Starting phenix.real_space_refine
on Tue Sep 24 06:54:20 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_27267.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_27267.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_27267.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_27267.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9n_27267/09_2024/8d9n_27267.cif"
  }
  resolution = 4.4
  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=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 4.63, per 1000 atoms: 0.64
  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: 1.80
  Conformation dependent library (CDL) restraints added in 968.4 milliseconds
  

  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: 0.74
  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: 1.63

  Time building geometry restraints manager: 2.09 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:             0.510
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.020
  Set scattering table:                    0.060
  Process input model:                     19.140
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.900
-------------------------------------------------------------------------------
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= 0.178
  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 (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: -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
 TRP   0.032   0.002   TRP A 680 
 HIS   0.001   0.000   HIS A 573 
 PHE   0.008   0.001   PHE B 513 
 TYR   0.006   0.001   TYR B 836 
 ARG   0.003   0.000   ARG A 869 

*********************** 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 fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 PHE cc_start: -0.0240 (t80) cc_final: -0.0486 (t80)
REVERT: B  861 CYS cc_start: 0.3385 (m) cc_final: 0.2829 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1403
  time to fit residues: 19.5666
Evaluate side-chains
  69 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0570
   chunk 52 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0020
   overall best weight:    0.5708

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0717
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7366  Z= 0.174
  Angle     :  0.623   9.165  10026  Z= 0.307
  Chirality :  0.043   0.167   1218
  Planarity :  0.005   0.050   1208
  Dihedral  :  4.368  20.609    960
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 890
  helix:  0.43 (0.23), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.27 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 866 
 HIS   0.003   0.001   HIS B 721 
 PHE   0.017   0.001   PHE A 489 
 TYR   0.011   0.001   TYR A 504 
 ARG   0.013   0.000   ARG A 869 

*********************** 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
  95 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  682 MET cc_start: -0.2666 (mmp) cc_final: -0.2981 (mmm)
REVERT: A  739 MET cc_start: 0.3790 (mpp) cc_final: 0.2906 (mpp)
REVERT: B  739 MET cc_start: 0.3192 (mpp) cc_final: 0.2450 (mpp)
REVERT: B  861 CYS cc_start: 0.3166 (m) cc_final: 0.2788 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1254
  time to fit residues: 18.3458
Evaluate side-chains
  62 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 81 optimal weight:    0.4980
   chunk 88 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    2.4988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0586
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7366  Z= 0.213
  Angle     :  0.613   6.045  10026  Z= 0.307
  Chirality :  0.043   0.175   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.212  18.213    960
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.28 (0.29), residues: 890
  helix:  0.58 (0.23), residues: 562
  sheet:  None (None), residues: 0
  loop : -1.50 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 866 
 HIS   0.002   0.001   HIS A 565 
 PHE   0.019   0.001   PHE B 807 
 TYR   0.007   0.001   TYR A 842 
 ARG   0.001   0.000   ARG B 850 

*********************** 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
  86 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.1333 (mtp) cc_final: 0.0540 (mtp)
REVERT: B  861 CYS cc_start: 0.3394 (m) cc_final: 0.3053 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1313
  time to fit residues: 17.2564
Evaluate side-chains
  59 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.7986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0602
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7366  Z= 0.176
  Angle     :  0.587   6.853  10026  Z= 0.287
  Chirality :  0.043   0.162   1218
  Planarity :  0.005   0.050   1208
  Dihedral  :  4.207  18.018    960
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  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 (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: -0.12 (0.29), residues: 890
  helix:  0.69 (0.22), residues: 581
  sheet:  None (None), residues: 0
  loop : -1.52 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 510 
 HIS   0.001   0.001   HIS A 573 
 PHE   0.021   0.001   PHE B 513 
 TYR   0.009   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 869 

*********************** 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
  77 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3845 (mmp) cc_final: 0.3638 (mmp)
REVERT: A  635 MET cc_start: 0.1163 (mtp) cc_final: 0.0410 (mtp)
REVERT: B  635 MET cc_start: 0.1255 (mtp) cc_final: 0.0687 (mtp)
REVERT: B  861 CYS cc_start: 0.3499 (m) cc_final: 0.3055 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1349
  time to fit residues: 16.1361
Evaluate side-chains
  58 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 64 optimal weight:    0.2980
   chunk 35 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   chunk 60 optimal weight:   20.0000
   chunk 0 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0656
moved from start:          0.2788

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= 0.140
  Angle     :  0.580   6.831  10026  Z= 0.272
  Chirality :  0.043   0.163   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.069  17.454    960
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -0.01 (0.29), residues: 890
  helix:  0.78 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -1.45 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 866 
 HIS   0.002   0.000   HIS B 852 
 PHE   0.016   0.001   PHE A 513 
 TYR   0.005   0.001   TYR B 842 
 ARG   0.002   0.000   ARG B 850 

*********************** 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
  83 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3846 (mmp) cc_final: 0.3622 (mmp)
REVERT: A  635 MET cc_start: 0.1318 (mtp) cc_final: 0.0547 (mtp)
REVERT: B  861 CYS cc_start: 0.3832 (m) cc_final: 0.3253 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1296
  time to fit residues: 16.6416
Evaluate side-chains
  60 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0636
moved from start:          0.3036

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= 0.151
  Angle     :  0.592   6.212  10026  Z= 0.283
  Chirality :  0.043   0.156   1218
  Planarity :  0.005   0.049   1208
  Dihedral  :  4.049  17.990    960
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.08 (0.30), residues: 890
  helix:  0.83 (0.23), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.37 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 510 
 HIS   0.002   0.000   HIS B 852 
 PHE   0.030   0.001   PHE A 513 
 TYR   0.006   0.001   TYR B 842 
 ARG   0.002   0.000   ARG A 508 

*********************** 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
  81 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3767 (mmp) cc_final: 0.3551 (mmp)
REVERT: A  635 MET cc_start: 0.1426 (mtp) cc_final: 0.0678 (mtp)
REVERT: B  635 MET cc_start: 0.1590 (mtp) cc_final: 0.1045 (mtp)
REVERT: B  861 CYS cc_start: 0.3835 (m) cc_final: 0.3289 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1321
  time to fit residues: 16.3321
Evaluate side-chains
  59 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0050
   chunk 86 optimal weight:    0.0870
   chunk 54 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0870
   overall best weight:    0.4354

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0677
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7366  Z= 0.136
  Angle     :  0.597   6.431  10026  Z= 0.275
  Chirality :  0.043   0.155   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  3.976  17.253    960
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  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 (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:  0.13 (0.30), residues: 890
  helix:  0.75 (0.22), residues: 591
  sheet:  None (None), residues: 0
  loop : -1.15 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 866 
 HIS   0.003   0.000   HIS A 852 
 PHE   0.015   0.001   PHE A 489 
 TYR   0.006   0.001   TYR B 842 
 ARG   0.001   0.000   ARG A 869 

*********************** 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
  84 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  635 MET cc_start: 0.1310 (mtp) cc_final: 0.0569 (mtp)
REVERT: B  635 MET cc_start: 0.1396 (mtp) cc_final: 0.0800 (pmm)
REVERT: B  861 CYS cc_start: 0.3802 (m) cc_final: 0.3276 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1318
  time to fit residues: 16.9528
Evaluate side-chains
  59 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    9.9990
   chunk 68 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0635
moved from start:          0.3315

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= 0.153
  Angle     :  0.600   6.817  10026  Z= 0.283
  Chirality :  0.043   0.154   1218
  Planarity :  0.005   0.048   1208
  Dihedral  :  3.977  17.488    960
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.91
  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 (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:  0.19 (0.30), residues: 890
  helix:  0.78 (0.22), residues: 591
  sheet:  None (None), residues: 0
  loop : -1.11 (0.40), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 866 
 HIS   0.003   0.001   HIS A 852 
 PHE   0.016   0.001   PHE B 489 
 TYR   0.006   0.001   TYR B 842 
 ARG   0.001   0.000   ARG A 869 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3871 (mmp) cc_final: 0.3584 (mmp)
REVERT: A  635 MET cc_start: 0.1342 (mtp) cc_final: 0.0584 (mtp)
REVERT: B  635 MET cc_start: 0.1369 (mtp) cc_final: 0.0867 (mtp)
REVERT: B  861 CYS cc_start: 0.3862 (m) cc_final: 0.3289 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1353
  time to fit residues: 17.2366
Evaluate side-chains
  60 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0170
   chunk 48 optimal weight:    0.0010
   chunk 35 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0060
   chunk 73 optimal weight:    0.0870
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.1818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0681
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7366  Z= 0.138
  Angle     :  0.624   7.953  10026  Z= 0.286
  Chirality :  0.043   0.154   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  4.016  16.875    960
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  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 (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:  0.18 (0.30), residues: 890
  helix:  0.74 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.04 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 680 
 HIS   0.007   0.001   HIS A 852 
 PHE   0.017   0.001   PHE B 489 
 TYR   0.006   0.001   TYR B 842 
 ARG   0.002   0.000   ARG A 536 

*********************** 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
  86 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3875 (mmp) cc_final: 0.3656 (mmp)
REVERT: A  635 MET cc_start: 0.1102 (mtp) cc_final: 0.0464 (mtp)
REVERT: B  635 MET cc_start: 0.1436 (mtp) cc_final: 0.0880 (pmm)
REVERT: B  861 CYS cc_start: 0.3778 (m) cc_final: 0.3265 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1384
  time to fit residues: 18.1801
Evaluate side-chains
  64 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 71 optimal weight:    0.1980
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.4984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0624
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7366  Z= 0.158
  Angle     :  0.617   6.692  10026  Z= 0.291
  Chirality :  0.043   0.151   1218
  Planarity :  0.005   0.048   1208
  Dihedral  :  3.994  17.254    960
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.63 %
    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 (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:  0.34 (0.30), residues: 890
  helix:  0.85 (0.23), residues: 595
  sheet:  None (None), residues: 0
  loop : -0.97 (0.40), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 680 
 HIS   0.006   0.001   HIS A 852 
 PHE   0.015   0.001   PHE B 489 
 TYR   0.006   0.001   TYR B 842 
 ARG   0.002   0.000   ARG A 869 

********************** 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
  84 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 MET cc_start: 0.3817 (mmp) cc_final: 0.3566 (mmp)
REVERT: A  635 MET cc_start: 0.1153 (mtp) cc_final: 0.0512 (mtp)
REVERT: B  635 MET cc_start: 0.1672 (mtp) cc_final: 0.1227 (mtp)
REVERT: B  861 CYS cc_start: 0.3877 (m) cc_final: 0.3360 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1279
  time to fit residues: 16.4938
Evaluate side-chains
  59 residues out of total 798 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0870
   chunk 19 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0770
   chunk 29 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 62 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0000
   overall best weight:    0.2920

-------------------------------------------------------------------------------
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 = 0.5716 r_free = 0.5716 target = 0.247337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.223505 restraints weight = 42348.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.224320 restraints weight = 32992.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.224321 restraints weight = 26053.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.5360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0567
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7366  Z= 0.136
  Angle     :  0.625   7.363  10026  Z= 0.287
  Chirality :  0.043   0.172   1218
  Planarity :  0.005   0.047   1208
  Dihedral  :  3.948  17.120    960
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.30), residues: 890
  helix:  0.84 (0.22), residues: 597
  sheet:  None (None), residues: 0
  loop : -0.93 (0.40), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 680 
 HIS   0.007   0.001   HIS A 852 
 PHE   0.018   0.001   PHE B 489 
 TYR   0.007   0.001   TYR B 842 
 ARG   0.001   0.000   ARG B 799 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1416.80 seconds
wall clock time: 25 minutes 38.84 seconds (1538.84 seconds total)