Starting phenix.real_space_refine
on Sat Aug 23 05:35:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f75_28895/08_2025/8f75_28895.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f75_28895/08_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_28895/08_2025/8f75_28895.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f75_28895/08_2025/8f75_28895.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f75_28895/08_2025/8f75_28895.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f75_28895/08_2025/8f75_28895.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9899
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "F"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3257
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 17, 'TRANS': 386}
  Time building chain proxies: 2.42, per 1000 atoms: 0.24
  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: 0.88
  Conformation dependent library (CDL) restraints added in 370.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.34
  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: 1.05

  Time building geometry restraints manager: 1.18 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:             4.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.570
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (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
 ARG   0.006   0.001   ARG B 749 
 TYR   0.017   0.001   TYR F 756 
 PHE   0.029   0.002   PHE F 609 
 TRP   0.033   0.003   TRP A 475 
 HIS   0.009   0.001   HIS B 499 

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

*********************** 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  : 0.411 
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: 0.1039
  time to fit residues: 53.6109
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  : 0.431 
-------------------------------------------------------------------------------
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 108 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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
** B 650 HIS ** 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 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: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.084479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.071942 restraints weight = 66206.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.073108 restraints weight = 45695.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.073994 restraints weight = 31764.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.074280 restraints weight = 24878.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.074466 restraints weight = 21954.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10071  Z= 0.204
  Angle     :  0.808  12.289  13642  Z= 0.401
  Chirality :  0.047   0.226   1633
  Planarity :  0.006   0.054   1715
  Dihedral  :  5.226  22.658   1305
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 23.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 22.93 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.66 (0.24), residues: 1212
  helix: -2.41 (0.25), residues: 373
  sheet: -2.49 (0.37), residues: 182
  loop : -1.02 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 781 
 TYR   0.020   0.002   TYR A 689 
 PHE   0.019   0.002   PHE B 682 
 TRP   0.017   0.002   TRP A 475 
 HIS   0.007   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (10071)
  covalent geometry    : angle       0.80835 (13642)
  hydrogen bonds       : bond        0.04643 (  242)
  hydrogen bonds       : angle       7.20948 (  513)

*********************** 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
  281 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 221
  time to evaluate  : 0.444 
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: 0.7815 (OUTLIER) cc_final: 0.7241 (m)
REVERT: A  710 LEU cc_start: 0.8598 (tp) cc_final: 0.8092 (mt)
REVERT: A  712 ASN cc_start: 0.8059 (m-40) cc_final: 0.7705 (t0)
REVERT: A  791 PHE cc_start: 0.7617 (t80) cc_final: 0.7178 (t80)
REVERT: A  794 LEU cc_start: 0.9176 (mt) cc_final: 0.8949 (mt)
REVERT: A  802 LEU cc_start: 0.9068 (tp) cc_final: 0.8685 (tp)
REVERT: B  403 ARG cc_start: 0.5673 (OUTLIER) cc_final: 0.5063 (ptt-90)
REVERT: B  434 MET cc_start: 0.6808 (tmm) cc_final: 0.6118 (tmm)
REVERT: B  575 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7630 (m-40)
REVERT: B  599 ILE cc_start: 0.8417 (mm) cc_final: 0.7940 (mp)
REVERT: B  620 ASP cc_start: 0.6599 (t0) cc_final: 0.5860 (m-30)
REVERT: B  621 LEU cc_start: 0.8434 (mt) cc_final: 0.8088 (mt)
REVERT: B  687 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8025 (tp)
REVERT: F  516 LEU cc_start: 0.9268 (mt) cc_final: 0.8642 (tp)
REVERT: F  521 LEU cc_start: 0.9039 (mt) cc_final: 0.8834 (mt)
REVERT: F  541 LEU cc_start: 0.5602 (mt) cc_final: 0.5286 (mt)
REVERT: F  550 LYS cc_start: 0.9332 (tmtt) cc_final: 0.8863 (mptt)
REVERT: F  588 MET cc_start: 0.8339 (mmm) cc_final: 0.7786 (mmm)
REVERT: F  591 LEU cc_start: 0.7382 (mm) cc_final: 0.5690 (tp)
REVERT: F  611 LEU cc_start: 0.7388 (mm) cc_final: 0.6732 (mp)
REVERT: F  612 LEU cc_start: 0.7512 (mt) cc_final: 0.7188 (pp)
REVERT: F  665 LEU cc_start: 0.8256 (tp) cc_final: 0.7994 (mt)
REVERT: F  680 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.5375 (m-80)
REVERT: F  687 TYR cc_start: 0.7133 (t80) cc_final: 0.6762 (t80)
REVERT: F  688 LEU cc_start: 0.9369 (mt) cc_final: 0.9108 (mt)
REVERT: F  701 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7568 (tp30)
REVERT: F  704 VAL cc_start: 0.7443 (t) cc_final: 0.6393 (t)
  outliers start: 60
  outliers final: 26
  residues processed: 262
  average time/residue: 0.1025
  time to fit residues: 36.7006
Evaluate side-chains
  209 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  543 LEU
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  784 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  454 GLU
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  684 CYS
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 66 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 56 optimal weight:    0.4980
   chunk 67 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0050
   chunk 107 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.0396

-------------------------------------------------------------------------------
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**
B 575 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**
** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 729 GLN
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 = 0.084072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.071965 restraints weight = 68436.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.073007 restraints weight = 45595.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.073792 restraints weight = 32875.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.074035 restraints weight = 26326.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.074161 restraints weight = 23835.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10071  Z= 0.143
  Angle     :  0.736  17.763  13642  Z= 0.359
  Chirality :  0.045   0.229   1633
  Planarity :  0.005   0.051   1715
  Dihedral  :  4.983  20.165   1303
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.28 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.52 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.55 (0.24), residues: 1212
  helix: -2.22 (0.25), residues: 370
  sheet: -2.32 (0.38), residues: 183
  loop : -1.06 (0.26), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 603 
 TYR   0.017   0.002   TYR B 653 
 PHE   0.017   0.002   PHE A 443 
 TRP   0.014   0.002   TRP F 645 
 HIS   0.006   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10071)
  covalent geometry    : angle       0.73569 (13642)
  hydrogen bonds       : bond        0.03866 (  242)
  hydrogen bonds       : angle       6.72513 (  513)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 196
  time to evaluate  : 0.395 
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: A  433 PHE cc_start: 0.7436 (t80) cc_final: 0.7038 (t80)
REVERT: A  496 ARG cc_start: 0.7371 (mmt-90) cc_final: 0.7169 (mmt-90)
REVERT: A  648 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7156 (m-10)
REVERT: A  710 LEU cc_start: 0.8350 (tp) cc_final: 0.8032 (mt)
REVERT: A  712 ASN cc_start: 0.7932 (m-40) cc_final: 0.7677 (m-40)
REVERT: A  737 HIS cc_start: 0.7807 (m170) cc_final: 0.7501 (m-70)
REVERT: A  802 LEU cc_start: 0.8967 (tp) cc_final: 0.8745 (tp)
REVERT: B  403 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.4467 (ptt-90)
REVERT: B  434 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5731 (tmm)
REVERT: B  475 TRP cc_start: 0.7133 (m-10) cc_final: 0.6700 (m-10)
REVERT: B  599 ILE cc_start: 0.8483 (mm) cc_final: 0.8150 (mp)
REVERT: B  700 LEU cc_start: 0.4861 (tt) cc_final: 0.3708 (tp)
REVERT: B  749 ARG cc_start: 0.4210 (OUTLIER) cc_final: 0.3891 (ttp80)
REVERT: F  458 MET cc_start: 0.7159 (tpp) cc_final: 0.6924 (tpt)
REVERT: F  516 LEU cc_start: 0.9203 (mt) cc_final: 0.8492 (tp)
REVERT: F  541 LEU cc_start: 0.5439 (mt) cc_final: 0.5000 (mt)
REVERT: F  550 LYS cc_start: 0.9346 (tmtt) cc_final: 0.8932 (tptp)
REVERT: F  588 MET cc_start: 0.8237 (mmm) cc_final: 0.7650 (mmm)
REVERT: F  591 LEU cc_start: 0.7229 (mm) cc_final: 0.5635 (tp)
REVERT: F  611 LEU cc_start: 0.7537 (mm) cc_final: 0.6757 (mt)
REVERT: F  612 LEU cc_start: 0.7338 (mt) cc_final: 0.7052 (pp)
REVERT: F  687 TYR cc_start: 0.7410 (t80) cc_final: 0.7105 (t80)
REVERT: F  688 LEU cc_start: 0.9366 (mt) cc_final: 0.9113 (mt)
REVERT: F  701 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7451 (tp30)
  outliers start: 53
  outliers final: 28
  residues processed: 234
  average time/residue: 0.0822
  time to fit residues: 27.1872
Evaluate side-chains
  208 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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  591 VAL
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  402 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  723 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  689 ASP
Chi-restraints excluded: chain F residue  734 LEU
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 57 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 65 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
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 554 ASN
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 709 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 718 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.082518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.070446 restraints weight = 68522.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.071101 restraints weight = 47027.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.071870 restraints weight = 34996.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.072132 restraints weight = 28590.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.072478 restraints weight = 25947.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.5429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10071  Z= 0.162
  Angle     :  0.729  14.030  13642  Z= 0.353
  Chirality :  0.045   0.173   1633
  Planarity :  0.005   0.063   1715
  Dihedral  :  4.989  19.146   1303
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 22.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.25 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.24), residues: 1212
  helix: -2.11 (0.25), residues: 370
  sheet: -2.42 (0.37), residues: 201
  loop : -1.02 (0.26), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 550 
 TYR   0.020   0.002   TYR B 653 
 PHE   0.017   0.002   PHE A 682 
 TRP   0.020   0.002   TRP A 475 
 HIS   0.016   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (10071)
  covalent geometry    : angle       0.72876 (13642)
  hydrogen bonds       : bond        0.03545 (  242)
  hydrogen bonds       : angle       6.57733 (  513)

*********************** 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
  226 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 173
  time to evaluate  : 0.343 
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: A  648 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7117 (m-10)
REVERT: A  677 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7231 (tp)
REVERT: A  710 LEU cc_start: 0.8338 (tp) cc_final: 0.8006 (mt)
REVERT: A  720 ILE cc_start: 0.8612 (mm) cc_final: 0.8252 (mm)
REVERT: A  734 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7987 (mmm-85)
REVERT: B  403 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.4339 (ptt-90)
REVERT: B  434 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6041 (tmm)
REVERT: B  550 ARG cc_start: 0.8565 (ttt-90) cc_final: 0.8236 (tmt-80)
REVERT: B  551 LEU cc_start: 0.7991 (tp) cc_final: 0.7366 (tp)
REVERT: B  684 CYS cc_start: 0.5228 (OUTLIER) cc_final: 0.4942 (m)
REVERT: B  749 ARG cc_start: 0.4275 (OUTLIER) cc_final: 0.3496 (tmt170)
REVERT: B  761 LEU cc_start: 0.6982 (mt) cc_final: 0.6380 (mt)
REVERT: B  762 ARG cc_start: 0.7469 (mmp-170) cc_final: 0.7229 (mmp-170)
REVERT: F  516 LEU cc_start: 0.9180 (mt) cc_final: 0.8539 (tp)
REVERT: F  529 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6309 (tt)
REVERT: F  541 LEU cc_start: 0.5476 (mt) cc_final: 0.5050 (mt)
REVERT: F  550 LYS cc_start: 0.9372 (tmtt) cc_final: 0.8974 (tptp)
REVERT: F  588 MET cc_start: 0.8145 (mmm) cc_final: 0.7662 (mmm)
REVERT: F  591 LEU cc_start: 0.7058 (mm) cc_final: 0.5476 (tp)
REVERT: F  611 LEU cc_start: 0.7447 (mm) cc_final: 0.7028 (mp)
REVERT: F  688 LEU cc_start: 0.9377 (mt) cc_final: 0.9093 (mt)
REVERT: F  701 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7472 (tp30)
  outliers start: 53
  outliers final: 28
  residues processed: 209
  average time/residue: 0.0980
  time to fit residues: 28.3171
Evaluate side-chains
  189 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  677 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  402 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  498 LEU
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
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  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  529 ILE
Chi-restraints excluded: chain F residue  560 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
Chi-restraints excluded: chain F residue  800 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 117 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 94 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.3322

-------------------------------------------------------------------------------
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 737 HIS
A 758 GLN
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4131 r_free = 0.4131 target = 0.082317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.070592 restraints weight = 68194.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.071144 restraints weight = 46665.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.071737 restraints weight = 35778.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.071942 restraints weight = 30220.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.072077 restraints weight = 27963.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.5771

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= 0.138
  Angle     :  0.720  13.325  13642  Z= 0.342
  Chirality :  0.045   0.191   1633
  Planarity :  0.005   0.055   1715
  Dihedral  :  4.866  19.533   1303
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 24.78 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.24), residues: 1212
  helix: -2.06 (0.26), residues: 378
  sheet: -2.30 (0.38), residues: 200
  loop : -1.07 (0.26), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 749 
 TYR   0.023   0.002   TYR F 687 
 PHE   0.016   0.002   PHE A 682 
 TRP   0.028   0.002   TRP A 475 
 HIS   0.008   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10071)
  covalent geometry    : angle       0.72001 (13642)
  hydrogen bonds       : bond        0.03286 (  242)
  hydrogen bonds       : angle       6.39228 (  513)

*********************** 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
  226 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 0.330 
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: 0.7614 (t80) cc_final: 0.7363 (t80)
REVERT: A  441 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7235 (m)
REVERT: A  496 ARG cc_start: 0.7411 (mmt-90) cc_final: 0.7188 (mmt-90)
REVERT: A  572 LEU cc_start: 0.8402 (mt) cc_final: 0.8196 (mt)
REVERT: A  595 GLU cc_start: 0.7849 (mp0) cc_final: 0.6622 (mp0)
REVERT: A  620 ASP cc_start: 0.8026 (t0) cc_final: 0.7772 (m-30)
REVERT: A  648 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.7140 (m-10)
REVERT: A  710 LEU cc_start: 0.8290 (tp) cc_final: 0.7933 (mt)
REVERT: A  720 ILE cc_start: 0.8674 (mm) cc_final: 0.8351 (mm)
REVERT: A  791 PHE cc_start: 0.6991 (t80) cc_final: 0.6731 (t80)
REVERT: B  403 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.3590 (ptt-90)
REVERT: B  477 TYR cc_start: 0.6906 (m-10) cc_final: 0.6245 (m-10)
REVERT: B  550 ARG cc_start: 0.8471 (ttt-90) cc_final: 0.8185 (tpt-90)
REVERT: B  551 LEU cc_start: 0.8074 (tp) cc_final: 0.7574 (tp)
REVERT: B  596 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7740 (mt)
REVERT: B  684 CYS cc_start: 0.5961 (OUTLIER) cc_final: 0.2980 (m)
REVERT: B  710 LEU cc_start: 0.8376 (tp) cc_final: 0.7823 (mp)
REVERT: B  749 ARG cc_start: 0.4210 (OUTLIER) cc_final: 0.3454 (tmt170)
REVERT: F  458 MET cc_start: 0.6784 (tpt) cc_final: 0.6561 (tpt)
REVERT: F  550 LYS cc_start: 0.9385 (tmtt) cc_final: 0.9013 (tptp)
REVERT: F  687 TYR cc_start: 0.7491 (t80) cc_final: 0.7186 (t80)
REVERT: F  688 LEU cc_start: 0.9368 (mt) cc_final: 0.9161 (mt)
REVERT: F  701 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7587 (tp30)
  outliers start: 55
  outliers final: 26
  residues processed: 213
  average time/residue: 0.0835
  time to fit residues: 24.6959
Evaluate side-chains
  183 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  441 THR
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 B residue  403 ARG
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  458 ASP
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  619 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 F residue  451 LEU
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  606 HIS
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  677 SER
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 7 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   chunk 115 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 625 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.081801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.070345 restraints weight = 68668.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.070626 restraints weight = 45630.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.071234 restraints weight = 36235.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.071419 restraints weight = 32214.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.071605 restraints weight = 29848.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.6078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10071  Z= 0.142
  Angle     :  0.723  12.534  13642  Z= 0.344
  Chirality :  0.045   0.337   1633
  Planarity :  0.005   0.053   1715
  Dihedral  :  4.914  20.419   1303
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 21.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 26.19 %
    Favored  : 69.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.24), residues: 1212
  helix: -2.02 (0.26), residues: 379
  sheet: -2.45 (0.36), residues: 211
  loop : -0.99 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 749 
 TYR   0.014   0.002   TYR F 687 
 PHE   0.031   0.002   PHE B 635 
 TRP   0.033   0.002   TRP A 475 
 HIS   0.017   0.001   HIS F 606 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (10071)
  covalent geometry    : angle       0.72293 (13642)
  hydrogen bonds       : bond        0.03197 (  242)
  hydrogen bonds       : angle       6.30313 (  513)

*********************** 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
  207 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 159
  time to evaluate  : 0.279 
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: 0.7750 (t80) cc_final: 0.7349 (t80)
REVERT: A  546 LEU cc_start: 0.8458 (tp) cc_final: 0.8169 (tp)
REVERT: A  620 ASP cc_start: 0.8070 (t0) cc_final: 0.7834 (m-30)
REVERT: A  648 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7160 (m-10)
REVERT: A  677 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7325 (tp)
REVERT: A  710 LEU cc_start: 0.8411 (tp) cc_final: 0.7931 (mt)
REVERT: A  720 ILE cc_start: 0.8718 (mm) cc_final: 0.8447 (mm)
REVERT: B  403 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.3609 (ptt-90)
REVERT: B  550 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.8151 (tpt-90)
REVERT: B  551 LEU cc_start: 0.8146 (tp) cc_final: 0.7535 (tp)
REVERT: B  596 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7764 (mt)
REVERT: B  684 CYS cc_start: 0.5265 (OUTLIER) cc_final: 0.3524 (m)
REVERT: B  710 LEU cc_start: 0.8411 (tp) cc_final: 0.7933 (mp)
REVERT: B  749 ARG cc_start: 0.4352 (OUTLIER) cc_final: 0.3624 (tmt170)
REVERT: B  761 LEU cc_start: 0.6645 (mt) cc_final: 0.6230 (mt)
REVERT: B  762 ARG cc_start: 0.7534 (mmp-170) cc_final: 0.7264 (mmp-170)
REVERT: F  458 MET cc_start: 0.6830 (tpt) cc_final: 0.6613 (tpt)
REVERT: F  550 LYS cc_start: 0.9412 (tmtt) cc_final: 0.9056 (tptp)
REVERT: F  611 LEU cc_start: 0.7553 (mm) cc_final: 0.7022 (mt)
REVERT: F  687 TYR cc_start: 0.7584 (t80) cc_final: 0.7211 (t80)
REVERT: F  688 LEU cc_start: 0.9369 (mt) cc_final: 0.9157 (mt)
REVERT: F  701 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7615 (tp30)
  outliers start: 48
  outliers final: 27
  residues processed: 196
  average time/residue: 0.0768
  time to fit residues: 21.0396
Evaluate side-chains
  179 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  536 VAL
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  677 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  438 ILE
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  619 ILE
Chi-restraints excluded: chain B residue  650 HIS
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 F residue  451 LEU
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  677 SER
Chi-restraints excluded: chain F residue  689 ASP
Chi-restraints excluded: chain F residue  743 VAL
Chi-restraints excluded: chain F residue  800 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 81 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 592 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 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 = 0.4131 r_free = 0.4131 target = 0.082252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.070467 restraints weight = 67644.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.071151 restraints weight = 44811.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.071636 restraints weight = 35886.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.072199 restraints weight = 28129.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.072222 restraints weight = 25453.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.6321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10071  Z= 0.120
  Angle     :  0.727  13.058  13642  Z= 0.343
  Chirality :  0.045   0.273   1633
  Planarity :  0.005   0.056   1715
  Dihedral  :  4.824  18.842   1303
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 27.24 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.24), residues: 1212
  helix: -2.00 (0.26), residues: 380
  sheet: -2.32 (0.38), residues: 201
  loop : -1.11 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 749 
 TYR   0.010   0.001   TYR F 710 
 PHE   0.020   0.002   PHE B 635 
 TRP   0.024   0.002   TRP A 475 
 HIS   0.007   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10071)
  covalent geometry    : angle       0.72664 (13642)
  hydrogen bonds       : bond        0.03042 (  242)
  hydrogen bonds       : angle       6.19656 (  513)

*********************** 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
  199 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 160
  time to evaluate  : 0.420 
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: A  433 PHE cc_start: 0.7785 (t80) cc_final: 0.7357 (t80)
REVERT: A  546 LEU cc_start: 0.8320 (tp) cc_final: 0.8069 (tp)
REVERT: A  572 LEU cc_start: 0.8340 (mt) cc_final: 0.8035 (mt)
REVERT: A  620 ASP cc_start: 0.7946 (t0) cc_final: 0.7699 (m-30)
REVERT: A  648 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7222 (m-10)
REVERT: A  677 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7313 (tp)
REVERT: A  710 LEU cc_start: 0.8245 (tp) cc_final: 0.7790 (mt)
REVERT: B  403 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.4881 (ptt-90)
REVERT: B  475 TRP cc_start: 0.7314 (m-10) cc_final: 0.7018 (m-10)
REVERT: B  550 ARG cc_start: 0.8495 (ttt-90) cc_final: 0.8088 (tpt-90)
REVERT: B  551 LEU cc_start: 0.8149 (tp) cc_final: 0.7447 (tp)
REVERT: B  596 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7683 (mt)
REVERT: B  707 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6200 (mm)
REVERT: B  741 ASN cc_start: 0.7828 (m-40) cc_final: 0.6740 (m110)
REVERT: B  749 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3927 (tmt170)
REVERT: B  761 LEU cc_start: 0.6685 (mt) cc_final: 0.6302 (mt)
REVERT: B  762 ARG cc_start: 0.7534 (mmp-170) cc_final: 0.7274 (mmp-170)
REVERT: F  550 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9066 (tptp)
REVERT: F  687 TYR cc_start: 0.7533 (t80) cc_final: 0.7050 (t80)
REVERT: F  688 LEU cc_start: 0.9365 (mt) cc_final: 0.9152 (mt)
REVERT: F  701 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7605 (tp30)
  outliers start: 39
  outliers final: 22
  residues processed: 188
  average time/residue: 0.1081
  time to fit residues: 28.0796
Evaluate side-chains
  178 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  448 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  656 ILE
Chi-restraints excluded: chain A residue  677 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
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  683 TYR
Chi-restraints excluded: chain B residue  707 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  462 THR
Chi-restraints excluded: chain F residue  496 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 48 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 65 optimal weight:    0.3980
   chunk 103 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.7582

-------------------------------------------------------------------------------
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 608 HIS
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 636 GLN
B 660 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4103 r_free = 0.4103 target = 0.080902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.069760 restraints weight = 69348.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.069425 restraints weight = 50283.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.070122 restraints weight = 40935.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.070520 restraints weight = 33440.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.070676 restraints weight = 30264.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.6694

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= 0.150
  Angle     :  0.739  12.205  13642  Z= 0.351
  Chirality :  0.046   0.277   1633
  Planarity :  0.005   0.056   1715
  Dihedral  :  4.893  18.640   1303
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 27.33 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.61 (0.24), residues: 1212
  helix: -2.10 (0.25), residues: 387
  sheet: -2.33 (0.37), residues: 206
  loop : -1.11 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 514 
 TYR   0.011   0.001   TYR F 710 
 PHE   0.017   0.002   PHE B 635 
 TRP   0.021   0.002   TRP A 475 
 HIS   0.004   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10071)
  covalent geometry    : angle       0.73918 (13642)
  hydrogen bonds       : bond        0.03019 (  242)
  hydrogen bonds       : angle       6.24780 (  513)

*********************** 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
  194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 153
  time to evaluate  : 0.414 
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  433 PHE cc_start: 0.7633 (t80) cc_final: 0.7227 (t80)
REVERT: A  496 ARG cc_start: 0.7317 (mmt-90) cc_final: 0.7106 (mpt180)
REVERT: A  546 LEU cc_start: 0.8295 (tp) cc_final: 0.7995 (tp)
REVERT: A  648 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7159 (m-10)
REVERT: A  710 LEU cc_start: 0.8342 (tp) cc_final: 0.8040 (mt)
REVERT: A  801 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7630 (tpt90)
REVERT: B  403 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.3469 (ptt-90)
REVERT: B  410 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7009 (mp0)
REVERT: B  475 TRP cc_start: 0.7385 (m-10) cc_final: 0.6843 (m-10)
REVERT: B  551 LEU cc_start: 0.8175 (tp) cc_final: 0.7005 (tp)
REVERT: B  596 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7533 (mt)
REVERT: B  707 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6139 (mm)
REVERT: B  761 LEU cc_start: 0.6614 (mt) cc_final: 0.6125 (mt)
REVERT: B  762 ARG cc_start: 0.7647 (mmp-170) cc_final: 0.7329 (mmp-170)
REVERT: F  550 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9151 (tptp)
REVERT: F  680 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6152 (m-80)
REVERT: F  687 TYR cc_start: 0.7680 (t80) cc_final: 0.7190 (t80)
REVERT: F  688 LEU cc_start: 0.9383 (mt) cc_final: 0.9062 (mt)
REVERT: F  701 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7643 (tp30)
  outliers start: 41
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1159
  time to fit residues: 28.8352
Evaluate side-chains
  171 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  448 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  426 ASP
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  596 LEU
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  683 TYR
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  496 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 113 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 94 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    2.2984

-------------------------------------------------------------------------------
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**
B 575 ASN
B 696 ASN
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** 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 = 0.4085 r_free = 0.4085 target = 0.080059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.068612 restraints weight = 69362.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.069029 restraints weight = 48456.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.069511 restraints weight = 37790.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.069751 restraints weight = 32046.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.069885 restraints weight = 29643.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.7070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10071  Z= 0.173
  Angle     :  0.770  11.743  13642  Z= 0.368
  Chirality :  0.047   0.362   1633
  Planarity :  0.005   0.059   1715
  Dihedral  :  5.037  22.876   1303
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 22.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 28.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.24), residues: 1212
  helix: -2.16 (0.25), residues: 389
  sheet: -2.47 (0.37), residues: 205
  loop : -1.17 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 539 
 TYR   0.032   0.002   TYR B 477 
 PHE   0.034   0.002   PHE B 728 
 TRP   0.020   0.002   TRP A 475 
 HIS   0.010   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10071)
  covalent geometry    : angle       0.76982 (13642)
  hydrogen bonds       : bond        0.03219 (  242)
  hydrogen bonds       : angle       6.29726 (  513)

*********************** 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
  187 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.456 
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: 0.7588 (t80) cc_final: 0.7386 (t80)
REVERT: A  546 LEU cc_start: 0.8371 (tp) cc_final: 0.8100 (tp)
REVERT: A  648 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7205 (m-10)
REVERT: A  710 LEU cc_start: 0.8318 (tp) cc_final: 0.8013 (mt)
REVERT: B  403 ARG cc_start: 0.5463 (OUTLIER) cc_final: 0.3651 (ptt-90)
REVERT: B  410 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7220 (mp0)
REVERT: B  474 LEU cc_start: 0.8373 (tp) cc_final: 0.8129 (tp)
REVERT: B  596 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7305 (mt)
REVERT: B  761 LEU cc_start: 0.6879 (mt) cc_final: 0.6419 (mt)
REVERT: B  762 ARG cc_start: 0.7656 (mmp-170) cc_final: 0.7395 (mmp-170)
REVERT: F  520 TYR cc_start: 0.8482 (m-80) cc_final: 0.8203 (m-80)
REVERT: F  550 LYS cc_start: 0.9454 (tmtt) cc_final: 0.8883 (mppt)
REVERT: F  680 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6717 (m-80)
REVERT: F  687 TYR cc_start: 0.7413 (t80) cc_final: 0.6983 (t80)
REVERT: F  688 LEU cc_start: 0.9315 (mt) cc_final: 0.9092 (mt)
  outliers start: 42
  outliers final: 28
  residues processed: 173
  average time/residue: 0.1107
  time to fit residues: 26.6640
Evaluate side-chains
  170 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  448 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  426 ASP
Chi-restraints excluded: chain B residue  438 ILE
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  619 ILE
Chi-restraints excluded: chain B residue  627 LYS
Chi-restraints excluded: chain B residue  650 HIS
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  451 LEU
Chi-restraints excluded: chain F residue  462 THR
Chi-restraints excluded: chain F residue  496 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:    0.2980
   chunk 103 optimal weight:    1.9990
   chunk 117 optimal weight:    0.0000
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 79 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0000
   overall best weight:    0.2788

-------------------------------------------------------------------------------
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**
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.081691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.070280 restraints weight = 68252.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.070648 restraints weight = 48941.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.071254 restraints weight = 36414.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.071464 restraints weight = 32675.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.071534 restraints weight = 29726.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.7185

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= 0.127
  Angle     :  0.811  13.566  13642  Z= 0.374
  Chirality :  0.047   0.306   1633
  Planarity :  0.005   0.053   1715
  Dihedral  :  4.914  21.036   1303
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 30.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.90 (0.24), residues: 1212
  helix: -2.23 (0.24), residues: 404
  sheet: -2.50 (0.36), residues: 214
  loop : -1.31 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 496 
 TYR   0.031   0.002   TYR B 477 
 PHE   0.016   0.001   PHE B 635 
 TRP   0.018   0.002   TRP A 475 
 HIS   0.009   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10071)
  covalent geometry    : angle       0.81125 (13642)
  hydrogen bonds       : bond        0.02916 (  242)
  hydrogen bonds       : angle       6.10115 (  513)

********************** 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: 24
    poor density    : 149
  time to evaluate  : 0.291 
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  433 PHE cc_start: 0.7662 (t80) cc_final: 0.7254 (t80)
REVERT: A  546 LEU cc_start: 0.8341 (tp) cc_final: 0.8139 (tp)
REVERT: A  648 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7207 (m-10)
REVERT: A  710 LEU cc_start: 0.8320 (tp) cc_final: 0.8057 (mt)
REVERT: B  403 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.4693 (ptt-90)
REVERT: B  575 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6335 (t0)
REVERT: B  596 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7224 (mt)
REVERT: B  761 LEU cc_start: 0.6669 (mt) cc_final: 0.6193 (mt)
REVERT: B  762 ARG cc_start: 0.7627 (mmp-170) cc_final: 0.7354 (mmp-170)
REVERT: F  687 TYR cc_start: 0.7398 (t80) cc_final: 0.6928 (t80)
  outliers start: 24
  outliers final: 19
  residues processed: 165
  average time/residue: 0.0917
  time to fit residues: 21.4874
Evaluate side-chains
  159 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  648 TYR
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  438 ILE
Chi-restraints excluded: chain B residue  562 VAL
Chi-restraints excluded: chain B residue  575 ASN
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  619 ILE
Chi-restraints excluded: chain B residue  627 LYS
Chi-restraints excluded: chain B residue  683 TYR
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  496 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  672 VAL
Chi-restraints excluded: chain F residue  689 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 17 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 758 GLN
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 532 ASN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 799 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.081312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.069739 restraints weight = 69022.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.069765 restraints weight = 49754.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.070572 restraints weight = 42118.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.071172 restraints weight = 31090.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.071246 restraints weight = 27664.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.7372

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= 0.127
  Angle     :  0.787  11.837  13642  Z= 0.368
  Chirality :  0.047   0.297   1633
  Planarity :  0.005   0.075   1715
  Dihedral  :  4.861  21.197   1303
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 19.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 30.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.91 (0.24), residues: 1212
  helix: -2.32 (0.24), residues: 412
  sheet: -2.35 (0.37), residues: 208
  loop : -1.31 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 804 
 TYR   0.030   0.001   TYR B 477 
 PHE   0.014   0.001   PHE B 635 
 TRP   0.018   0.002   TRP A 803 
 HIS   0.013   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10071)
  covalent geometry    : angle       0.78668 (13642)
  hydrogen bonds       : bond        0.02879 (  242)
  hydrogen bonds       : angle       6.07528 (  513)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1846.60 seconds
wall clock time: 32 minutes 44.39 seconds (1964.39 seconds total)