Starting phenix.real_space_refine
on Mon Jul 28 04:44:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dra_27675/07_2025/8dra_27675.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9899
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "F"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3257
          Classifications: {'peptide': 404}
          Link IDs: {'PTRANS': 17, 'TRANS': 386}
  Time building chain proxies: 7.38, per 1000 atoms: 0.75
  Number of scatterers: 9899
  At special positions: 0
  Unit cell: (119.472, 114.232, 92.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1785      8.00
     N    1713      7.00
     C    6369      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      33.2% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 411
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.637A  pdb=" N   PHE A 443 " --> pdb=" O   PRO A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 467
      removed outlier: 3.527A  pdb=" N   ILE A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
    Processing helix  chain 'A' and resid 536 through 542
      removed outlier: 3.889A  pdb=" N   GLY A 539 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ARG A 541 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 566
      removed outlier: 3.694A  pdb=" N   THR A 563 " --> pdb=" O   PRO A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 3.911A  pdb=" N   LYS A 588 " --> pdb=" O   ASN A 585 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LYS A 589 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 613
    Processing helix  chain 'A' and resid 629 through 638
      removed outlier: 3.954A  pdb=" N   ILE A 633 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN A 636 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.606A  pdb=" N   CYS A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 706
    Processing helix  chain 'A' and resid 724 through 730
      removed outlier: 3.644A  pdb=" N   CYS A 730 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 753
      removed outlier: 3.549A  pdb=" N   VAL A 750 " --> pdb=" O   PRO A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
      removed outlier: 3.655A  pdb=" N   CYS A 776 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 793
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'B' and resid 403 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 440 through 445
    Processing helix  chain 'B' and resid 462 through 468
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.647A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.878A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE B 508 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 586 through 590
      removed outlier: 4.011A  pdb=" N   LYS B 589 " --> pdb=" O   SER B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 613
      removed outlier: 3.512A  pdb=" N   LEU B 613 " --> pdb=" O   ILE B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 638
      removed outlier: 3.756A  pdb=" N   HIS B 637 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.718A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B 661 " --> pdb=" O   ILE B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.866A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 705
      removed outlier: 3.619A  pdb=" N   ILE B 704 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 724 through 729
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.638A  pdb=" N   VAL B 750 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 776
      removed outlier: 3.510A  pdb=" N   CYS B 776 " --> pdb=" O   LEU B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'F' and resid 401 through 409
    Processing helix  chain 'F' and resid 410 through 418
    Processing helix  chain 'F' and resid 460 through 466
      removed outlier: 3.649A  pdb=" N   ILE F 463 " --> pdb=" O   PRO F 460 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 482 through 493
    Processing helix  chain 'F' and resid 502 through 506
    Processing helix  chain 'F' and resid 508 through 513
      removed outlier: 3.710A  pdb=" N   TYR F 511 " --> pdb=" O   PRO F 508 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LEU F 513 " --> pdb=" O   MET F 510 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 534 through 540
      removed outlier: 4.042A  pdb=" N   ARG F 539 " --> pdb=" O   GLU F 536 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 557 through 563
      removed outlier: 3.573A  pdb=" N   VAL F 561 " --> pdb=" O   PRO F 557 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 582 through 587
    Processing helix  chain 'F' and resid 605 through 610
    Processing helix  chain 'F' and resid 629 through 636
      removed outlier: 4.564A  pdb=" N   GLN F 634 " --> pdb=" O   VAL F 631 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 653 through 659
      removed outlier: 3.797A  pdb=" N   ILE F 656 " --> pdb=" O   PRO F 653 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU F 659 " --> pdb=" O   ILE F 656 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 676 through 682
      removed outlier: 3.938A  pdb=" N   PHE F 680 " --> pdb=" O   PRO F 676 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   CYS F 682 " --> pdb=" O   HIS F 678 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 699 through 705
      removed outlier: 3.537A  pdb=" N   ILE F 702 " --> pdb=" O   PRO F 699 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLY F 703 " --> pdb=" O   PRO F 700 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 724 through 728
    Processing helix  chain 'F' and resid 768 through 774
      removed outlier: 3.696A  pdb=" N   CYS F 774 " --> pdb=" O   LEU F 771 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 785 through 791
    Processing helix  chain 'F' and resid 793 through 802
      removed outlier: 3.839A  pdb=" N   MET F 800 " --> pdb=" O   VAL F 796 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.379A  pdb=" N   LEU A 428 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LYS A 452 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   LEU A 430 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   GLU A 454 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   LEU A 432 " --> pdb=" O   GLU A 454 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU A 451 " --> pdb=" O   TRP A 475 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   LEU A 453 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU A 572 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ILE A 599 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ILE A 574 " --> pdb=" O   ILE A 599 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU A 596 " --> pdb=" O   ASP A 620 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ILE A 619 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 461
      removed outlier: 6.351A  pdb=" N   VAL A 459 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668
      removed outlier: 3.660A  pdb=" N   ASP A 691 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760
      removed outlier: 6.341A  pdb=" N   ILE A 759 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.518A  pdb=" N   LEU B 428 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LYS B 452 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   LEU B 430 " --> pdb=" O   LYS B 452 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   GLU B 454 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 432 " --> pdb=" O   GLU B 454 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU B 498 " --> pdb=" O   HIS B 522 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   THR B 524 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B 500 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU B 667 " --> pdb=" O   ASP B 691 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461
    Processing sheet with id=AA7, first strand: chain 'B' and resid 712 through 714
      removed outlier: 7.029A  pdb=" N   LEU B 713 " --> pdb=" O   HIS B 737 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 419 through 420
      removed outlier: 6.080A  pdb=" N   LEU F 426 " --> pdb=" O   SER F 448 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   LYS F 450 " --> pdb=" O   LEU F 426 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LEU F 428 " --> pdb=" O   LYS F 450 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   GLU F 452 " --> pdb=" O   LEU F 428 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU F 430 " --> pdb=" O   GLU F 452 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU F 449 " --> pdb=" O   CYS F 473 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   HIS F 475 " --> pdb=" O   LEU F 449 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   LEU F 451 " --> pdb=" O   HIS F 475 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU F 472 " --> pdb=" O   SER F 497 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS F 499 " --> pdb=" O   LEU F 472 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU F 474 " --> pdb=" O   LYS F 499 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   MET F 570 " --> pdb=" O   GLU F 595 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL F 597 " --> pdb=" O   MET F 570 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   VAL F 572 " --> pdb=" O   VAL F 597 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU F 617 " --> pdb=" O   LYS F 643 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LYS F 735 " --> pdb=" O   PHE F 711 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP F 758 " --> pdb=" O   LEU F 734 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU F 757 " --> pdb=" O   VAL F 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 457 through 459
      removed outlier: 5.735A  pdb=" N   VAL F 457 " --> pdb=" O   LYS F 480 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    238 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.12

  Time building geometry restraints manager: 3.12 seconds

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

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

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.180
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.870
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  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:3.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.0000

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

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.23), residues: 1212
  helix: -2.86 (0.22), residues: 369
  sheet: -2.58 (0.37), residues: 182
  loop : -1.18 (0.24), residues: 661

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

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

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 377
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 GLU cc_start: 0.8049 (pm20) cc_final: 0.7523 (pm20)
REVERT: A  534 TYR cc_start: 0.7233 (m-80) cc_final: 0.6984 (m-10)
REVERT: A  540 LEU cc_start: 0.9316 (mt) cc_final: 0.9112 (mt)
REVERT: A  616 LEU cc_start: 0.7902 (mt) cc_final: 0.7360 (mt)
REVERT: A  624 ASN cc_start: 0.8522 (m-40) cc_final: 0.8190 (m-40)
REVERT: A  626 LEU cc_start: 0.8220 (mt) cc_final: 0.7558 (mp)
REVERT: A  682 PHE cc_start: 0.8523 (m-10) cc_final: 0.8263 (m-80)
REVERT: B  503 THR cc_start: 0.8813 (m) cc_final: 0.8599 (p)
REVERT: B  570 GLN cc_start: 0.7773 (mt0) cc_final: 0.7380 (mm110)
REVERT: B  623 ASP cc_start: 0.7996 (t0) cc_final: 0.7507 (t0)
REVERT: B  637 HIS cc_start: 0.7817 (m90) cc_final: 0.6765 (t-90)
REVERT: B  644 LEU cc_start: 0.8857 (pt) cc_final: 0.8576 (tp)
REVERT: B  648 TYR cc_start: 0.8373 (m-80) cc_final: 0.8084 (m-10)
REVERT: B  664 LEU cc_start: 0.9077 (tp) cc_final: 0.8836 (tp)
REVERT: B  682 PHE cc_start: 0.8600 (m-80) cc_final: 0.8219 (m-80)
REVERT: F  428 LEU cc_start: 0.9160 (mt) cc_final: 0.8958 (mt)
REVERT: F  476 GLN cc_start: 0.7831 (mp-120) cc_final: 0.6511 (mm-40)
REVERT: F  490 LYS cc_start: 0.9409 (tttt) cc_final: 0.9146 (ttpp)
REVERT: F  504 ARG cc_start: 0.8292 (tpt170) cc_final: 0.8074 (tpt90)
REVERT: F  545 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8508 (mmmt)
REVERT: F  567 LEU cc_start: 0.7844 (tp) cc_final: 0.7428 (tp)
REVERT: F  637 ARG cc_start: 0.7585 (ptp90) cc_final: 0.7343 (ptp90)
REVERT: F  777 LEU cc_start: 0.7998 (tp) cc_final: 0.7533 (tp)
  outliers start: 4
  outliers final: 0
  residues processed: 378
  average time/residue: 0.2594
  time to fit residues: 130.2978
Evaluate side-chains
  218 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0040
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 478 HIS
B 650 HIS
F 402 GLN
** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 558 GLN
F 635 HIS
F 693 ASN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.116882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.096014 restraints weight = 34688.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.097034 restraints weight = 21576.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.098171 restraints weight = 16332.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10071  Z= 0.165
  Angle     :  0.738   8.784  13642  Z= 0.360
  Chirality :  0.047   0.367   1633
  Planarity :  0.005   0.073   1715
  Dihedral  :  5.034  23.773   1303
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.87 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.23), residues: 1212
  helix: -2.51 (0.24), residues: 360
  sheet: -2.71 (0.35), residues: 191
  loop : -1.00 (0.25), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 647 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.020   0.002   PHE F 609 
 TYR   0.021   0.002   TYR F 646 
 ARG   0.008   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  238)
  hydrogen bonds       : angle       7.11011 (  504)
  covalent geometry    : bond        0.00371 (10071)
  covalent geometry    : angle       0.73767 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 221
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8133 (pt)
REVERT: A  534 TYR cc_start: 0.5830 (m-80) cc_final: 0.5396 (m-10)
REVERT: A  646 LEU cc_start: 0.9175 (mt) cc_final: 0.8926 (mt)
REVERT: F  446 LEU cc_start: 0.8758 (tp) cc_final: 0.8541 (tp)
REVERT: F  452 GLU cc_start: 0.7584 (tt0) cc_final: 0.7354 (tt0)
REVERT: F  504 ARG cc_start: 0.8327 (tpt170) cc_final: 0.8104 (tpt90)
REVERT: F  567 LEU cc_start: 0.7697 (tp) cc_final: 0.6983 (tp)
REVERT: F  570 MET cc_start: 0.8404 (tmm) cc_final: 0.7997 (tpp)
REVERT: F  599 CYS cc_start: 0.8527 (m) cc_final: 0.8310 (m)
REVERT: F  616 GLU cc_start: 0.8008 (pt0) cc_final: 0.7794 (pt0)
REVERT: F  638 LYS cc_start: 0.6975 (mttt) cc_final: 0.6557 (ptmt)
REVERT: F  686 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7041 (ptp-170)
  outliers start: 40
  outliers final: 18
  residues processed: 247
  average time/residue: 0.2251
  time to fit residues: 77.9582
Evaluate side-chains
  207 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  512 ILE
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  757 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 68 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 625 ASN
A 711 GLN
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 532 ASN
** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 584 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 = 0.4095 r_free = 0.4095 target = 0.112930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.090492 restraints weight = 33827.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.091401 restraints weight = 21359.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.091977 restraints weight = 14927.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10071  Z= 0.171
  Angle     :  0.700  10.091  13642  Z= 0.343
  Chirality :  0.046   0.302   1633
  Planarity :  0.005   0.050   1715
  Dihedral  :  5.078  22.308   1303
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 24.43 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.24), residues: 1212
  helix: -2.48 (0.25), residues: 360
  sheet: -2.52 (0.36), residues: 192
  loop : -0.98 (0.25), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 647 
 HIS   0.005   0.001   HIS F 655 
 PHE   0.021   0.002   PHE F 609 
 TYR   0.014   0.002   TYR F 756 
 ARG   0.007   0.001   ARG A 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  238)
  hydrogen bonds       : angle       6.54213 (  504)
  covalent geometry    : bond        0.00393 (10071)
  covalent geometry    : angle       0.69974 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 188
  time to evaluate  : 1.118 
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  407 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8429 (mp)
REVERT: B  438 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8612 (mp)
REVERT: B  550 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7817 (mtt-85)
REVERT: B  667 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (tp)
REVERT: B  700 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7049 (tt)
REVERT: F  446 LEU cc_start: 0.8823 (tp) cc_final: 0.8604 (tp)
REVERT: F  504 ARG cc_start: 0.8399 (tpt170) cc_final: 0.8009 (tpt90)
REVERT: F  567 LEU cc_start: 0.7768 (tp) cc_final: 0.7319 (tp)
REVERT: F  570 MET cc_start: 0.8608 (tmm) cc_final: 0.8146 (tmm)
REVERT: F  588 MET cc_start: 0.7575 (mmm) cc_final: 0.7309 (mmm)
REVERT: F  599 CYS cc_start: 0.8560 (m) cc_final: 0.8334 (m)
REVERT: F  617 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (mt)
REVERT: F  638 LYS cc_start: 0.7199 (mttt) cc_final: 0.6791 (ptmt)
REVERT: F  643 LYS cc_start: 0.8109 (mttt) cc_final: 0.7664 (mttm)
REVERT: F  686 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6919 (ptp-170)
REVERT: F  711 PHE cc_start: 0.8105 (t80) cc_final: 0.7819 (t80)
  outliers start: 60
  outliers final: 34
  residues processed: 227
  average time/residue: 0.1937
  time to fit residues: 63.7741
Evaluate side-chains
  202 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 162
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  568 HIS
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  667 LEU
Chi-restraints excluded: chain B residue  687 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  496 LEU
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  679 LEU
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  757 LEU
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 117 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 598 HIS
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.111177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.089026 restraints weight = 33622.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.089590 restraints weight = 22657.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.090717 restraints weight = 15993.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10071  Z= 0.190
  Angle     :  0.707  10.731  13642  Z= 0.345
  Chirality :  0.046   0.263   1633
  Planarity :  0.005   0.047   1715
  Dihedral  :  5.061  20.426   1303
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 20.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 25.48 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.24), residues: 1212
  helix: -2.51 (0.25), residues: 355
  sheet: -2.52 (0.36), residues: 193
  loop : -0.99 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 645 
 HIS   0.006   0.001   HIS B 499 
 PHE   0.021   0.002   PHE F 609 
 TYR   0.015   0.002   TYR B 689 
 ARG   0.005   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  238)
  hydrogen bonds       : angle       6.40142 (  504)
  covalent geometry    : bond        0.00438 (10071)
  covalent geometry    : angle       0.70655 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 175
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8504 (mp)
REVERT: A  626 LEU cc_start: 0.8616 (mt) cc_final: 0.8116 (mt)
REVERT: B  438 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8687 (mp)
REVERT: B  550 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7837 (mtt-85)
REVERT: B  667 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7950 (tp)
REVERT: B  700 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6970 (tt)
REVERT: B  754 THR cc_start: 0.5252 (OUTLIER) cc_final: 0.4840 (p)
REVERT: F  446 LEU cc_start: 0.8841 (tp) cc_final: 0.8619 (tp)
REVERT: F  504 ARG cc_start: 0.8349 (tpt170) cc_final: 0.8092 (tpt90)
REVERT: F  545 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8229 (mmmt)
REVERT: F  588 MET cc_start: 0.7564 (mmm) cc_final: 0.7229 (mmm)
REVERT: F  599 CYS cc_start: 0.8562 (m) cc_final: 0.8215 (m)
REVERT: F  616 GLU cc_start: 0.8331 (pt0) cc_final: 0.8107 (pt0)
REVERT: F  617 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: F  638 LYS cc_start: 0.7276 (mttt) cc_final: 0.6885 (ptmt)
REVERT: F  643 LYS cc_start: 0.8113 (mttt) cc_final: 0.7658 (mttm)
REVERT: F  686 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6907 (ptp-170)
REVERT: F  756 TYR cc_start: 0.7068 (t80) cc_final: 0.6622 (t80)
  outliers start: 58
  outliers final: 28
  residues processed: 214
  average time/residue: 0.1807
  time to fit residues: 57.1562
Evaluate side-chains
  183 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  667 LEU
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  744 GLN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  652 ILE
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 114 optimal weight:    0.0670
   chunk 85 optimal weight:    4.9990
   chunk 17 optimal weight:    0.1980
   chunk 76 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0020
   chunk 65 optimal weight:    0.0770
   overall best weight:    0.2484

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.114012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.092209 restraints weight = 33256.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.093045 restraints weight = 21607.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.094284 restraints weight = 15075.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10071  Z= 0.117
  Angle     :  0.700  10.875  13642  Z= 0.327
  Chirality :  0.045   0.223   1633
  Planarity :  0.004   0.046   1715
  Dihedral  :  4.841  21.260   1303
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.94 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.68 (0.24), residues: 1212
  helix: -2.48 (0.24), residues: 369
  sheet: -2.56 (0.37), residues: 198
  loop : -0.92 (0.25), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 645 
 HIS   0.004   0.001   HIS F 678 
 PHE   0.016   0.001   PHE F 609 
 TYR   0.010   0.002   TYR A 534 
 ARG   0.004   0.000   ARG F 797 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  238)
  hydrogen bonds       : angle       6.03917 (  504)
  covalent geometry    : bond        0.00268 (10071)
  covalent geometry    : angle       0.70022 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  553 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.7990 (p)
REVERT: A  626 LEU cc_start: 0.8489 (mt) cc_final: 0.8012 (mp)
REVERT: B  550 ARG cc_start: 0.8391 (mtt90) cc_final: 0.7956 (mmt90)
REVERT: B  754 THR cc_start: 0.5272 (OUTLIER) cc_final: 0.4937 (p)
REVERT: F  476 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6924 (mm110)
REVERT: F  504 ARG cc_start: 0.8355 (tpt170) cc_final: 0.8021 (tpt90)
REVERT: F  545 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8406 (mmmt)
REVERT: F  599 CYS cc_start: 0.8147 (m) cc_final: 0.7899 (m)
REVERT: F  611 LEU cc_start: 0.8678 (mm) cc_final: 0.8472 (mm)
REVERT: F  614 LEU cc_start: 0.8798 (tt) cc_final: 0.8146 (tt)
REVERT: F  616 GLU cc_start: 0.8259 (pt0) cc_final: 0.7991 (pt0)
REVERT: F  617 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7658 (mt)
REVERT: F  638 LYS cc_start: 0.7302 (mttt) cc_final: 0.7009 (ptmt)
REVERT: F  643 LYS cc_start: 0.8080 (mttt) cc_final: 0.7708 (mttm)
REVERT: F  756 TYR cc_start: 0.6917 (t80) cc_final: 0.6425 (t80)
  outliers start: 43
  outliers final: 26
  residues processed: 200
  average time/residue: 0.1986
  time to fit residues: 56.8795
Evaluate side-chains
  191 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  591 VAL
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  727 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  510 MET
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0870
   chunk 57 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    2.5964

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 ASN
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 693 ASN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 750 ASN
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.108901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.087883 restraints weight = 34006.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.088148 restraints weight = 25001.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.088916 restraints weight = 18534.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  10071  Z= 0.234
  Angle     :  0.769  18.538  13642  Z= 0.368
  Chirality :  0.047   0.222   1633
  Planarity :  0.005   0.047   1715
  Dihedral  :  5.092  20.009   1303
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 23.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 25.83 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.24), residues: 1212
  helix: -2.64 (0.24), residues: 368
  sheet: -2.67 (0.35), residues: 209
  loop : -0.86 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 647 
 HIS   0.007   0.001   HIS F 655 
 PHE   0.017   0.002   PHE A 682 
 TYR   0.015   0.002   TYR F 646 
 ARG   0.005   0.001   ARG F 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  238)
  hydrogen bonds       : angle       6.29244 (  504)
  covalent geometry    : bond        0.00535 (10071)
  covalent geometry    : angle       0.76931 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 160
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  591 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8104 (t)
REVERT: A  626 LEU cc_start: 0.8562 (mt) cc_final: 0.7888 (mt)
REVERT: A  649 ASN cc_start: 0.7543 (t0) cc_final: 0.6632 (t0)
REVERT: B  426 ASP cc_start: 0.8294 (m-30) cc_final: 0.7912 (t70)
REVERT: B  438 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8787 (mp)
REVERT: B  550 ARG cc_start: 0.8392 (mtt90) cc_final: 0.7730 (mtt-85)
REVERT: B  673 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7787 (tmtt)
REVERT: B  720 ILE cc_start: 0.7272 (mm) cc_final: 0.7061 (mm)
REVERT: B  754 THR cc_start: 0.5462 (OUTLIER) cc_final: 0.5110 (p)
REVERT: F  499 LYS cc_start: 0.7990 (tptp) cc_final: 0.7534 (tptp)
REVERT: F  504 ARG cc_start: 0.8402 (tpt90) cc_final: 0.8104 (tpt90)
REVERT: F  545 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8225 (mmmt)
REVERT: F  617 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8150 (mt)
REVERT: F  633 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7736 (t80)
REVERT: F  638 LYS cc_start: 0.7404 (mttt) cc_final: 0.7062 (ptmt)
REVERT: F  643 LYS cc_start: 0.8188 (mttt) cc_final: 0.7791 (mttm)
REVERT: F  727 PHE cc_start: 0.8552 (t80) cc_final: 0.8278 (m-80)
REVERT: F  756 TYR cc_start: 0.7385 (t80) cc_final: 0.7070 (t80)
  outliers start: 70
  outliers final: 40
  residues processed: 204
  average time/residue: 0.1920
  time to fit residues: 57.8183
Evaluate side-chains
  197 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 151
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  715 VAL
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  541 LEU
Chi-restraints excluded: chain F residue  561 VAL
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  645 TRP
Chi-restraints excluded: chain F residue  686 ARG
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  705 LEU
Chi-restraints excluded: chain F residue  719 GLU
Chi-restraints excluded: chain F residue  753 PHE
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 114 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 606 HIS
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.111336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.090651 restraints weight = 34200.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.090794 restraints weight = 22336.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.091695 restraints weight = 17872.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.5259

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= 0.133
  Angle     :  0.695  16.029  13642  Z= 0.328
  Chirality :  0.045   0.205   1633
  Planarity :  0.004   0.046   1715
  Dihedral  :  4.858  20.853   1303
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 28.73 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.24), residues: 1212
  helix: -2.62 (0.23), residues: 379
  sheet: -2.52 (0.37), residues: 203
  loop : -0.96 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 647 
 HIS   0.004   0.001   HIS F 655 
 PHE   0.014   0.001   PHE F 609 
 TYR   0.012   0.002   TYR B 668 
 ARG   0.008   0.001   ARG B 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  238)
  hydrogen bonds       : angle       6.01607 (  504)
  covalent geometry    : bond        0.00310 (10071)
  covalent geometry    : angle       0.69459 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 162
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  626 LEU cc_start: 0.8520 (mt) cc_final: 0.7879 (mt)
REVERT: A  649 ASN cc_start: 0.7342 (t0) cc_final: 0.6613 (t0)
REVERT: B  430 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8317 (mp)
REVERT: B  438 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8819 (mp)
REVERT: B  550 ARG cc_start: 0.8334 (mtt90) cc_final: 0.7958 (mmt90)
REVERT: B  569 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6588 (mp)
REVERT: B  673 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7431 (tptp)
REVERT: B  720 ILE cc_start: 0.7157 (mm) cc_final: 0.6937 (mm)
REVERT: B  754 THR cc_start: 0.5437 (OUTLIER) cc_final: 0.5117 (p)
REVERT: F  499 LYS cc_start: 0.7835 (tptp) cc_final: 0.7576 (tptp)
REVERT: F  504 ARG cc_start: 0.8450 (tpt90) cc_final: 0.8103 (tpt90)
REVERT: F  538 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7525 (mm)
REVERT: F  545 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8306 (mmmt)
REVERT: F  588 MET cc_start: 0.7365 (mmp) cc_final: 0.6692 (mmm)
REVERT: F  598 HIS cc_start: 0.8765 (t-170) cc_final: 0.8362 (t70)
REVERT: F  611 LEU cc_start: 0.8658 (mm) cc_final: 0.8413 (mm)
REVERT: F  617 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8176 (mt)
REVERT: F  633 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7423 (t80)
REVERT: F  638 LYS cc_start: 0.7511 (mttt) cc_final: 0.7195 (ptmt)
REVERT: F  643 LYS cc_start: 0.8109 (mttt) cc_final: 0.7780 (mttm)
REVERT: F  727 PHE cc_start: 0.8550 (t80) cc_final: 0.8306 (m-80)
REVERT: F  756 TYR cc_start: 0.7440 (t80) cc_final: 0.7052 (t80)
  outliers start: 50
  outliers final: 33
  residues processed: 188
  average time/residue: 0.2853
  time to fit residues: 77.6030
Evaluate side-chains
  193 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  534 TYR
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  569 LEU
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  644 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  432 MET
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  538 LEU
Chi-restraints excluded: chain F residue  561 VAL
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  752 LEU
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 116 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 729 GLN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.110807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.090797 restraints weight = 34229.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.090909 restraints weight = 22769.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.091690 restraints weight = 19603.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  10071  Z= 0.151
  Angle     :  0.703  16.954  13642  Z= 0.331
  Chirality :  0.045   0.205   1633
  Planarity :  0.004   0.045   1715
  Dihedral  :  4.763  19.822   1303
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 29.79 %
    Favored  : 65.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.23), residues: 1212
  helix: -2.71 (0.23), residues: 384
  sheet: -2.48 (0.37), residues: 203
  loop : -1.03 (0.25), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 647 
 HIS   0.007   0.001   HIS A 608 
 PHE   0.025   0.002   PHE B 728 
 TYR   0.016   0.002   TYR F 646 
 ARG   0.021   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  238)
  hydrogen bonds       : angle       6.07041 (  504)
  covalent geometry    : bond        0.00357 (10071)
  covalent geometry    : angle       0.70311 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 159
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  591 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8090 (t)
REVERT: A  626 LEU cc_start: 0.8595 (mt) cc_final: 0.7938 (mt)
REVERT: A  649 ASN cc_start: 0.7419 (t0) cc_final: 0.6559 (t0)
REVERT: B  426 ASP cc_start: 0.8293 (m-30) cc_final: 0.7922 (t70)
REVERT: B  438 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8819 (mp)
REVERT: B  506 LYS cc_start: 0.8701 (tptt) cc_final: 0.8153 (tppt)
REVERT: B  550 ARG cc_start: 0.8395 (mtt90) cc_final: 0.7832 (mtt-85)
REVERT: B  590 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7246 (pmm)
REVERT: B  673 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7427 (tptp)
REVERT: B  754 THR cc_start: 0.5329 (OUTLIER) cc_final: 0.5031 (p)
REVERT: F  476 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.5851 (mm-40)
REVERT: F  504 ARG cc_start: 0.8473 (tpt90) cc_final: 0.8090 (tpt90)
REVERT: F  545 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8275 (mmmt)
REVERT: F  588 MET cc_start: 0.7495 (mmp) cc_final: 0.7037 (mmm)
REVERT: F  598 HIS cc_start: 0.8786 (t-170) cc_final: 0.8387 (t70)
REVERT: F  617 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8224 (mt)
REVERT: F  633 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7263 (t80)
REVERT: F  638 LYS cc_start: 0.7486 (mttt) cc_final: 0.7169 (ptmt)
REVERT: F  693 ASN cc_start: 0.7497 (m-40) cc_final: 0.7203 (m110)
  outliers start: 49
  outliers final: 37
  residues processed: 184
  average time/residue: 0.3414
  time to fit residues: 90.3803
Evaluate side-chains
  199 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 154
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  644 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  683 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  476 GLN
Chi-restraints excluded: chain F residue  516 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  752 LEU
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0770
   chunk 69 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0870
   overall best weight:    0.5716

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 650 HIS
B 758 GLN
F 558 GLN
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.112490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.091692 restraints weight = 34196.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.092592 restraints weight = 22525.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.093621 restraints weight = 16861.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10071  Z= 0.114
  Angle     :  0.703  15.024  13642  Z= 0.328
  Chirality :  0.044   0.196   1633
  Planarity :  0.004   0.045   1715
  Dihedral  :  4.600  20.366   1303
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 30.67 %
    Favored  : 65.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.23), residues: 1212
  helix: -2.59 (0.23), residues: 385
  sheet: -2.42 (0.37), residues: 201
  loop : -1.01 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 411 
 HIS   0.007   0.001   HIS A 608 
 PHE   0.012   0.001   PHE B 728 
 TYR   0.011   0.002   TYR F 511 
 ARG   0.011   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03044 (  238)
  hydrogen bonds       : angle       5.84384 (  504)
  covalent geometry    : bond        0.00267 (10071)
  covalent geometry    : angle       0.70266 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 1.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  591 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8108 (t)
REVERT: A  626 LEU cc_start: 0.8418 (mt) cc_final: 0.7818 (mt)
REVERT: A  649 ASN cc_start: 0.7204 (t0) cc_final: 0.6500 (t0)
REVERT: B  430 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8358 (mp)
REVERT: B  506 LYS cc_start: 0.8660 (tptt) cc_final: 0.8101 (tppt)
REVERT: B  550 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7764 (mtt-85)
REVERT: B  590 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7314 (pmm)
REVERT: B  673 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7385 (tptp)
REVERT: B  754 THR cc_start: 0.5280 (OUTLIER) cc_final: 0.5025 (p)
REVERT: F  504 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8047 (tpt90)
REVERT: F  545 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8236 (mmmt)
REVERT: F  581 MET cc_start: 0.7186 (ppp) cc_final: 0.6281 (ppp)
REVERT: F  588 MET cc_start: 0.7408 (mmp) cc_final: 0.6868 (mmm)
REVERT: F  598 HIS cc_start: 0.8757 (t-170) cc_final: 0.8398 (t70)
REVERT: F  617 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (mt)
REVERT: F  633 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7018 (t80)
REVERT: F  638 LYS cc_start: 0.7445 (mttt) cc_final: 0.7191 (ptmt)
REVERT: F  646 TYR cc_start: 0.6814 (m-80) cc_final: 0.6542 (m-10)
  outliers start: 43
  outliers final: 29
  residues processed: 188
  average time/residue: 0.2866
  time to fit residues: 75.2186
Evaluate side-chains
  194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  644 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain B residue  756 LEU
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  752 LEU
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.111071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.090752 restraints weight = 34575.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.090903 restraints weight = 22363.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.091709 restraints weight = 19094.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.5792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10071  Z= 0.147
  Angle     :  0.728  13.570  13642  Z= 0.342
  Chirality :  0.045   0.196   1633
  Planarity :  0.005   0.054   1715
  Dihedral  :  4.709  20.917   1303
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 31.55 %
    Favored  : 65.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.24), residues: 1212
  helix: -2.51 (0.24), residues: 378
  sheet: -2.27 (0.37), residues: 200
  loop : -0.97 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP F 645 
 HIS   0.007   0.001   HIS A 608 
 PHE   0.013   0.002   PHE B 728 
 TYR   0.021   0.002   TYR B 689 
 ARG   0.005   0.001   ARG B 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03114 (  238)
  hydrogen bonds       : angle       5.95152 (  504)
  covalent geometry    : bond        0.00346 (10071)
  covalent geometry    : angle       0.72845 (13642)

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

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 160
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  591 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8120 (t)
REVERT: A  626 LEU cc_start: 0.8459 (mt) cc_final: 0.7889 (mt)
REVERT: A  649 ASN cc_start: 0.7335 (t0) cc_final: 0.6490 (t0)
REVERT: B  426 ASP cc_start: 0.8323 (m-30) cc_final: 0.7954 (t70)
REVERT: B  430 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8359 (mp)
REVERT: B  438 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8787 (mp)
REVERT: B  506 LYS cc_start: 0.8642 (tptt) cc_final: 0.8383 (tppt)
REVERT: B  550 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7772 (mtt-85)
REVERT: B  590 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7430 (pmm)
REVERT: B  673 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7393 (tptp)
REVERT: B  754 THR cc_start: 0.5246 (OUTLIER) cc_final: 0.5005 (p)
REVERT: F  504 ARG cc_start: 0.8357 (tpt90) cc_final: 0.7951 (tpt90)
REVERT: F  545 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8224 (mmmt)
REVERT: F  581 MET cc_start: 0.7395 (ppp) cc_final: 0.6482 (ppp)
REVERT: F  588 MET cc_start: 0.7463 (mmp) cc_final: 0.7018 (mmm)
REVERT: F  598 HIS cc_start: 0.8735 (t-170) cc_final: 0.8387 (t70)
REVERT: F  617 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8241 (mt)
REVERT: F  633 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6984 (t80)
REVERT: F  638 LYS cc_start: 0.7646 (mttt) cc_final: 0.7336 (ptmt)
  outliers start: 38
  outliers final: 29
  residues processed: 181
  average time/residue: 0.2049
  time to fit residues: 53.4318
Evaluate side-chains
  194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASP
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  591 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  609 SER
Chi-restraints excluded: chain A residue  611 PHE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  590 MET
Chi-restraints excluded: chain B residue  613 LEU
Chi-restraints excluded: chain B residue  644 LEU
Chi-restraints excluded: chain B residue  673 LYS
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  709 ASN
Chi-restraints excluded: chain B residue  754 THR
Chi-restraints excluded: chain F residue  449 LEU
Chi-restraints excluded: chain F residue  617 LEU
Chi-restraints excluded: chain F residue  627 ILE
Chi-restraints excluded: chain F residue  633 PHE
Chi-restraints excluded: chain F residue  694 ASP
Chi-restraints excluded: chain F residue  697 PHE
Chi-restraints excluded: chain F residue  708 LEU
Chi-restraints excluded: chain F residue  752 LEU
Chi-restraints excluded: chain F residue  784 VAL
Chi-restraints excluded: chain F residue  789 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0370
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 111 optimal weight:    0.2980
   overall best weight:    0.6462

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

Flipped N/Q/H residues before XYZ refinement:
A 431 HIS
** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 HIS
B 494 ASN
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.112352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.091671 restraints weight = 34482.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.092356 restraints weight = 22605.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.093286 restraints weight = 17457.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10071  Z= 0.119
  Angle     :  0.710  13.988  13642  Z= 0.330
  Chirality :  0.044   0.190   1633
  Planarity :  0.004   0.048   1715
  Dihedral  :  4.583  21.100   1303
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 30.84 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.24), residues: 1212
  helix: -2.46 (0.24), residues: 385
  sheet: -2.27 (0.37), residues: 201
  loop : -1.00 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP F 645 
 HIS   0.007   0.001   HIS A 608 
 PHE   0.023   0.001   PHE B 728 
 TYR   0.012   0.001   TYR F 687 
 ARG   0.005   0.000   ARG B 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02926 (  238)
  hydrogen bonds       : angle       5.81781 (  504)
  covalent geometry    : bond        0.00279 (10071)
  covalent geometry    : angle       0.70967 (13642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3770.00 seconds
wall clock time: 68 minutes 34.05 seconds (4114.05 seconds total)