Starting phenix.real_space_refine
on Wed Sep 17 08:40:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9n_27267/09_2025/8d9n_27267.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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    4840      2.51       5
     N    1126      2.21       5
     O    1188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7186
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3594
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 24, 'TRANS': 426}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3592
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 24, 'TRANS': 426}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
  Residues with excluded nonbonded symmetry interactions: 382
    residue:
      pdb=" N   SER A 420 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER A 420 " occ=0.00
    residue:
      pdb=" N   PRO A 421 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO A 421 " occ=0.00
    residue:
      pdb=" N   SER A 425 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER A 425 " occ=0.00
    residue:
      pdb=" N   ALA A 426 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 426 " occ=0.00
    residue:
      pdb=" N   PHE A 429 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 429 " occ=0.00
    residue:
      pdb=" N   TYR A 431 " occ=0.00
      ... (10 atoms not shown)
      pdb=" OH  TYR A 431 " occ=0.00
    residue:
      pdb=" N   PHE A 432 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 432 " occ=0.00
    residue:
      pdb=" N   ALA A 433 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 433 " occ=0.00
    residue:
      pdb=" N   ALA A 434 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 434 " occ=0.00
    residue:
      pdb=" N   PRO A 437 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO A 437 " occ=0.00
    residue:
      pdb=" N   ALA A 438 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 438 " occ=0.00
    residue:
      pdb=" N   PHE A 441 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 441 " occ=0.00
    ... (remaining 370 not shown)
  Time building chain proxies: 2.14, per 1000 atoms: 0.30
  Number of scatterers: 7186
  At special positions: 0
  Unit cell: (121.04, 77.52, 84.32, 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    1188      8.00
     N    1126      7.00
     C    4840      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 457.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      70.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 420 through 449
      removed outlier: 3.795A  pdb=" N   ILE A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 3.875A  pdb=" N   THR A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 471
      removed outlier: 3.632A  pdb=" N   ALA A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN A 465 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 500
      removed outlier: 3.536A  pdb=" N   THR A 499 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN A 500 " --> pdb=" O   PHE A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 525
      removed outlier: 3.559A  pdb=" N   VAL A 520 " --> pdb=" O   ILE A 516 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE A 525 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 534
      removed outlier: 4.545A  pdb=" N   LEU A 530 " --> pdb=" O   GLY A 527 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 534 " --> pdb=" O   VAL A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 565
      removed outlier: 3.928A  pdb=" N   ILE A 541 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A 543 " --> pdb=" O   GLN A 539 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE A 544 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 545 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ILE A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR A 554 " --> pdb=" O   PHE A 550 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 555 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS A 557 " --> pdb=" O   GLU A 553 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU A 558 " --> pdb=" O   THR A 554 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 611
      removed outlier: 3.513A  pdb=" N   THR A 599 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A 600 " --> pdb=" O   MET A 596 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 625
      removed outlier: 3.631A  pdb=" N   ARG A 620 " --> pdb=" O   PRO A 616 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ILE A 623 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 631
    Processing helix  chain 'A' and resid 632 through 642
    Processing helix  chain 'A' and resid 678 through 682
    Processing helix  chain 'A' and resid 686 through 703
      removed outlier: 3.620A  pdb=" N   LEU A 691 " --> pdb=" O   LEU A 687 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL A 692 " --> pdb=" O   PRO A 688 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A 701 " --> pdb=" O   PHE A 697 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR A 703 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 734
    Processing helix  chain 'A' and resid 776 through 791
      removed outlier: 3.590A  pdb=" N   SER A 780 " --> pdb=" O   GLU A 776 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY A 781 " --> pdb=" O   GLN A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 802 through 820
      removed outlier: 3.664A  pdb=" N   LEU A 806 " --> pdb=" O   PRO A 802 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU A 818 " --> pdb=" O   GLY A 814 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 820 " --> pdb=" O   THR A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 832
      removed outlier: 3.874A  pdb=" N   LEU A 829 " --> pdb=" O   ASP A 825 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 871
      removed outlier: 3.688A  pdb=" N   HIS A 852 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 853 " --> pdb=" O   TRP A 849 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 854 " --> pdb=" O   ARG A 850 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   CYS A 861 " --> pdb=" O   THR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 884
      removed outlier: 3.700A  pdb=" N   LEU A 884 " --> pdb=" O   PHE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 891
      removed outlier: 3.757A  pdb=" N   LEU A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 897
      removed outlier: 3.717A  pdb=" N   ILE A 896 " --> pdb=" O   LEU A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 903
    Processing helix  chain 'B' and resid 421 through 449
      removed outlier: 3.795A  pdb=" N   ILE B 428 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
      removed outlier: 3.875A  pdb=" N   THR B 440 " --> pdb=" O   THR B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 471
      removed outlier: 3.632A  pdb=" N   ALA B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN B 465 " --> pdb=" O   SER B 461 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ILE B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 500
      removed outlier: 3.536A  pdb=" N   THR B 499 " --> pdb=" O   SER B 495 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN B 500 " --> pdb=" O   PHE B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 525
      removed outlier: 3.559A  pdb=" N   VAL B 520 " --> pdb=" O   ILE B 516 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 521 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL B 522 " --> pdb=" O   LEU B 518 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE B 525 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 534
      removed outlier: 4.545A  pdb=" N   LEU B 530 " --> pdb=" O   GLY B 527 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE B 534 " --> pdb=" O   VAL B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 565
      removed outlier: 3.928A  pdb=" N   ILE B 541 " --> pdb=" O   TYR B 537 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B 543 " --> pdb=" O   GLN B 539 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE B 544 " --> pdb=" O   GLU B 540 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B 545 " --> pdb=" O   ILE B 541 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ILE B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR B 554 " --> pdb=" O   PHE B 550 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE B 555 " --> pdb=" O   ILE B 551 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS B 557 " --> pdb=" O   GLU B 553 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU B 558 " --> pdb=" O   THR B 554 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL B 559 " --> pdb=" O   PHE B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 611
      removed outlier: 3.512A  pdb=" N   THR B 599 " --> pdb=" O   LEU B 595 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE B 600 " --> pdb=" O   MET B 596 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN B 611 " --> pdb=" O   ARG B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 625
      removed outlier: 3.632A  pdb=" N   ARG B 620 " --> pdb=" O   PRO B 616 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ILE B 623 " --> pdb=" O   LEU B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 631
    Processing helix  chain 'B' and resid 632 through 642
    Processing helix  chain 'B' and resid 678 through 682
    Processing helix  chain 'B' and resid 686 through 703
      removed outlier: 3.622A  pdb=" N   LEU B 691 " --> pdb=" O   LEU B 687 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   VAL B 692 " --> pdb=" O   PRO B 688 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN B 701 " --> pdb=" O   PHE B 697 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ILE B 702 " --> pdb=" O   LEU B 698 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   THR B 703 " --> pdb=" O   GLU B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 734
    Processing helix  chain 'B' and resid 776 through 791
      removed outlier: 3.590A  pdb=" N   SER B 780 " --> pdb=" O   GLU B 776 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLY B 781 " --> pdb=" O   GLN B 777 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 794 through 799
    Processing helix  chain 'B' and resid 802 through 820
      removed outlier: 3.664A  pdb=" N   LEU B 806 " --> pdb=" O   PRO B 802 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU B 818 " --> pdb=" O   GLY B 814 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 820 " --> pdb=" O   THR B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 823 through 832
      removed outlier: 3.875A  pdb=" N   LEU B 829 " --> pdb=" O   ASP B 825 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 831 " --> pdb=" O   VAL B 827 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 847 through 871
      removed outlier: 3.689A  pdb=" N   HIS B 852 " --> pdb=" O   THR B 848 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU B 853 " --> pdb=" O   TRP B 849 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE B 854 " --> pdb=" O   ARG B 850 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   CYS B 861 " --> pdb=" O   THR B 857 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 877 through 884
      removed outlier: 3.700A  pdb=" N   LEU B 884 " --> pdb=" O   PHE B 880 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 884 through 891
      removed outlier: 3.757A  pdb=" N   LEU B 888 " --> pdb=" O   LEU B 884 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 892 through 897
      removed outlier: 3.718A  pdb=" N   ILE B 896 " --> pdb=" O   LEU B 892 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 898 through 903
    Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481
    Processing sheet with id=AA2, first strand: chain 'B' and resid 480 through 481

    361 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.02

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2134
        1.34 -     1.46: 1632
        1.46 -     1.58: 3540
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 7366
  Sorted by residual:
  bond pdb=" N   VAL B 784 "
       pdb=" CA  VAL B 784 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.19e-02 7.06e+03 7.83e+00
  bond pdb=" N   ILE B 728 "
       pdb=" CA  ILE B 728 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.17e-02 7.31e+03 6.94e+00
  bond pdb=" N   ILE A 549 "
       pdb=" CA  ILE A 549 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.031 1.30e-02 5.92e+03 5.83e+00
  bond pdb=" N   HIS B 721 "
       pdb=" CA  HIS B 721 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.38e+00
  bond pdb=" N   LEU A 545 "
       pdb=" CA  LEU A 545 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.96e+00
  ... (remaining 7361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 9412
        1.07 -     2.13: 452
        2.13 -     3.20: 117
        3.20 -     4.27: 39
        4.27 -     5.33: 6
  Bond angle restraints: 10026
  Sorted by residual:
  angle pdb=" CA  ILE B 728 "
        pdb=" C   ILE B 728 "
        pdb=" O   ILE B 728 "
      ideal   model   delta    sigma   weight residual
     121.17  117.43    3.74 1.06e+00 8.90e-01 1.25e+01
  angle pdb=" CA  LEU B 515 "
        pdb=" C   LEU B 515 "
        pdb=" O   LEU B 515 "
      ideal   model   delta    sigma   weight residual
     120.20  116.77    3.43 1.12e+00 7.97e-01 9.40e+00
  angle pdb=" CA  ILE A 549 "
        pdb=" C   ILE A 549 "
        pdb=" O   ILE A 549 "
      ideal   model   delta    sigma   weight residual
     120.47  117.34    3.13 1.08e+00 8.57e-01 8.38e+00
  angle pdb=" CA  VAL B 784 "
        pdb=" C   VAL B 784 "
        pdb=" O   VAL B 784 "
      ideal   model   delta    sigma   weight residual
     120.95  117.97    2.98 1.04e+00 9.25e-01 8.19e+00
  angle pdb=" CA  LEU A 545 "
        pdb=" C   LEU A 545 "
        pdb=" O   LEU A 545 "
      ideal   model   delta    sigma   weight residual
     120.42  117.54    2.88 1.06e+00 8.90e-01 7.39e+00
  ... (remaining 10021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 3926
       16.05 -    32.09: 303
       32.09 -    48.14: 76
       48.14 -    64.19: 19
       64.19 -    80.23: 8
  Dihedral angle restraints: 4332
    sinusoidal: 1718
      harmonic: 2614
  Sorted by residual:
  dihedral pdb=" CA  MET A 635 "
           pdb=" C   MET A 635 "
           pdb=" N   VAL A 636 "
           pdb=" CA  VAL A 636 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.32   24.68     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  MET B 635 "
           pdb=" C   MET B 635 "
           pdb=" N   VAL B 636 "
           pdb=" CA  VAL B 636 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.38   24.62     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  LEU B 590 "
           pdb=" C   LEU B 590 "
           pdb=" N   LEU B 591 "
           pdb=" CA  LEU B 591 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.35   19.65     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 904
       0.042 -    0.083: 240
       0.083 -    0.125: 63
       0.125 -    0.166: 8
       0.166 -    0.208: 3
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CA  ILE A 549 "
            pdb=" N   ILE A 549 "
            pdb=" C   ILE A 549 "
            pdb=" CB  ILE A 549 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE B 707 "
            pdb=" N   ILE B 707 "
            pdb=" C   ILE B 707 "
            pdb=" CB  ILE B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" CA  VAL B 747 "
            pdb=" N   VAL B 747 "
            pdb=" C   VAL B 747 "
            pdb=" CB  VAL B 747 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 1215 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 680 "    0.012 2.00e-02 2.50e+03   1.18e-02 3.47e+00
        pdb=" CG  TRP A 680 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 680 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 680 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 680 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 680 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 680 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 680 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 680 "   -0.012 2.00e-02 2.50e+03   1.17e-02 3.43e+00
        pdb=" CG  TRP B 680 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 680 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 680 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 680 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 680 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 680 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 680 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 680 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 680 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 840 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO B 841 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 841 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 841 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 96
        2.67 -     3.22: 7349
        3.22 -     3.78: 10655
        3.78 -     4.34: 14552
        4.34 -     4.90: 22673
  Nonbonded interactions: 55325
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 696 "
            pdb=" OG  SER B 700 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" O   ILE A 696 "
            pdb=" OG  SER A 700 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OH  TYR A 431 "
            pdb=" OG  SER A 791 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OH  TYR B 431 "
            pdb=" OG  SER B 791 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   VAL B 479 "
            pdb=" OG1 THR B 745 "
     model   vdw
     2.183 3.040
  ... (remaining 55320 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' and (resid 420 through 706 or (resid 707 and (name N or name CA or na \ 
me C or name CB or name CG1 or name CG2 or name CD1)) or resid 720 through 746 o \ 
r (resid 747 and (name N or name CA or name C or name CB or name CG1 or name CG2 \ 
)) or resid 775 through 909))
  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=0.00 max=1.00 mean=0.30
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:             0.570
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.910
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0695
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   0.037   7366  Z= 0.150
  Angle     :  0.600   5.335  10026  Z= 0.336
  Chirality :  0.042   0.208   1218
  Planarity :  0.005   0.043   1208
  Dihedral  : 13.205  80.232   2640
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.38 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.29), residues: 890
  helix:  0.12 (0.24), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.38 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 869 
 TYR   0.006   0.001   TYR B 836 
 PHE   0.008   0.001   PHE B 513 
 TRP   0.032   0.002   TRP A 680 
 HIS   0.001   0.000   HIS A 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7366)
  covalent geometry    : angle       0.59969 (10026)
  hydrogen bonds       : bond        0.20680 (  361)
  hydrogen bonds       : angle       7.05944 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 PHE cc_start: -0.0240 (t80) cc_final: -0.0475 (t80)
REVERT: A  861 CYS cc_start: 0.2646 (m) cc_final: 0.2192 (p)
REVERT: B  861 CYS cc_start: 0.3385 (m) cc_final: 0.2825 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0663
  time to fit residues: 9.4635
Evaluate side-chains
  70 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    3.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5678 r_free = 0.5678 target = 0.244971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.5199 r_free = 0.5199 target = 0.215729 restraints weight = 41466.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5226 r_free = 0.5226 target = 0.218451 restraints weight = 33663.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.220987 restraints weight = 27680.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.5276 r_free = 0.5276 target = 0.223171 restraints weight = 23657.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.5307 r_free = 0.5307 target = 0.225182 restraints weight = 20706.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.5194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0367
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7366  Z= 0.209
  Angle     :  0.669   6.264  10026  Z= 0.344
  Chirality :  0.043   0.157   1218
  Planarity :  0.006   0.049   1208
  Dihedral  :  4.397  19.844    960
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.29), residues: 890
  helix:  0.55 (0.23), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.56 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 869 
 TYR   0.007   0.001   TYR A 504 
 PHE   0.017   0.002   PHE A 489 
 TRP   0.012   0.002   TRP A 866 
 HIS   0.003   0.001   HIS B 565 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7366)
  covalent geometry    : angle       0.66897 (10026)
  hydrogen bonds       : bond        0.04804 (  361)
  hydrogen bonds       : angle       4.87042 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  739 MET cc_start: 0.4348 (mpp) cc_final: 0.3389 (mpp)
REVERT: A  861 CYS cc_start: 0.4206 (m) cc_final: 0.3927 (p)
REVERT: B  739 MET cc_start: 0.4012 (mpp) cc_final: 0.2965 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0605
  time to fit residues: 7.4668
Evaluate side-chains
  57 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 76 optimal weight:    0.1980
   chunk 22 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 858 GLN
B 858 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5684 r_free = 0.5684 target = 0.244797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5220 r_free = 0.5220 target = 0.216232 restraints weight = 40330.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5243 r_free = 0.5243 target = 0.218480 restraints weight = 32590.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.5267 r_free = 0.5267 target = 0.221389 restraints weight = 26681.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.224057 restraints weight = 22699.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.225207 restraints weight = 20057.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.5321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0459
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7366  Z= 0.113
  Angle     :  0.599   7.264  10026  Z= 0.290
  Chirality :  0.044   0.173   1218
  Planarity :  0.005   0.049   1208
  Dihedral  :  4.300  19.104    960
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.29), residues: 890
  helix:  0.73 (0.23), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.32 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.005   0.001   TYR A 842 
 PHE   0.018   0.001   PHE B 489 
 TRP   0.014   0.001   TRP A 866 
 HIS   0.002   0.001   HIS B 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7366)
  covalent geometry    : angle       0.59930 (10026)
  hydrogen bonds       : bond        0.04025 (  361)
  hydrogen bonds       : angle       4.36334 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  739 MET cc_start: 0.3404 (mpp) cc_final: 0.3204 (mpp)
REVERT: A  861 CYS cc_start: 0.3871 (m) cc_final: 0.3534 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0601
  time to fit residues: 8.7838
Evaluate side-chains
  64 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0870
   chunk 48 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    1.4564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5700 r_free = 0.5700 target = 0.246551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5348 r_free = 0.5348 target = 0.222261 restraints weight = 41638.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.5350 r_free = 0.5350 target = 0.223120 restraints weight = 33588.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.223975 restraints weight = 26489.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.5363 r_free = 0.5363 target = 0.224945 restraints weight = 23568.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5374 r_free = 0.5374 target = 0.226359 restraints weight = 21175.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.5374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0541
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7366  Z= 0.117
  Angle     :  0.579   6.460  10026  Z= 0.284
  Chirality :  0.043   0.161   1218
  Planarity :  0.005   0.049   1208
  Dihedral  :  4.206  18.837    960
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.29), residues: 890
  helix:  0.81 (0.23), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.50 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 869 
 TYR   0.009   0.001   TYR A 842 
 PHE   0.015   0.001   PHE B 489 
 TRP   0.012   0.001   TRP A 866 
 HIS   0.001   0.000   HIS B 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7366)
  covalent geometry    : angle       0.57938 (10026)
  hydrogen bonds       : bond        0.03592 (  361)
  hydrogen bonds       : angle       4.10837 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 CYS cc_start: 0.3840 (m) cc_final: 0.3538 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0613
  time to fit residues: 8.0338
Evaluate side-chains
  55 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   chunk 76 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5704 r_free = 0.5704 target = 0.246549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5251 r_free = 0.5251 target = 0.216518 restraints weight = 41958.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5242 r_free = 0.5242 target = 0.217960 restraints weight = 36771.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 93)----------------|
| r_work = 0.5236 r_free = 0.5236 target = 0.220802 restraints weight = 30692.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5252 r_free = 0.5252 target = 0.222400 restraints weight = 26791.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.5268 r_free = 0.5268 target = 0.223863 restraints weight = 23600.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.5116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0344
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7366  Z= 0.136
  Angle     :  0.592   6.484  10026  Z= 0.290
  Chirality :  0.043   0.161   1218
  Planarity :  0.005   0.046   1208
  Dihedral  :  4.156  18.129    960
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.29), residues: 890
  helix:  0.88 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.52 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 850 
 TYR   0.005   0.001   TYR A 842 
 PHE   0.016   0.001   PHE A 513 
 TRP   0.017   0.001   TRP A 866 
 HIS   0.001   0.001   HIS A 573 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7366)
  covalent geometry    : angle       0.59231 (10026)
  hydrogen bonds       : bond        0.03323 (  361)
  hydrogen bonds       : angle       4.03369 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  739 MET cc_start: 0.3750 (mpp) cc_final: 0.3477 (mpp)
REVERT: A  861 CYS cc_start: 0.4585 (m) cc_final: 0.4326 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0618
  time to fit residues: 7.9863
Evaluate side-chains
  56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0470
   chunk 63 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 60 optimal weight:   20.0000
   chunk 50 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    2.0086

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

Flipped N/Q/H residues before XYZ refinement:
A 822 GLN
B 822 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5708 r_free = 0.5708 target = 0.246558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.217972 restraints weight = 42793.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5273 r_free = 0.5273 target = 0.220191 restraints weight = 35189.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.220007 restraints weight = 32323.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.220902 restraints weight = 31805.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5289 r_free = 0.5289 target = 0.223620 restraints weight = 26169.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.5288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0384
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7366  Z= 0.130
  Angle     :  0.602   6.322  10026  Z= 0.292
  Chirality :  0.043   0.157   1218
  Planarity :  0.005   0.048   1208
  Dihedral  :  4.135  18.550    960
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.26 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.30), residues: 890
  helix:  0.97 (0.23), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.46 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 869 
 TYR   0.006   0.001   TYR B 646 
 PHE   0.017   0.001   PHE B 489 
 TRP   0.018   0.002   TRP A 866 
 HIS   0.002   0.000   HIS A 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7366)
  covalent geometry    : angle       0.60191 (10026)
  hydrogen bonds       : bond        0.03189 (  361)
  hydrogen bonds       : angle       3.95931 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 CYS cc_start: 0.4578 (m) cc_final: 0.4250 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0581
  time to fit residues: 7.5634
Evaluate side-chains
  54 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.5764

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5709 r_free = 0.5709 target = 0.246570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5330 r_free = 0.5330 target = 0.221127 restraints weight = 42887.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5331 r_free = 0.5331 target = 0.221943 restraints weight = 32073.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.223048 restraints weight = 26352.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.5348 r_free = 0.5348 target = 0.224151 restraints weight = 22644.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5358 r_free = 0.5358 target = 0.225614 restraints weight = 20203.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.5358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0466
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7366  Z= 0.114
  Angle     :  0.608   6.079  10026  Z= 0.289
  Chirality :  0.043   0.155   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.113  17.534    960
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.30), residues: 890
  helix:  1.02 (0.23), residues: 575
  sheet:  None (None), residues: 0
  loop : -1.30 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 850 
 TYR   0.005   0.001   TYR A 842 
 PHE   0.016   0.001   PHE A 489 
 TRP   0.016   0.001   TRP A 866 
 HIS   0.003   0.001   HIS A 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7366)
  covalent geometry    : angle       0.60781 (10026)
  hydrogen bonds       : bond        0.03110 (  361)
  hydrogen bonds       : angle       3.81232 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 CYS cc_start: 0.3883 (m) cc_final: 0.3478 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0586
  time to fit residues: 7.5005
Evaluate side-chains
  56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 85 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0870
   overall best weight:    0.6964

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5712 r_free = 0.5712 target = 0.246807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223031 restraints weight = 42852.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223757 restraints weight = 34120.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223777 restraints weight = 27107.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223781 restraints weight = 27018.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223783 restraints weight = 27000.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.5147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0538
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7366  Z= 0.103
  Angle     :  0.621   7.370  10026  Z= 0.289
  Chirality :  0.043   0.156   1218
  Planarity :  0.005   0.048   1208
  Dihedral  :  4.070  18.182    960
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.30), residues: 890
  helix:  0.96 (0.22), residues: 587
  sheet:  None (None), residues: 0
  loop : -1.11 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 850 
 TYR   0.005   0.001   TYR A 842 
 PHE   0.019   0.001   PHE B 489 
 TRP   0.015   0.001   TRP A 866 
 HIS   0.003   0.001   HIS A 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7366)
  covalent geometry    : angle       0.62090 (10026)
  hydrogen bonds       : bond        0.03017 (  361)
  hydrogen bonds       : angle       3.75616 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 CYS cc_start: 0.3894 (m) cc_final: 0.3494 (p)
REVERT: B  545 LEU cc_start: -0.6428 (pp) cc_final: -0.6702 (pp)
REVERT: B  693 PHE cc_start: -0.0088 (t80) cc_final: -0.0862 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0566
  time to fit residues: 7.3907
Evaluate side-chains
  60 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 89 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5704 r_free = 0.5704 target = 0.246260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5283 r_free = 0.5283 target = 0.217719 restraints weight = 42522.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5307 r_free = 0.5307 target = 0.218975 restraints weight = 38760.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.220619 restraints weight = 33485.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5317 r_free = 0.5317 target = 0.222262 restraints weight = 28782.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5298 r_free = 0.5298 target = 0.222903 restraints weight = 26125.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.5298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0388
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7366  Z= 0.110
  Angle     :  0.617   6.401  10026  Z= 0.292
  Chirality :  0.044   0.182   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.093  17.494    960
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.30), residues: 890
  helix:  1.00 (0.22), residues: 591
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 536 
 TYR   0.005   0.001   TYR A 842 
 PHE   0.016   0.001   PHE B 489 
 TRP   0.013   0.001   TRP A 866 
 HIS   0.003   0.001   HIS A 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7366)
  covalent geometry    : angle       0.61730 (10026)
  hydrogen bonds       : bond        0.03037 (  361)
  hydrogen bonds       : angle       3.72014 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  861 CYS cc_start: 0.4433 (m) cc_final: 0.4111 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0591
  time to fit residues: 7.5605
Evaluate side-chains
  56 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5698 r_free = 0.5698 target = 0.245704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.5260 r_free = 0.5260 target = 0.216458 restraints weight = 42675.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.5284 r_free = 0.5284 target = 0.219836 restraints weight = 34737.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.5247 r_free = 0.5247 target = 0.221367 restraints weight = 29524.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.5266 r_free = 0.5266 target = 0.223418 restraints weight = 24563.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.5283 r_free = 0.5283 target = 0.225012 restraints weight = 21633.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.5156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0284
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7366  Z= 0.135
  Angle     :  0.655   6.647  10026  Z= 0.312
  Chirality :  0.044   0.159   1218
  Planarity :  0.005   0.048   1208
  Dihedral  :  4.136  17.977    960
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.30), residues: 890
  helix:  1.12 (0.23), residues: 586
  sheet:  None (None), residues: 0
  loop : -1.06 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 826 
 TYR   0.006   0.001   TYR A 552 
 PHE   0.016   0.001   PHE A 489 
 TRP   0.012   0.001   TRP B 680 
 HIS   0.002   0.001   HIS B 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7366)
  covalent geometry    : angle       0.65511 (10026)
  hydrogen bonds       : bond        0.03121 (  361)
  hydrogen bonds       : angle       3.74062 ( 1047)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  447 ASP cc_start: -0.5451 (p0) cc_final: -0.5698 (p0)
REVERT: A  861 CYS cc_start: 0.4654 (m) cc_final: 0.4323 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0588
  time to fit residues: 7.2114
Evaluate side-chains
  53 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0470
   chunk 74 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5701 r_free = 0.5701 target = 0.245736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.220371 restraints weight = 42869.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.220888 restraints weight = 36655.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.5341 r_free = 0.5341 target = 0.221632 restraints weight = 29282.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.221731 restraints weight = 25928.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.221731 restraints weight = 25577.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.5341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0495
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7366  Z= 0.105
  Angle     :  0.643   7.275  10026  Z= 0.298
  Chirality :  0.044   0.154   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.162  18.547    960
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.30), residues: 890
  helix:  1.05 (0.23), residues: 593
  sheet:  None (None), residues: 0
  loop : -0.87 (0.41), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 799 
 TYR   0.006   0.001   TYR A 552 
 PHE   0.018   0.001   PHE A 489 
 TRP   0.061   0.002   TRP B 680 
 HIS   0.004   0.001   HIS A 852 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7366)
  covalent geometry    : angle       0.64338 (10026)
  hydrogen bonds       : bond        0.03025 (  361)
  hydrogen bonds       : angle       3.58281 ( 1047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1224.94 seconds
wall clock time: 21 minutes 35.86 seconds (1295.86 seconds total)