Starting phenix.real_space_refine
on Sun Jun  8 22:59:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f75_28895/06_2025/8f75_28895.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.044
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 17 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.91, per 1000 atoms: 0.70
  Number of scatterers: 9899
  At special positions: 0
  Unit cell: (128.904, 112.136, 91.176, 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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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
      33.3% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  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: 3.528A  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: 3.888A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
      removed outlier: 3.695A  pdb=" N   THR A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 3.910A  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: 3.645A  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: 3.656A  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 420
    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: 3.648A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.877A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
      removed outlier: 3.582A  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: 4.012A  pdb=" N   LYS B 589 " --> pdb=" O   SER B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
      removed outlier: 3.513A  pdb=" N   LEU B 613 " --> pdb=" O   ILE B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 638
      removed outlier: 3.757A  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: 3.539A  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: 3.637A  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: 3.711A  pdb=" N   TYR F 511 " --> pdb=" O   PRO F 508 " (cutoff:3.500A)
      removed outlier: 3.859A  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: 3.574A  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: 3.939A  pdb=" N   PHE F 680 " --> pdb=" O   PRO F 676 " (cutoff:3.500A)
      removed outlier: 4.094A  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: 4.001A  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: 3.838A  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: 6.378A  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: 6.796A  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: 5.946A  pdb=" N   ILE A 574 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU A 596 " --> pdb=" O   ASP A 620 " (cutoff:3.500A)
      removed outlier: 7.037A  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: 6.352A  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: 6.342A  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 421 through 422
      removed outlier: 6.517A  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: 6.979A  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: 6.793A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 476 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B 498 " --> pdb=" O   HIS B 522 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   THR B 524 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ILE B 500 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 6.832A  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: 7.163A  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: 7.107A  pdb=" N   HIS F 475 " --> pdb=" O   LEU F 449 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU F 451 " --> pdb=" O   HIS F 475 " (cutoff:3.500A)
      removed outlier: 6.665A  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: 6.887A  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: 3.893A  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

    242 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 2.90 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: 3157
        1.34 -     1.46: 1064
        1.46 -     1.57: 5806
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 10071
  Sorted by residual:
  bond pdb=" N   THR B 412 "
       pdb=" CA  THR B 412 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.037 1.31e-02 5.83e+03 7.89e+00
  bond pdb=" N   ARG B 688 "
       pdb=" CA  ARG B 688 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.17e-02 7.31e+03 7.65e+00
  bond pdb=" N   ILE A 606 "
       pdb=" CA  ILE A 606 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.23e-02 6.61e+03 7.57e+00
  bond pdb=" N   HIS A 608 "
       pdb=" CA  HIS A 608 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.44e+00
  bond pdb=" N   ASP B 414 "
       pdb=" CA  ASP B 414 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.37e+00
  ... (remaining 10066 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 13156
        1.94 -     3.88: 402
        3.88 -     5.83: 56
        5.83 -     7.77: 21
        7.77 -     9.71: 7
  Bond angle restraints: 13642
  Sorted by residual:
  angle pdb=" N   ARG B 685 "
        pdb=" CA  ARG B 685 "
        pdb=" C   ARG B 685 "
      ideal   model   delta    sigma   weight residual
     113.16  122.65   -9.49 1.24e+00 6.50e-01 5.86e+01
  angle pdb=" CA  LYS F 555 "
        pdb=" CB  LYS F 555 "
        pdb=" CG  LYS F 555 "
      ideal   model   delta    sigma   weight residual
     114.10  122.85   -8.75 2.00e+00 2.50e-01 1.91e+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  108.07    4.10 9.50e-01 1.11e+00 1.87e+01
  angle pdb=" CA  LEU B 687 "
        pdb=" C   LEU B 687 "
        pdb=" O   LEU B 687 "
      ideal   model   delta    sigma   weight residual
     122.64  117.83    4.81 1.25e+00 6.40e-01 1.48e+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  116.86   -6.46 1.70e+00 3.46e-01 1.44e+01
  ... (remaining 13637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5500
       17.82 -    35.63: 576
       35.63 -    53.45: 148
       53.45 -    71.26: 22
       71.26 -    89.08: 4
  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  159.64   20.36     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 -160.78  -19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  LYS A 552 "
           pdb=" C   LYS A 552 "
           pdb=" N   SER A 553 "
           pdb=" CA  SER A 553 "
      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 -    0.055: 1299
       0.055 -    0.111: 279
       0.111 -    0.166: 46
       0.166 -    0.222: 5
       0.222 -    0.277: 4
  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 1.92e+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 1.53e+00
  chirality pdb=" CA  ILE A 606 "
            pdb=" N   ILE A 606 "
            pdb=" C   ILE A 606 "
            pdb=" CB  ILE A 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (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   7.19e-02 8.27e+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   6.00e-02 5.76e+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   1.44e-02 5.17e+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: 2062
        2.79 -     3.31: 9318
        3.31 -     3.84: 16982
        3.84 -     4.37: 21247
        4.37 -     4.90: 33546
  Nonbonded interactions: 83155
  Sorted by model distance:
  nonbonded pdb=" O   ILE F 556 "
            pdb=" ND2 ASN F 584 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" O   TRP A 411 "
            pdb=" OG1 THR A 441 "
     model   vdw
     2.271 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
     2.310 3.120
  nonbonded pdb=" NH1 ARG B 749 "
            pdb=" OE1 GLU B 752 "
     model   vdw
     2.313 3.120
  ... (remaining 83150 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:             4.640
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.670
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10071  Z= 0.228
  Angle     :  0.804   9.710  13642  Z= 0.453
  Chirality :  0.049   0.277   1633
  Planarity :  0.006   0.072   1715
  Dihedral  : 15.362  89.081   3886
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 19.24 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.23), residues: 1212
  helix: -2.75 (0.23), residues: 369
  sheet: -2.58 (0.37), residues: 182
  loop : -1.19 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 475 
 HIS   0.009   0.001   HIS B 499 
 PHE   0.029   0.002   PHE F 609 
 TYR   0.017   0.001   TYR F 756 
 ARG   0.006   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22425 (  242)
  hydrogen bonds       : angle       8.83777 (  513)
  covalent geometry    : bond        0.00385 (10071)
  covalent geometry    : angle       0.80378 (13642)

*********************** 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
  392 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 385
  time to evaluate  : 1.234 
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: A  430 LEU cc_start: 0.8195 (tp) cc_final: 0.7310 (mt)
REVERT: A  448 LEU cc_start: 0.8331 (tp) cc_final: 0.7879 (tp)
REVERT: A  471 LEU cc_start: 0.8452 (tt) cc_final: 0.8162 (tp)
REVERT: A  546 LEU cc_start: 0.8464 (tp) cc_final: 0.8127 (tp)
REVERT: A  569 LEU cc_start: 0.8404 (mt) cc_final: 0.8129 (mt)
REVERT: A  572 LEU cc_start: 0.8994 (tp) cc_final: 0.8558 (tp)
REVERT: A  611 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6730 (m-80)
REVERT: A  621 LEU cc_start: 0.8903 (mt) cc_final: 0.8654 (mt)
REVERT: A  623 ASP cc_start: 0.8758 (t0) cc_final: 0.8031 (t70)
REVERT: A  643 CYS cc_start: 0.7469 (t) cc_final: 0.7090 (m)
REVERT: A  710 LEU cc_start: 0.9117 (tp) cc_final: 0.8611 (mt)
REVERT: A  720 ILE cc_start: 0.9366 (mt) cc_final: 0.9148 (mm)
REVERT: A  736 LEU cc_start: 0.9170 (mt) cc_final: 0.8951 (mt)
REVERT: A  794 LEU cc_start: 0.9110 (mt) cc_final: 0.8784 (mt)
REVERT: A  799 LYS cc_start: 0.9261 (mtmt) cc_final: 0.9034 (ttmt)
REVERT: B  443 PHE cc_start: 0.7575 (m-10) cc_final: 0.7304 (m-80)
REVERT: B  475 TRP cc_start: 0.8269 (m-10) cc_final: 0.7400 (m-10)
REVERT: B  513 TYR cc_start: 0.6183 (m-80) cc_final: 0.5371 (m-10)
REVERT: B  549 LEU cc_start: 0.9121 (tp) cc_final: 0.8833 (tp)
REVERT: F  458 MET cc_start: 0.7017 (tpt) cc_final: 0.6781 (tpt)
REVERT: F  505 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6343 (mm-30)
REVERT: F  516 LEU cc_start: 0.8752 (mt) cc_final: 0.8371 (tp)
REVERT: F  550 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8804 (mppt)
REVERT: F  581 MET cc_start: 0.7455 (tpp) cc_final: 0.7084 (tpp)
REVERT: F  583 ASN cc_start: 0.8785 (m-40) cc_final: 0.8530 (p0)
REVERT: F  594 LEU cc_start: 0.8165 (tp) cc_final: 0.7671 (tp)
REVERT: F  612 LEU cc_start: 0.7415 (mt) cc_final: 0.6945 (pp)
REVERT: F  623 ASN cc_start: 0.7476 (m-40) cc_final: 0.6586 (p0)
REVERT: F  642 LEU cc_start: 0.7566 (tp) cc_final: 0.7240 (tp)
REVERT: F  644 LEU cc_start: 0.9414 (mt) cc_final: 0.9202 (tt)
REVERT: F  701 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7095 (tp30)
REVERT: F  704 VAL cc_start: 0.7392 (t) cc_final: 0.6964 (t)
REVERT: F  777 LEU cc_start: 0.8244 (tp) cc_final: 0.8037 (tt)
  outliers start: 7
  outliers final: 0
  residues processed: 389
  average time/residue: 0.2716
  time to fit residues: 138.5129
Evaluate side-chains
  228 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  611 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0770
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0170
   chunk 94 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0000
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 ASN
A 636 GLN
A 637 HIS
A 755 ASN
B 409 ASN
B 478 HIS
B 575 ASN
** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 758 GLN
F 515 ASN
F 606 HIS
F 635 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.085343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.073006 restraints weight = 65931.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.074100 restraints weight = 44695.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.074784 restraints weight = 34302.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10071  Z= 0.178
  Angle     :  0.782  12.130  13642  Z= 0.389
  Chirality :  0.046   0.206   1633
  Planarity :  0.006   0.052   1715
  Dihedral  :  5.166  22.823   1305
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 22.76 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.24), residues: 1212
  helix: -2.33 (0.25), residues: 368
  sheet: -2.55 (0.37), residues: 179
  loop : -1.13 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 475 
 HIS   0.007   0.001   HIS A 694 
 PHE   0.020   0.002   PHE B 682 
 TYR   0.021   0.002   TYR A 689 
 ARG   0.010   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04649 (  242)
  hydrogen bonds       : angle       7.20462 (  513)
  covalent geometry    : bond        0.00399 (10071)
  covalent geometry    : angle       0.78229 (13642)

*********************** 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
  284 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 225
  time to evaluate  : 1.157 
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: symmetry clash
REVERT: A  441 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7109 (m)
REVERT: A  710 LEU cc_start: 0.8565 (tp) cc_final: 0.7904 (mt)
REVERT: A  712 ASN cc_start: 0.7952 (m-40) cc_final: 0.7583 (t0)
REVERT: A  732 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (mmtm)
REVERT: A  736 LEU cc_start: 0.9005 (mt) cc_final: 0.8730 (mp)
REVERT: A  737 HIS cc_start: 0.7947 (m170) cc_final: 0.7523 (m-70)
REVERT: A  791 PHE cc_start: 0.7575 (t80) cc_final: 0.7081 (t80)
REVERT: A  794 LEU cc_start: 0.9161 (mt) cc_final: 0.8929 (mt)
REVERT: A  802 LEU cc_start: 0.9078 (tp) cc_final: 0.8678 (tp)
REVERT: B  434 MET cc_start: 0.6669 (tmm) cc_final: 0.5915 (tmm)
REVERT: B  575 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7647 (m-40)
REVERT: B  599 ILE cc_start: 0.8468 (mm) cc_final: 0.8006 (mp)
REVERT: B  620 ASP cc_start: 0.6487 (t0) cc_final: 0.5784 (m-30)
REVERT: B  621 LEU cc_start: 0.8345 (mt) cc_final: 0.7978 (mt)
REVERT: B  687 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7981 (tp)
REVERT: F  516 LEU cc_start: 0.9240 (mt) cc_final: 0.8590 (tp)
REVERT: F  521 LEU cc_start: 0.9031 (mt) cc_final: 0.8806 (mt)
REVERT: F  541 LEU cc_start: 0.5527 (mt) cc_final: 0.5053 (mt)
REVERT: F  550 LYS cc_start: 0.9321 (tmtt) cc_final: 0.8854 (mptt)
REVERT: F  588 MET cc_start: 0.8302 (mmm) cc_final: 0.7643 (mmm)
REVERT: F  591 LEU cc_start: 0.7335 (mm) cc_final: 0.5645 (tp)
REVERT: F  611 LEU cc_start: 0.7386 (mm) cc_final: 0.6722 (mm)
REVERT: F  612 LEU cc_start: 0.7546 (mt) cc_final: 0.7280 (pp)
REVERT: F  665 LEU cc_start: 0.8248 (tp) cc_final: 0.7985 (mt)
REVERT: F  680 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5261 (m-80)
REVERT: F  687 TYR cc_start: 0.7102 (t80) cc_final: 0.6766 (t80)
REVERT: F  688 LEU cc_start: 0.9365 (mt) cc_final: 0.9100 (mt)
REVERT: F  701 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7462 (tp30)
REVERT: F  704 VAL cc_start: 0.7574 (t) cc_final: 0.6799 (t)
  outliers start: 59
  outliers final: 23
  residues processed: 265
  average time/residue: 0.2372
  time to fit residues: 85.2753
Evaluate side-chains
  210 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  732 LYS
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  575 ASN
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  687 LEU
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  758 GLN
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  560 VAL
Chi-restraints excluded: chain F residue  563 VAL
Chi-restraints excluded: chain F residue  593 GLU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  680 PHE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  734 LEU
Chi-restraints excluded: chain F residue  743 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 ASN
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 575 ASN
** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 758 GLN
F 606 HIS
** 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 = 0.4163 r_free = 0.4163 target = 0.084012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.071903 restraints weight = 69077.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.072823 restraints weight = 46801.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.073580 restraints weight = 35293.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10071  Z= 0.151
  Angle     :  0.742  17.292  13642  Z= 0.362
  Chirality :  0.045   0.223   1633
  Planarity :  0.005   0.050   1715
  Dihedral  :  4.978  20.230   1303
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 22.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.36 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 23.99 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.24), residues: 1212
  helix: -2.15 (0.25), residues: 363
  sheet: -2.31 (0.38), residues: 183
  loop : -1.09 (0.25), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 645 
 HIS   0.005   0.001   HIS B 431 
 PHE   0.030   0.002   PHE B 635 
 TYR   0.018   0.002   TYR B 653 
 ARG   0.011   0.001   ARG F 603 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (  242)
  hydrogen bonds       : angle       6.77614 (  513)
  covalent geometry    : bond        0.00342 (10071)
  covalent geometry    : angle       0.74215 (13642)

*********************** 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
  246 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 192
  time to evaluate  : 1.750 
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: A  433 PHE cc_start: 0.7442 (t80) cc_final: 0.7036 (t80)
REVERT: A  648 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7039 (m-10)
REVERT: A  710 LEU cc_start: 0.8386 (tp) cc_final: 0.8036 (mt)
REVERT: A  712 ASN cc_start: 0.7931 (m-40) cc_final: 0.7616 (t0)
REVERT: A  736 LEU cc_start: 0.8942 (mt) cc_final: 0.8204 (mt)
REVERT: A  802 LEU cc_start: 0.8963 (tp) cc_final: 0.8722 (tp)
REVERT: B  403 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.4696 (ptt-90)
REVERT: B  434 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5790 (tmm)
REVERT: B  684 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.3506 (m)
REVERT: B  749 ARG cc_start: 0.4214 (OUTLIER) cc_final: 0.3861 (ttp80)
REVERT: F  458 MET cc_start: 0.7177 (tpp) cc_final: 0.6975 (tpt)
REVERT: F  516 LEU cc_start: 0.9235 (mt) cc_final: 0.8538 (tp)
REVERT: F  541 LEU cc_start: 0.5494 (mt) cc_final: 0.5011 (mt)
REVERT: F  550 LYS cc_start: 0.9350 (tmtt) cc_final: 0.8927 (tptp)
REVERT: F  588 MET cc_start: 0.8313 (mmm) cc_final: 0.7702 (mmm)
REVERT: F  591 LEU cc_start: 0.7263 (mm) cc_final: 0.5633 (tp)
REVERT: F  611 LEU cc_start: 0.7600 (mm) cc_final: 0.6793 (mt)
REVERT: F  612 LEU cc_start: 0.7333 (mt) cc_final: 0.7059 (pp)
REVERT: F  665 LEU cc_start: 0.8287 (tp) cc_final: 0.8086 (mt)
REVERT: F  687 TYR cc_start: 0.7437 (t80) cc_final: 0.7134 (t80)
REVERT: F  688 LEU cc_start: 0.9370 (mt) cc_final: 0.9094 (mt)
REVERT: F  701 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7415 (tp30)
  outliers start: 54
  outliers final: 29
  residues processed: 231
  average time/residue: 0.2897
  time to fit residues: 93.6275
Evaluate side-chains
  204 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 1.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  560 VAL
Chi-restraints excluded: chain F residue  563 VAL
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  734 LEU
Chi-restraints excluded: chain F residue  743 VAL
Chi-restraints excluded: chain F residue  783 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 117 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 696 ASN
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** 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 = 0.4120 r_free = 0.4120 target = 0.081753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.069548 restraints weight = 66570.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.070536 restraints weight = 42235.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.071102 restraints weight = 31907.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.5517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10071  Z= 0.179
  Angle     :  0.747  14.853  13642  Z= 0.362
  Chirality :  0.046   0.230   1633
  Planarity :  0.005   0.063   1715
  Dihedral  :  5.062  19.200   1303
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 23.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 23.99 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.24), residues: 1212
  helix: -2.07 (0.26), residues: 364
  sheet: -2.44 (0.37), residues: 202
  loop : -1.13 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 475 
 HIS   0.027   0.002   HIS B 614 
 PHE   0.021   0.002   PHE B 635 
 TYR   0.019   0.002   TYR B 653 
 ARG   0.007   0.001   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  242)
  hydrogen bonds       : angle       6.59839 (  513)
  covalent geometry    : bond        0.00400 (10071)
  covalent geometry    : angle       0.74687 (13642)

*********************** 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
  236 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 175
  time to evaluate  : 1.457 
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: A  433 PHE cc_start: 0.7634 (t80) cc_final: 0.7278 (t80)
REVERT: A  496 ARG cc_start: 0.7358 (mmt-90) cc_final: 0.7107 (mmt-90)
REVERT: A  571 LYS cc_start: 0.8979 (mptt) cc_final: 0.8659 (mmtt)
REVERT: A  648 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7039 (m-10)
REVERT: A  710 LEU cc_start: 0.8378 (tp) cc_final: 0.8017 (mt)
REVERT: B  403 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.3511 (ptt-90)
REVERT: B  434 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6551 (tmm)
REVERT: B  550 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.8120 (ttt-90)
REVERT: B  551 LEU cc_start: 0.8006 (tp) cc_final: 0.7520 (tp)
REVERT: B  700 LEU cc_start: 0.4658 (tt) cc_final: 0.3464 (tp)
REVERT: B  749 ARG cc_start: 0.4294 (OUTLIER) cc_final: 0.3505 (tmt170)
REVERT: B  761 LEU cc_start: 0.6654 (mt) cc_final: 0.6244 (mt)
REVERT: B  762 ARG cc_start: 0.7474 (mmp-170) cc_final: 0.7236 (mmp-170)
REVERT: F  516 LEU cc_start: 0.9212 (mt) cc_final: 0.8588 (tp)
REVERT: F  541 LEU cc_start: 0.5540 (mt) cc_final: 0.5098 (mt)
REVERT: F  550 LYS cc_start: 0.9372 (tmtt) cc_final: 0.8992 (tptp)
REVERT: F  588 MET cc_start: 0.8243 (mmm) cc_final: 0.7670 (mmm)
REVERT: F  591 LEU cc_start: 0.7043 (mm) cc_final: 0.5401 (tp)
REVERT: F  611 LEU cc_start: 0.7807 (mm) cc_final: 0.6944 (mt)
REVERT: F  612 LEU cc_start: 0.7295 (mt) cc_final: 0.6995 (pp)
REVERT: F  627 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5554 (mt)
REVERT: F  680 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.5897 (m-80)
REVERT: F  688 LEU cc_start: 0.9398 (mt) cc_final: 0.9104 (mt)
REVERT: F  701 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7556 (tp30)
  outliers start: 61
  outliers final: 36
  residues processed: 217
  average time/residue: 0.3204
  time to fit residues: 96.8359
Evaluate side-chains
  195 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 1.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  498 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  654 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  560 VAL
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  677 SER
Chi-restraints excluded: chain F residue  680 PHE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  734 LEU
Chi-restraints excluded: chain F residue  743 VAL
Chi-restraints excluded: chain F residue  783 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.7982

-------------------------------------------------------------------------------
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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 716 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 = 0.4117 r_free = 0.4117 target = 0.081605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.069845 restraints weight = 67040.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.070428 restraints weight = 42804.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.071197 restraints weight = 32479.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.5901

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= 0.152
  Angle     :  0.721  12.913  13642  Z= 0.346
  Chirality :  0.045   0.281   1633
  Planarity :  0.005   0.057   1715
  Dihedral  :  4.972  20.179   1303
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.22 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.24), residues: 1212
  helix: -2.03 (0.26), residues: 371
  sheet: -2.48 (0.36), residues: 210
  loop : -0.99 (0.26), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 475 
 HIS   0.020   0.002   HIS B 614 
 PHE   0.019   0.002   PHE B 635 
 TYR   0.024   0.002   TYR F 687 
 ARG   0.007   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03365 (  242)
  hydrogen bonds       : angle       6.30606 (  513)
  covalent geometry    : bond        0.00344 (10071)
  covalent geometry    : angle       0.72108 (13642)

*********************** 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
  218 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 162
  time to evaluate  : 1.513 
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: A  433 PHE cc_start: 0.7666 (t80) cc_final: 0.7340 (t80)
REVERT: A  496 ARG cc_start: 0.7459 (mmt-90) cc_final: 0.7232 (mmt-90)
REVERT: A  572 LEU cc_start: 0.8477 (mt) cc_final: 0.8233 (mt)
REVERT: A  595 GLU cc_start: 0.7760 (mp0) cc_final: 0.6195 (mp0)
REVERT: A  648 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7179 (m-10)
REVERT: A  710 LEU cc_start: 0.8304 (tp) cc_final: 0.7974 (mt)
REVERT: B  403 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.3735 (ptt-90)
REVERT: B  434 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.5930 (tmm)
REVERT: B  453 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8401 (mm)
REVERT: B  551 LEU cc_start: 0.8076 (tp) cc_final: 0.7569 (tp)
REVERT: B  684 CYS cc_start: 0.5489 (OUTLIER) cc_final: 0.3582 (m)
REVERT: B  749 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.3483 (tmt170)
REVERT: F  458 MET cc_start: 0.6813 (tpt) cc_final: 0.6596 (tpt)
REVERT: F  495 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7501 (t)
REVERT: F  550 LYS cc_start: 0.9402 (tmtt) cc_final: 0.9023 (tptp)
REVERT: F  611 LEU cc_start: 0.7829 (mm) cc_final: 0.7235 (mt)
REVERT: F  627 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5589 (mt)
REVERT: F  687 TYR cc_start: 0.7484 (t80) cc_final: 0.7144 (t80)
REVERT: F  688 LEU cc_start: 0.9418 (mt) cc_final: 0.9161 (mt)
REVERT: F  701 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7597 (tp30)
  outliers start: 56
  outliers final: 31
  residues processed: 200
  average time/residue: 0.3494
  time to fit residues: 95.2213
Evaluate side-chains
  180 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  650 HIS
Chi-restraints excluded: chain B residue  654 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  495 VAL
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  734 LEU
Chi-restraints excluded: chain F residue  743 VAL
Chi-restraints excluded: chain F residue  783 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 116 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 HIS
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** 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 = 0.4093 r_free = 0.4093 target = 0.080297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.069036 restraints weight = 68485.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.069217 restraints weight = 48797.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.069581 restraints weight = 41286.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.6377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10071  Z= 0.176
  Angle     :  0.743  12.182  13642  Z= 0.357
  Chirality :  0.046   0.238   1633
  Planarity :  0.005   0.058   1715
  Dihedral  :  5.074  21.754   1303
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 23.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 26.54 %
    Favored  : 68.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.24), residues: 1212
  helix: -2.06 (0.26), residues: 372
  sheet: -2.52 (0.36), residues: 216
  loop : -1.01 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 475 
 HIS   0.024   0.002   HIS B 614 
 PHE   0.020   0.002   PHE B 635 
 TYR   0.016   0.002   TYR F 687 
 ARG   0.007   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  242)
  hydrogen bonds       : angle       6.23484 (  513)
  covalent geometry    : bond        0.00397 (10071)
  covalent geometry    : angle       0.74279 (13642)

*********************** 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
  211 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 155
  time to evaluate  : 1.417 
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: A  433 PHE cc_start: 0.7656 (t80) cc_final: 0.7355 (t80)
REVERT: A  546 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8239 (tp)
REVERT: A  571 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8612 (mmtm)
REVERT: A  595 GLU cc_start: 0.7635 (mp0) cc_final: 0.7078 (mp0)
REVERT: A  648 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7054 (m-10)
REVERT: A  710 LEU cc_start: 0.8347 (tp) cc_final: 0.7976 (mt)
REVERT: B  403 ARG cc_start: 0.5511 (OUTLIER) cc_final: 0.3284 (ptt-90)
REVERT: B  434 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6623 (tmm)
REVERT: B  453 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8393 (mm)
REVERT: B  684 CYS cc_start: 0.5690 (OUTLIER) cc_final: 0.3802 (m)
REVERT: B  749 ARG cc_start: 0.4296 (OUTLIER) cc_final: 0.3567 (tmt170)
REVERT: B  762 ARG cc_start: 0.7562 (mmp-170) cc_final: 0.7305 (mmp-170)
REVERT: F  458 MET cc_start: 0.6797 (tpt) cc_final: 0.6593 (tpt)
REVERT: F  550 LYS cc_start: 0.9457 (tmtt) cc_final: 0.9081 (tptp)
REVERT: F  611 LEU cc_start: 0.7697 (mm) cc_final: 0.7000 (mt)
REVERT: F  627 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5664 (mt)
REVERT: F  680 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6279 (m-80)
REVERT: F  687 TYR cc_start: 0.7543 (t80) cc_final: 0.7168 (t80)
REVERT: F  688 LEU cc_start: 0.9398 (mt) cc_final: 0.9135 (mt)
REVERT: F  701 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7637 (tp30)
REVERT: F  778 LYS cc_start: 0.8529 (tppt) cc_final: 0.7685 (tptt)
  outliers start: 56
  outliers final: 31
  residues processed: 197
  average time/residue: 0.2263
  time to fit residues: 61.8278
Evaluate side-chains
  184 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 143
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  571 LYS
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  498 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  650 HIS
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  469 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  680 PHE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  743 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 114 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:   10.0000
   overall best weight:    2.4584

-------------------------------------------------------------------------------
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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 592 ASN
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.079793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.067924 restraints weight = 69251.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.068434 restraints weight = 49725.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.068830 restraints weight = 39154.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.6803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10071  Z= 0.179
  Angle     :  0.746  12.381  13642  Z= 0.359
  Chirality :  0.046   0.288   1633
  Planarity :  0.005   0.063   1715
  Dihedral  :  5.150  20.518   1303
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 25.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.63 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.24), residues: 1212
  helix: -2.11 (0.25), residues: 374
  sheet: -2.57 (0.35), residues: 217
  loop : -1.04 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 645 
 HIS   0.016   0.001   HIS B 614 
 PHE   0.020   0.002   PHE B 635 
 TYR   0.012   0.002   TYR F 687 
 ARG   0.007   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  242)
  hydrogen bonds       : angle       6.20672 (  513)
  covalent geometry    : bond        0.00405 (10071)
  covalent geometry    : angle       0.74557 (13642)

*********************** 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
  205 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 147
  time to evaluate  : 1.150 
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: A  496 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.7021 (mpt180)
REVERT: A  546 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8251 (tp)
REVERT: A  572 LEU cc_start: 0.8525 (mt) cc_final: 0.8231 (mt)
REVERT: A  595 GLU cc_start: 0.7554 (mp0) cc_final: 0.7127 (mp0)
REVERT: A  648 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7187 (m-10)
REVERT: A  710 LEU cc_start: 0.8392 (tp) cc_final: 0.7895 (mt)
REVERT: A  734 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.8012 (mmm-85)
REVERT: B  403 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.3438 (ptt-90)
REVERT: B  434 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6621 (tmm)
REVERT: B  453 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8573 (mm)
REVERT: B  550 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.7162 (ttt-90)
REVERT: B  596 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: B  684 CYS cc_start: 0.5497 (OUTLIER) cc_final: 0.3778 (m)
REVERT: B  710 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7771 (mm)
REVERT: B  749 ARG cc_start: 0.4355 (OUTLIER) cc_final: 0.3940 (ttp80)
REVERT: B  762 ARG cc_start: 0.7706 (mmp-170) cc_final: 0.7438 (mmp-170)
REVERT: F  401 LYS cc_start: 0.4054 (OUTLIER) cc_final: 0.3253 (mtmm)
REVERT: F  458 MET cc_start: 0.6851 (tpt) cc_final: 0.6643 (tpt)
REVERT: F  550 LYS cc_start: 0.9463 (tmtt) cc_final: 0.9099 (tptp)
REVERT: F  611 LEU cc_start: 0.7684 (mm) cc_final: 0.7160 (mt)
REVERT: F  680 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6898 (m-80)
REVERT: F  687 TYR cc_start: 0.7459 (t80) cc_final: 0.6986 (t80)
REVERT: F  688 LEU cc_start: 0.9406 (mt) cc_final: 0.9151 (mt)
REVERT: F  778 LYS cc_start: 0.8622 (tppt) cc_final: 0.7563 (tptt)
  outliers start: 58
  outliers final: 32
  residues processed: 189
  average time/residue: 0.2377
  time to fit residues: 61.3144
Evaluate side-chains
  178 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 135
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  627 LYS
Chi-restraints excluded: chain B residue  650 HIS
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  401 LYS
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  469 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  680 PHE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  743 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 636 GLN
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 711 GLN
F 606 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.078989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.067575 restraints weight = 70034.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.067951 restraints weight = 45187.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.068264 restraints weight = 35533.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.7195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10071  Z= 0.195
  Angle     :  0.769  12.556  13642  Z= 0.369
  Chirality :  0.047   0.246   1633
  Planarity :  0.005   0.064   1715
  Dihedral  :  5.252  19.835   1303
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 26.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 27.59 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.24), residues: 1212
  helix: -2.30 (0.24), residues: 382
  sheet: -2.41 (0.37), residues: 205
  loop : -1.28 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 475 
 HIS   0.011   0.001   HIS B 614 
 PHE   0.022   0.002   PHE B 635 
 TYR   0.012   0.002   TYR B 653 
 ARG   0.007   0.001   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  242)
  hydrogen bonds       : angle       6.32761 (  513)
  covalent geometry    : bond        0.00441 (10071)
  covalent geometry    : angle       0.76871 (13642)

*********************** 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
  189 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 139
  time to evaluate  : 1.182 
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: A  572 LEU cc_start: 0.8572 (mt) cc_final: 0.8315 (mt)
REVERT: A  648 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7261 (m-10)
REVERT: A  710 LEU cc_start: 0.8325 (tp) cc_final: 0.7777 (mt)
REVERT: A  737 HIS cc_start: 0.8306 (m-70) cc_final: 0.8074 (m-70)
REVERT: B  403 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.3537 (ptt-90)
REVERT: B  434 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6714 (ppp)
REVERT: B  453 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8523 (mm)
REVERT: B  475 TRP cc_start: 0.7435 (m100) cc_final: 0.7181 (m-10)
REVERT: B  550 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.7217 (ttt-90)
REVERT: B  596 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7650 (mt)
REVERT: B  684 CYS cc_start: 0.5471 (OUTLIER) cc_final: 0.4032 (m)
REVERT: B  710 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7855 (mm)
REVERT: B  749 ARG cc_start: 0.4296 (OUTLIER) cc_final: 0.3822 (ttp80)
REVERT: B  762 ARG cc_start: 0.7757 (mmp-170) cc_final: 0.7470 (mmp-170)
REVERT: F  520 TYR cc_start: 0.8586 (m-80) cc_final: 0.8351 (m-80)
REVERT: F  544 LEU cc_start: 0.7258 (tp) cc_final: 0.6663 (tp)
REVERT: F  550 LYS cc_start: 0.9489 (tmtt) cc_final: 0.8818 (mppt)
REVERT: F  588 MET cc_start: 0.7827 (mmm) cc_final: 0.7395 (mmm)
REVERT: F  611 LEU cc_start: 0.7527 (mm) cc_final: 0.6897 (mt)
REVERT: F  680 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7080 (m-80)
REVERT: F  687 TYR cc_start: 0.7464 (t80) cc_final: 0.7037 (t80)
REVERT: F  688 LEU cc_start: 0.9398 (mt) cc_final: 0.9134 (mt)
REVERT: F  800 MET cc_start: 0.6135 (ppp) cc_final: 0.5843 (ppp)
  outliers start: 50
  outliers final: 33
  residues processed: 178
  average time/residue: 0.2210
  time to fit residues: 54.8455
Evaluate side-chains
  170 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  698 THR
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  426 ASP
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  650 HIS
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  733 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  793 THR
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  469 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  680 PHE
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  743 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 21 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 ASN
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 716 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 = 0.4092 r_free = 0.4092 target = 0.080571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.068638 restraints weight = 67120.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.069521 restraints weight = 45365.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.070048 restraints weight = 33202.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.7283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10071  Z= 0.130
  Angle     :  0.761  11.230  13642  Z= 0.359
  Chirality :  0.046   0.288   1633
  Planarity :  0.005   0.061   1715
  Dihedral  :  5.069  18.607   1303
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 21.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 28.73 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.24), residues: 1212
  helix: -2.26 (0.24), residues: 393
  sheet: -2.29 (0.38), residues: 205
  loop : -1.37 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 475 
 HIS   0.017   0.001   HIS F 566 
 PHE   0.035   0.002   PHE A 433 
 TYR   0.009   0.001   TYR F 710 
 ARG   0.006   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (  242)
  hydrogen bonds       : angle       6.12334 (  513)
  covalent geometry    : bond        0.00303 (10071)
  covalent geometry    : angle       0.76058 (13642)

*********************** 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
  179 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 1.137 
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  469 THR cc_start: 0.7814 (p) cc_final: 0.7598 (t)
REVERT: A  572 LEU cc_start: 0.8536 (mt) cc_final: 0.8270 (mt)
REVERT: A  648 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7165 (m-10)
REVERT: A  710 LEU cc_start: 0.8262 (tp) cc_final: 0.7895 (mt)
REVERT: A  737 HIS cc_start: 0.8125 (m-70) cc_final: 0.7895 (m-70)
REVERT: B  403 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.3514 (ptt-90)
REVERT: B  434 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6304 (tmm)
REVERT: B  453 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8541 (mm)
REVERT: B  475 TRP cc_start: 0.7309 (m-10) cc_final: 0.6790 (m-10)
REVERT: B  550 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7340 (tpt-90)
REVERT: B  596 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7609 (mt)
REVERT: B  684 CYS cc_start: 0.5747 (OUTLIER) cc_final: 0.4705 (m)
REVERT: B  710 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7911 (mm)
REVERT: B  749 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.4184 (ttp80)
REVERT: F  520 TYR cc_start: 0.8487 (m-80) cc_final: 0.8217 (m-80)
REVERT: F  550 LYS cc_start: 0.9469 (tmtt) cc_final: 0.8838 (mppt)
REVERT: F  588 MET cc_start: 0.7516 (mmm) cc_final: 0.7109 (mmm)
REVERT: F  611 LEU cc_start: 0.7694 (mm) cc_final: 0.6983 (mt)
REVERT: F  687 TYR cc_start: 0.7344 (t80) cc_final: 0.6931 (t80)
REVERT: F  688 LEU cc_start: 0.9343 (mt) cc_final: 0.9142 (mt)
  outliers start: 40
  outliers final: 27
  residues processed: 169
  average time/residue: 0.2246
  time to fit residues: 52.9421
Evaluate side-chains
  166 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  426 ASP
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  627 LYS
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  793 THR
Chi-restraints excluded: chain F residue  401 LYS
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  469 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  694 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 72 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0000
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.5790

-------------------------------------------------------------------------------
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 568 HIS
A 755 ASN
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 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 = 0.4075 r_free = 0.4075 target = 0.079901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.068097 restraints weight = 68957.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.068583 restraints weight = 50518.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.069114 restraints weight = 38444.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.7470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10071  Z= 0.147
  Angle     :  0.770  10.999  13642  Z= 0.368
  Chirality :  0.046   0.223   1633
  Planarity :  0.005   0.058   1715
  Dihedral  :  5.124  18.785   1303
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 22.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 29.53 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.24), residues: 1212
  helix: -2.16 (0.25), residues: 379
  sheet: -2.24 (0.37), residues: 210
  loop : -1.24 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 475 
 HIS   0.013   0.001   HIS F 566 
 PHE   0.018   0.002   PHE B 635 
 TYR   0.040   0.002   TYR B 477 
 ARG   0.009   0.001   ARG A 765 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  242)
  hydrogen bonds       : angle       6.09491 (  513)
  covalent geometry    : bond        0.00344 (10071)
  covalent geometry    : angle       0.77040 (13642)

********************** 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
  173 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 1.321 
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: A  572 LEU cc_start: 0.8494 (mt) cc_final: 0.8234 (mt)
REVERT: A  648 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7201 (m-10)
REVERT: A  710 LEU cc_start: 0.8268 (tp) cc_final: 0.8036 (mt)
REVERT: A  734 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7752 (mmm-85)
REVERT: A  737 HIS cc_start: 0.8250 (m-70) cc_final: 0.8021 (m-70)
REVERT: B  403 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.3541 (ptt-90)
REVERT: B  434 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6366 (tmm)
REVERT: B  453 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8621 (mm)
REVERT: B  596 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7623 (mt)
REVERT: B  684 CYS cc_start: 0.5546 (OUTLIER) cc_final: 0.4306 (m)
REVERT: B  749 ARG cc_start: 0.4657 (OUTLIER) cc_final: 0.4215 (ttp80)
REVERT: B  762 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7612 (mmp-170)
REVERT: F  520 TYR cc_start: 0.8559 (m-80) cc_final: 0.8276 (m-80)
REVERT: F  550 LYS cc_start: 0.9466 (tmtt) cc_final: 0.8864 (mppt)
REVERT: F  588 MET cc_start: 0.7555 (mmm) cc_final: 0.7140 (mmm)
REVERT: F  611 LEU cc_start: 0.7729 (mm) cc_final: 0.6987 (mt)
REVERT: F  687 TYR cc_start: 0.7486 (t80) cc_final: 0.7026 (t80)
REVERT: F  688 LEU cc_start: 0.9339 (mt) cc_final: 0.9136 (mt)
  outliers start: 34
  outliers final: 25
  residues processed: 167
  average time/residue: 0.2512
  time to fit residues: 59.7366
Evaluate side-chains
  167 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  426 ASP
Chi-restraints excluded: chain B residue  434 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  677 ILE
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  684 CYS
Chi-restraints excluded: chain B residue  749 ARG
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  793 THR
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  469 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  694 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0000
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 598 HIS
F 606 HIS
** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.078919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.067847 restraints weight = 69211.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.067755 restraints weight = 46413.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.068498 restraints weight = 37371.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.7881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10071  Z= 0.178
  Angle     :  0.793  11.284  13642  Z= 0.381
  Chirality :  0.047   0.290   1633
  Planarity :  0.005   0.070   1715
  Dihedral  :  5.263  17.990   1303
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 25.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 29.70 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.23), residues: 1212
  helix: -2.21 (0.25), residues: 386
  sheet: -2.34 (0.36), residues: 217
  loop : -1.40 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 645 
 HIS   0.012   0.001   HIS F 566 
 PHE   0.041   0.002   PHE A 433 
 TYR   0.038   0.002   TYR B 477 
 ARG   0.007   0.001   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  242)
  hydrogen bonds       : angle       6.11738 (  513)
  covalent geometry    : bond        0.00411 (10071)
  covalent geometry    : angle       0.79323 (13642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3958.82 seconds
wall clock time: 72 minutes 28.18 seconds (4348.18 seconds total)