydrogen bonds       : angle       5.99029 (  504)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.84 seconds
wall clock time: 30 minutes 47.92 seconds (1847.92 seconds total)