Starting phenix.real_space_refine
on Thu Feb 13 16:55:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtm_24683/02_2025/7rtm_24683.cif"
  }
  resolution = 3.4
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     Na      2      4.78       5
     C    6052      2.51       5
     N    1452      2.21       5
     O    1579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9161
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4520
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 30, 'TRANS': 540}
    Chain: "B"
      Number of atoms: 4519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4519
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 540}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 19
          Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 19
          Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1051
    residue:
      pdb=" N   LEU A 451 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 451 " occ=0.00
    residue:
      pdb=" N   PHE A 452 " occ=0.00
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 452 " occ=0.00
    residue:
      pdb=" N   GLY A 453 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 453 " occ=0.00
    residue:
      pdb=" N   GLY A 454 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 454 " occ=0.00
    residue:
      pdb=" N   LEU A 455 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 455 " occ=0.00
    residue:
      pdb=" N   VAL A 456 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 456 " occ=0.00
    residue:
      pdb=" N   LEU A 457 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 457 " occ=0.00
    residue:
      pdb=" N   ASP A 458 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 458 " occ=0.00
    residue:
      pdb=" N   VAL A 459 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 459 " occ=0.00
    residue:
      pdb=" N   LYS A 460 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 460 " occ=0.00
    residue:
      pdb=" N   ARG A 461 " occ=0.00
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 461 " occ=0.00
    residue:
      pdb=" N   LYS A 462 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 462 " occ=0.00
    ... (remaining 1039 not shown)
  Time building chain proxies: 5.77, per 1000 atoms: 0.63
  Number of scatterers: 9161
  At special positions: 0
  Unit cell: (130.54, 85.6, 108.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      76     16.00
     Na      2     11.00
     O    1579      8.00
     N    1452      7.00
     C    6052      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 636 " - pdb=" SG  CYS A 684 " distance=1.98
    Simple disulfide: pdb=" SG  CYS A 638 " - pdb=" SG  CYS A 672 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 636 " - pdb=" SG  CYS B 684 " distance=1.73
    Simple disulfide: pdb=" SG  CYS B 638 " - pdb=" SG  CYS B 672 " distance=2.00

  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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " NAG C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " NAG D   3 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      68.6% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 455 through 461
      removed outlier: 4.185A  pdb=" N   VAL A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 472
      removed outlier: 3.777A  pdb=" N   ARG A 471 " --> pdb=" O   TRP A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 491
      removed outlier: 3.814A  pdb=" N   CYS A 487 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A 491 " --> pdb=" O   CYS A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 504
      removed outlier: 3.791A  pdb=" N   ALA A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 528
      removed outlier: 3.570A  pdb=" N   LEU A 526 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 552
      removed outlier: 4.205A  pdb=" N   LEU A 542 " --> pdb=" O   THR A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 581
      removed outlier: 3.734A  pdb=" N   LEU A 562 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 580 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 589
    Processing helix  chain 'A' and resid 590 through 620
      removed outlier: 3.637A  pdb=" N   LEU A 600 " --> pdb=" O   ALA A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 634
      removed outlier: 4.355A  pdb=" N   SER A 632 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 655
      removed outlier: 3.640A  pdb=" N   HIS A 655 " --> pdb=" O   TYR A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 663
      removed outlier: 3.693A  pdb=" N   VAL A 662 " --> pdb=" O   THR A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 675
      removed outlier: 3.570A  pdb=" N   GLU A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 714
      removed outlier: 3.910A  pdb=" N   SER A 710 " --> pdb=" O   PHE A 706 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 714 " --> pdb=" O   SER A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 718
    Processing helix  chain 'A' and resid 722 through 732
      removed outlier: 4.137A  pdb=" N   THR A 728 " --> pdb=" O   ARG A 724 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 729 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER A 730 " --> pdb=" O   ARG A 726 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A 731 " --> pdb=" O   SER A 727 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A 732 " --> pdb=" O   THR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 748
    Processing helix  chain 'A' and resid 779 through 786
      removed outlier: 4.280A  pdb=" N   VAL A 783 " --> pdb=" O   PRO A 779 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE A 784 " --> pdb=" O   TRP A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 809
    Processing helix  chain 'A' and resid 820 through 838
    Processing helix  chain 'A' and resid 846 through 857
      removed outlier: 3.681A  pdb=" N   SER A 850 " --> pdb=" O   ALA A 846 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 857 " --> pdb=" O   HIS A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 892
      removed outlier: 3.579A  pdb=" N   MET A 884 " --> pdb=" O   VAL A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 919
      removed outlier: 3.959A  pdb=" N   LEU A 907 " --> pdb=" O   PRO A 903 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   LEU A 919 " --> pdb=" O   GLY A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 929
      removed outlier: 3.603A  pdb=" N   ASP A 926 " --> pdb=" O   ILE A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 947
      removed outlier: 3.579A  pdb=" N   HIS A 946 " --> pdb=" O   ILE A 942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 971
    Processing helix  chain 'A' and resid 980 through 996
      removed outlier: 3.868A  pdb=" N   ALA A 984 " --> pdb=" O   MET A 980 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 989 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET A 992 " --> pdb=" O   VAL A 988 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ASP A 993 " --> pdb=" O   ARG A 989 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU A 994 " --> pdb=" O   LYS A 990 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1002
    Processing helix  chain 'A' and resid 1009 through 1019
      removed outlier: 3.518A  pdb=" N   LYS A1013 " --> pdb=" O   PRO A1009 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 463
      removed outlier: 4.117A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 469
      removed outlier: 4.610A  pdb=" N   TRP B 467 " --> pdb=" O   ALA B 463 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   SER B 468 " --> pdb=" O   PRO B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 504
      removed outlier: 3.603A  pdb=" N   SER B 491 " --> pdb=" O   CYS B 487 " (cutoff:3.500A)
      Proline residue:  B 492  - end of helix
      removed outlier: 4.072A  pdb=" N   ALA B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 528
      removed outlier: 3.840A  pdb=" N   LEU B 526 " --> pdb=" O   ILE B 522 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA B 528 " --> pdb=" O   TYR B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 552
      removed outlier: 3.684A  pdb=" N   LEU B 542 " --> pdb=" O   THR B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 581
      removed outlier: 3.754A  pdb=" N   LEU B 562 " --> pdb=" O   SER B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.754A  pdb=" N   ILE B 589 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 620
    Processing helix  chain 'B' and resid 627 through 634
      removed outlier: 4.359A  pdb=" N   SER B 632 " --> pdb=" O   ASP B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 645 through 655
      removed outlier: 3.642A  pdb=" N   HIS B 655 " --> pdb=" O   TYR B 651 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 664
    Processing helix  chain 'B' and resid 668 through 673
      removed outlier: 3.922A  pdb=" N   GLN B 673 " --> pdb=" O   VAL B 669 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 693 through 714
      removed outlier: 3.661A  pdb=" N   ILE B 707 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER B 710 " --> pdb=" O   PHE B 706 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR B 714 " --> pdb=" O   SER B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 718
    Processing helix  chain 'B' and resid 722 through 727
      removed outlier: 3.658A  pdb=" N   ARG B 726 " --> pdb=" O   PRO B 722 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 748
    Processing helix  chain 'B' and resid 763 through 767
      removed outlier: 4.354A  pdb=" N   ASP B 766 " --> pdb=" O   PRO B 763 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASP B 767 " --> pdb=" O   THR B 764 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 763 through 767'
    Processing helix  chain 'B' and resid 779 through 786
      removed outlier: 4.576A  pdb=" N   VAL B 783 " --> pdb=" O   PRO B 779 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE B 784 " --> pdb=" O   TRP B 780 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 786 through 809
      removed outlier: 3.515A  pdb=" N   ILE B 795 " --> pdb=" O   LEU B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 838
      removed outlier: 3.797A  pdb=" N   ASP B 824 " --> pdb=" O   GLY B 820 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 846 through 857
      removed outlier: 3.732A  pdb=" N   SER B 850 " --> pdb=" O   ALA B 846 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU B 857 " --> pdb=" O   HIS B 853 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 880 through 891
    Processing helix  chain 'B' and resid 892 through 894
      No H-bonds generated for 'chain 'B' and resid 892 through 894'
    Processing helix  chain 'B' and resid 896 through 901
      removed outlier: 3.818A  pdb=" N   PHE B 901 " --> pdb=" O   ALA B 897 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 903 through 919
      removed outlier: 4.041A  pdb=" N   LEU B 907 " --> pdb=" O   PRO B 903 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LEU B 919 " --> pdb=" O   GLY B 915 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 929
      removed outlier: 4.187A  pdb=" N   ASP B 926 " --> pdb=" O   ILE B 922 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ARG B 927 " --> pdb=" O   GLN B 923 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 941 through 945
    Processing helix  chain 'B' and resid 948 through 972
    Processing helix  chain 'B' and resid 977 through 996
      removed outlier: 3.953A  pdb=" N   VAL B 982 " --> pdb=" O   PHE B 978 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU B 983 " --> pdb=" O   PRO B 979 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ALA B 984 " --> pdb=" O   MET B 980 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG B 989 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B 991 " --> pdb=" O   PHE B 987 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASP B 993 " --> pdb=" O   ARG B 989 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   LEU B 994 " --> pdb=" O   LYS B 990 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1001
    Processing helix  chain 'B' and resid 1009 through 1019
      removed outlier: 3.772A  pdb=" N   LYS B1013 " --> pdb=" O   PRO B1009 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 536
    Processing sheet with id=AA2, first strand: chain 'A' and resid 636 through 639
    Processing sheet with id=AA3, first strand: chain 'B' and resid 636 through 639

    487 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.16 -     1.32: 1448
        1.32 -     1.47: 3650
        1.47 -     1.63: 4191
        1.63 -     1.78: 21
        1.78 -     1.94: 101
  Bond restraints: 9411
  Sorted by residual:
  bond pdb=" CA  GLY B 501 "
       pdb=" C   GLY B 501 "
    ideal  model  delta    sigma   weight residual
    1.516  1.387  0.129 1.09e-02 8.42e+03 1.41e+02
  bond pdb=" NE  ARG A 471 "
       pdb=" CZ  ARG A 471 "
    ideal  model  delta    sigma   weight residual
    1.326  1.444 -0.118 1.10e-02 8.26e+03 1.15e+02
  bond pdb=" C   ALA A 897 "
       pdb=" N   VAL A 898 "
    ideal  model  delta    sigma   weight residual
    1.335  1.463 -0.129 1.26e-02 6.30e+03 1.04e+02
  bond pdb=" N   PHE B 702 "
       pdb=" CA  PHE B 702 "
    ideal  model  delta    sigma   weight residual
    1.459  1.345  0.114 1.17e-02 7.31e+03 9.44e+01
  bond pdb=" ND1 HIS B 625 "
       pdb=" CE1 HIS B 625 "
    ideal  model  delta    sigma   weight residual
    1.321  1.416 -0.095 1.00e-02 1.00e+04 9.11e+01
  ... (remaining 9406 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 8745
        2.78 -     5.55: 3033
        5.55 -     8.33: 827
        8.33 -    11.10: 163
       11.10 -    13.88: 27
  Bond angle restraints: 12795
  Sorted by residual:
  angle pdb=" N   VAL A 893 "
        pdb=" CA  VAL A 893 "
        pdb=" C   VAL A 893 "
      ideal   model   delta    sigma   weight residual
     113.53  102.71   10.82 9.80e-01 1.04e+00 1.22e+02
  angle pdb=" CA  ALA B 463 "
        pdb=" C   ALA B 463 "
        pdb=" N   PRO B 464 "
      ideal   model   delta    sigma   weight residual
     120.93  132.26  -11.33 1.06e+00 8.90e-01 1.14e+02
  angle pdb=" CA  ALA B 463 "
        pdb=" C   ALA B 463 "
        pdb=" O   ALA B 463 "
      ideal   model   delta    sigma   weight residual
     118.34  108.90    9.44 9.70e-01 1.06e+00 9.47e+01
  angle pdb=" N   GLN B 920 "
        pdb=" CA  GLN B 920 "
        pdb=" C   GLN B 920 "
      ideal   model   delta    sigma   weight residual
     113.23  101.30   11.93 1.24e+00 6.50e-01 9.26e+01
  angle pdb=" N   GLU B1010 "
        pdb=" CA  GLU B1010 "
        pdb=" C   GLU B1010 "
      ideal   model   delta    sigma   weight residual
     111.71  122.71  -11.00 1.15e+00 7.56e-01 9.15e+01
  ... (remaining 12790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.66: 5358
       24.66 -    49.31: 213
       49.31 -    73.97: 45
       73.97 -    98.62: 21
       98.62 -   123.28: 10
  Dihedral angle restraints: 5647
    sinusoidal: 2311
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" C   SER A 468 "
           pdb=" N   SER A 468 "
           pdb=" CA  SER A 468 "
           pdb=" CB  SER A 468 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.76   18.16     0      2.50e+00 1.60e-01 5.28e+01
  dihedral pdb=" N   MET B 981 "
           pdb=" C   MET B 981 "
           pdb=" CA  MET B 981 "
           pdb=" CB  MET B 981 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.52  -16.72     0      2.50e+00 1.60e-01 4.47e+01
  dihedral pdb=" C   GLU B1010 "
           pdb=" N   GLU B1010 "
           pdb=" CA  GLU B1010 "
           pdb=" CB  GLU B1010 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.66   16.06     0      2.50e+00 1.60e-01 4.13e+01
  ... (remaining 5644 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.147: 944
       0.147 -    0.294: 389
       0.294 -    0.442: 130
       0.442 -    0.589: 35
       0.589 -    0.736: 6
  Chirality restraints: 1504
  Sorted by residual:
  chirality pdb=" C1  NAG D   3 "
            pdb=" O4  NAG D   2 "
            pdb=" C2  NAG D   3 "
            pdb=" O5  NAG D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-02 2.50e+03 6.78e+02
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-02 2.50e+03 1.61e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 4.18e+01
  ... (remaining 1501 not shown)

  Planarity restraints: 1548
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   3 "    0.313 2.00e-02 2.50e+03   2.69e-01 9.04e+02
        pdb=" C7  NAG D   3 "   -0.075 2.00e-02 2.50e+03
        pdb=" C8  NAG D   3 "    0.167 2.00e-02 2.50e+03
        pdb=" N2  NAG D   3 "   -0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG D   3 "    0.070 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.305 2.00e-02 2.50e+03   2.63e-01 8.61e+02
        pdb=" C7  NAG D   2 "   -0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.449 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.214 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.270 2.00e-02 2.50e+03   2.30e-01 6.64e+02
        pdb=" C7  NAG D   1 "    0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.169 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.398 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1545 not shown)

  Histogram of nonbonded interaction distances:
        1.05 -     1.82: 8
        1.82 -     2.59: 171
        2.59 -     3.36: 11742
        3.36 -     4.13: 21331
        4.13 -     4.90: 37386
  Nonbonded interactions: 70638
  Sorted by model distance:
  nonbonded pdb=" CD2 HIS A 937 "
            pdb=" CB  PRO B 866 "
     model   vdw
     1.051 3.660
  nonbonded pdb=" O   ALA A 845 "
            pdb="NA    NA A1102 "
     model   vdw
     1.122 2.470
  nonbonded pdb=" O   LEU A 476 "
            pdb=" OD2 ASP A 731 "
     model   vdw
     1.520 3.040
  nonbonded pdb=" SG  CYS A 565 "
            pdb=" CD1 ILE A 775 "
     model   vdw
     1.625 3.820
  nonbonded pdb=" CD1 PHE A 484 "
            pdb=" CG1 VAL A 734 "
     model   vdw
     1.667 3.760
  ... (remaining 70633 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 451 through 772 or (resid 773 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 774 through 1021 or resid 1101 through 110 \ 
3))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.06
  Reset to 1.
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.000
  Set scattering table:                    0.090
  Process input model:                     23.590
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.350
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4590
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      :  0.031   0.131   9411  Z= 1.992
  Angle     :  3.049  13.876  12795  Z= 2.132
  Chirality :  0.185   0.736   1504
  Planarity :  0.028   0.269   1548
  Dihedral  : 16.560 123.278   3475
  Min Nonbonded Distance : 1.051

Molprobity Statistics.
  All-atom Clashscore : 36.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.77 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  :  9.29 %
    Favored  : 87.91 %
  Cbeta Deviations :  4.07 %
  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: -1.12 (0.23), residues: 1138
  helix:  0.06 (0.19), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.93 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.275   0.042   TRP B 467 
 HIS   0.043   0.007   HIS B 822 
 PHE   0.214   0.030   PHE B 955 
 TYR   0.184   0.042   TYR A 607 
 ARG   0.055   0.007   ARG B 637 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 352
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  988 VAL cc_start: 0.2821 (p) cc_final: 0.2144 (t)
REVERT: B  700 ILE cc_start: 0.4583 (mt) cc_final: 0.4293 (mt)
REVERT: B  881 THR cc_start: 0.4669 (p) cc_final: 0.4140 (p)
REVERT: B  988 VAL cc_start: 0.3922 (p) cc_final: 0.3317 (t)
  outliers start: 28
  outliers final: 5
  residues processed: 373
  average time/residue: 0.2073
  time to fit residues: 106.3445
Evaluate side-chains
  202 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 197
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  623 HIS
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  943 TYR
Chi-restraints excluded: chain B residue  657 ILE
Chi-restraints excluded: chain B residue  691 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 HIS
A 655 HIS
A 663 ASN
A 686 HIS
A 937 HIS
** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 627 GLN
B 643 ASN
B 646 ASN
B 676 HIS
B 686 HIS
B 822 HIS
B 855 ASN
B 869 GLN
B 923 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.145613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.130086 restraints weight = 28311.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 3.68
r_work: 0.4097 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9411  Z= 0.292
  Angle     :  0.903  11.555  12795  Z= 0.456
  Chirality :  0.050   0.231   1504
  Planarity :  0.007   0.068   1548
  Dihedral  : 13.051 109.635   1390
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.43 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.98 %
    Favored  : 79.72 %
  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: -0.51 (0.24), residues: 1138
  helix:  0.30 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop : -1.32 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 467 
 HIS   0.016   0.002   HIS A 630 
 PHE   0.023   0.003   PHE A 496 
 TYR   0.033   0.002   TYR B 486 
 ARG   0.006   0.001   ARG A 927 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 198
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 TYR cc_start: 0.7615 (t80) cc_final: 0.7359 (t80)
REVERT: A  663 ASN cc_start: 0.8211 (m110) cc_final: 0.7945 (p0)
REVERT: A  831 MET cc_start: 0.7211 (mmm) cc_final: 0.6544 (mmm)
REVERT: A  888 LEU cc_start: 0.8771 (tp) cc_final: 0.8081 (tp)
REVERT: A  923 GLN cc_start: 0.6840 (tt0) cc_final: 0.6625 (tt0)
REVERT: A  990 LYS cc_start: 0.6165 (tmtt) cc_final: 0.5587 (mmmt)
REVERT: A 1012 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8409 (mmpt)
REVERT: B  478 CYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7715 (p)
REVERT: B  615 HIS cc_start: 0.8371 (t70) cc_final: 0.7913 (m-70)
REVERT: B  643 ASN cc_start: 0.8323 (m-40) cc_final: 0.8056 (m110)
REVERT: B  700 ILE cc_start: 0.5853 (mt) cc_final: 0.5474 (mt)
REVERT: B  906 VAL cc_start: 0.5756 (p) cc_final: 0.4362 (t)
  outliers start: 33
  outliers final: 14
  residues processed: 222
  average time/residue: 0.1911
  time to fit residues: 60.6049
Evaluate side-chains
  175 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  737 THR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  828 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1012 LYS
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  478 CYS
Chi-restraints excluded: chain B residue  629 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue  844 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0030
   chunk 26 optimal weight:    6.9990
   chunk 19 optimal weight:   50.0000
   chunk 103 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0870
   chunk 23 optimal weight:    9.9990
   overall best weight:    0.5368

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 923 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.142452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.126233 restraints weight = 28716.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 3.71
r_work: 0.4040 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.5408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9411  Z= 0.213
  Angle     :  0.779  11.353  12795  Z= 0.386
  Chirality :  0.047   0.230   1504
  Planarity :  0.005   0.060   1548
  Dihedral  : 11.755 103.105   1383
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.22 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 17.58 %
    Favored  : 78.92 %
  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 (0.24), residues: 1138
  helix:  0.52 (0.19), residues: 699
  sheet:  None (None), residues: 0
  loop : -1.07 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 465 
 HIS   0.010   0.001   HIS A 630 
 PHE   0.016   0.002   PHE B 679 
 TYR   0.026   0.002   TYR A 634 
 ARG   0.012   0.001   ARG B 471 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 TYR cc_start: 0.7534 (t80) cc_final: 0.7156 (t80)
REVERT: A  624 MET cc_start: 0.7651 (tpt) cc_final: 0.6691 (ttp)
REVERT: A  673 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: A  851 ILE cc_start: 0.8302 (mm) cc_final: 0.8039 (mm)
REVERT: A  857 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7312 (pp)
REVERT: A  888 LEU cc_start: 0.8615 (tp) cc_final: 0.7844 (tp)
REVERT: A  923 GLN cc_start: 0.6759 (tt0) cc_final: 0.6556 (tt0)
REVERT: A  990 LYS cc_start: 0.6002 (tmtt) cc_final: 0.5293 (mmtp)
REVERT: A 1012 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8506 (mmpt)
REVERT: B  490 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7174 (ttt)
REVERT: B  615 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7771 (m-70)
REVERT: B  643 ASN cc_start: 0.8266 (m-40) cc_final: 0.7926 (m110)
REVERT: B  700 ILE cc_start: 0.6415 (mt) cc_final: 0.5800 (mt)
REVERT: B  831 MET cc_start: 0.7377 (mmm) cc_final: 0.7079 (mmm)
REVERT: B  906 VAL cc_start: 0.6196 (p) cc_final: 0.4877 (t)
  outliers start: 35
  outliers final: 15
  residues processed: 209
  average time/residue: 0.1805
  time to fit residues: 54.7850
Evaluate side-chains
  159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  824 ASP
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1012 LYS
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  602 CYS
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 36 optimal weight:    0.2980
   chunk 87 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 41 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.138804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.122201 restraints weight = 28379.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 3.68
r_work: 0.3980 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.6020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9411  Z= 0.197
  Angle     :  0.744   9.859  12795  Z= 0.361
  Chirality :  0.045   0.203   1504
  Planarity :  0.005   0.059   1548
  Dihedral  : 11.175  97.557   1383
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.18 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.88 %
    Favored  : 75.92 %
  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: -0.03 (0.24), residues: 1138
  helix:  0.65 (0.19), residues: 701
  sheet:  None (None), residues: 0
  loop : -1.04 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 652 
 HIS   0.007   0.001   HIS A 630 
 PHE   0.036   0.002   PHE A 987 
 TYR   0.022   0.001   TYR A 634 
 ARG   0.005   0.001   ARG B 507 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 145
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 TYR cc_start: 0.7751 (t80) cc_final: 0.7534 (t80)
REVERT: A  624 MET cc_start: 0.7721 (tpt) cc_final: 0.6704 (ttp)
REVERT: A  831 MET cc_start: 0.7484 (mmm) cc_final: 0.6704 (mmm)
REVERT: A  851 ILE cc_start: 0.8362 (mm) cc_final: 0.8102 (mm)
REVERT: A  888 LEU cc_start: 0.8625 (tp) cc_final: 0.8200 (tp)
REVERT: A  889 MET cc_start: 0.7439 (ptp) cc_final: 0.7230 (ptp)
REVERT: A  923 GLN cc_start: 0.6873 (tt0) cc_final: 0.6649 (tt0)
REVERT: A  987 PHE cc_start: 0.6349 (m-80) cc_final: 0.6148 (m-80)
REVERT: A  990 LYS cc_start: 0.6137 (tmtt) cc_final: 0.5421 (mmtp)
REVERT: B  490 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7372 (ttt)
REVERT: B  615 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7900 (t70)
REVERT: B  712 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8028 (mt)
  outliers start: 42
  outliers final: 21
  residues processed: 176
  average time/residue: 0.1616
  time to fit residues: 43.8814
Evaluate side-chains
  154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  881 THR
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain B residue  472 ASP
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  513 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  602 CYS
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  712 LEU
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  962 CYS
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 801 GLN
B 855 ASN
B 923 GLN
B 953 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.124808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.106193 restraints weight = 27924.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 3.57
r_work: 0.3712 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.7462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   9411  Z= 0.277
  Angle     :  0.789  10.963  12795  Z= 0.390
  Chirality :  0.048   0.254   1504
  Planarity :  0.006   0.055   1548
  Dihedral  : 10.148  85.921   1383
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.01 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 20.98 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.15 (0.24), residues: 1138
  helix:  0.60 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -1.24 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 465 
 HIS   0.036   0.003   HIS A 687 
 PHE   0.038   0.003   PHE A 987 
 TYR   0.015   0.002   TYR A 913 
 ARG   0.008   0.001   ARG A 989 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  486 TYR cc_start: 0.8159 (t80) cc_final: 0.7597 (t80)
REVERT: A  799 MET cc_start: 0.8130 (ptp) cc_final: 0.7899 (ptp)
REVERT: A  895 MET cc_start: 0.4330 (tmm) cc_final: 0.3988 (tmm)
REVERT: A  987 PHE cc_start: 0.6669 (m-80) cc_final: 0.6392 (m-80)
REVERT: A  990 LYS cc_start: 0.6406 (tmtt) cc_final: 0.5710 (mmtp)
REVERT: B  478 CYS cc_start: 0.8308 (t) cc_final: 0.7819 (p)
REVERT: B  615 HIS cc_start: 0.8678 (OUTLIER) cc_final: 0.8132 (t70)
REVERT: B  739 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6414 (m-80)
REVERT: B  931 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6640 (m-10)
  outliers start: 42
  outliers final: 30
  residues processed: 190
  average time/residue: 0.1551
  time to fit residues: 45.1417
Evaluate side-chains
  163 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  847 THR
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  513 SER
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  739 PHE
Chi-restraints excluded: chain B residue  750 VAL
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  857 LEU
Chi-restraints excluded: chain B residue  906 VAL
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  996 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   chunk 60 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 920 GLN
** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.119793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.100956 restraints weight = 27873.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 3.58
r_work: 0.3615 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.8214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   9411  Z= 0.269
  Angle     :  0.765  13.449  12795  Z= 0.371
  Chirality :  0.046   0.270   1504
  Planarity :  0.005   0.056   1548
  Dihedral  :  9.449  80.002   1383
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.75 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 22.38 %
    Favored  : 72.93 %
  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 (0.24), residues: 1138
  helix:  0.62 (0.19), residues: 715
  sheet:  None (None), residues: 0
  loop : -1.25 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 465 
 HIS   0.009   0.002   HIS B 686 
 PHE   0.026   0.002   PHE A 496 
 TYR   0.040   0.002   TYR B 486 
 ARG   0.004   0.001   ARG A 879 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
REVERT: A  486 TYR cc_start: 0.8352 (t80) cc_final: 0.8078 (t80)
REVERT: A  542 LEU cc_start: 0.8765 (pp) cc_final: 0.8529 (tt)
REVERT: A  701 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9063 (mt)
REVERT: A  831 MET cc_start: 0.8067 (mmm) cc_final: 0.7004 (mmm)
REVERT: A  969 ILE cc_start: 0.9137 (mm) cc_final: 0.8853 (mp)
REVERT: A  983 LEU cc_start: 0.7817 (mt) cc_final: 0.7242 (mt)
REVERT: A  987 PHE cc_start: 0.6825 (m-80) cc_final: 0.6456 (m-80)
REVERT: A  990 LYS cc_start: 0.6719 (tmtt) cc_final: 0.5960 (mmtm)
REVERT: B  490 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8203 (mmt)
REVERT: B  615 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8112 (t70)
REVERT: B  739 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6321 (m-80)
REVERT: B  931 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6816 (m-10)
  outliers start: 47
  outliers final: 27
  residues processed: 177
  average time/residue: 0.1607
  time to fit residues: 43.2615
Evaluate side-chains
  158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  847 THR
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  739 PHE
Chi-restraints excluded: chain B residue  760 VAL
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  857 LEU
Chi-restraints excluded: chain B residue  902 ILE
Chi-restraints excluded: chain B residue  930 LEU
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  962 CYS
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0570
   chunk 87 optimal weight:    0.6980
   chunk 109 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 920 GLN
A 923 GLN
A 959 GLN
B 646 ASN
** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.120045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.101168 restraints weight = 28476.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 3.66
r_work: 0.3627 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.8431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9411  Z= 0.189
  Angle     :  0.736  12.614  12795  Z= 0.349
  Chirality :  0.044   0.264   1504
  Planarity :  0.005   0.055   1548
  Dihedral  :  8.994  78.170   1382
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.57 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.88 %
    Favored  : 72.93 %
  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: -0.03 (0.25), residues: 1138
  helix:  0.74 (0.19), residues: 714
  sheet:  None (None), residues: 0
  loop : -1.28 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 664 
 HIS   0.005   0.001   HIS A 630 
 PHE   0.031   0.002   PHE A 496 
 TYR   0.011   0.001   TYR A 486 
 ARG   0.002   0.000   ARG A 563 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 148
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  542 LEU cc_start: 0.8769 (pp) cc_final: 0.8506 (tt)
REVERT: A  701 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9077 (mt)
REVERT: A  831 MET cc_start: 0.8097 (mmm) cc_final: 0.7077 (mmm)
REVERT: A  895 MET cc_start: 0.5306 (tmm) cc_final: 0.4660 (tmm)
REVERT: A  904 MET cc_start: 0.8862 (mmm) cc_final: 0.8451 (mmm)
REVERT: A  969 ILE cc_start: 0.9106 (mm) cc_final: 0.8811 (mp)
REVERT: A  990 LYS cc_start: 0.6713 (tmtt) cc_final: 0.5920 (mmtm)
REVERT: A 1008 MET cc_start: 0.8154 (ttp) cc_final: 0.7815 (ttp)
REVERT: B  490 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8272 (mtt)
REVERT: B  615 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8018 (t70)
REVERT: B  735 PHE cc_start: 0.6077 (t80) cc_final: 0.5856 (t80)
REVERT: B  739 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6257 (m-80)
REVERT: B  793 CYS cc_start: 0.7719 (t) cc_final: 0.7515 (t)
REVERT: B  931 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6837 (m-10)
REVERT: B 1012 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7280 (mmmm)
  outliers start: 42
  outliers final: 21
  residues processed: 177
  average time/residue: 0.1826
  time to fit residues: 47.3640
Evaluate side-chains
  158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain B residue  490 MET
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  739 PHE
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  906 VAL
Chi-restraints excluded: chain B residue  930 LEU
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  977 VAL
Chi-restraints excluded: chain B residue  996 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0030
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0270
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7450

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

Flipped N/Q/H residues before XYZ refinement:
A 920 GLN
B 855 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.118953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.099883 restraints weight = 28838.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.69
r_work: 0.3603 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.8727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9411  Z= 0.200
  Angle     :  0.745  12.116  12795  Z= 0.355
  Chirality :  0.044   0.266   1504
  Planarity :  0.005   0.055   1548
  Dihedral  :  8.551  76.689   1382
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.22 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 24.08 %
    Favored  : 72.73 %
  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: -0.04 (0.24), residues: 1138
  helix:  0.75 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -1.34 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 967 
 HIS   0.005   0.001   HIS A 630 
 PHE   0.039   0.002   PHE B 496 
 TYR   0.010   0.001   TYR A 486 
 ARG   0.006   0.000   ARG B 945 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 144
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  542 LEU cc_start: 0.8798 (pp) cc_final: 0.8524 (tt)
REVERT: A  701 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9103 (mt)
REVERT: A  969 ILE cc_start: 0.9118 (mm) cc_final: 0.8840 (mp)
REVERT: A  987 PHE cc_start: 0.6787 (m-80) cc_final: 0.6462 (m-80)
REVERT: A  990 LYS cc_start: 0.6660 (tmtt) cc_final: 0.5878 (mmtm)
REVERT: A 1008 MET cc_start: 0.8236 (ttp) cc_final: 0.7881 (ttp)
REVERT: B  478 CYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8115 (p)
REVERT: B  615 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7953 (t70)
REVERT: B  735 PHE cc_start: 0.6120 (t80) cc_final: 0.5891 (t80)
REVERT: B  739 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6153 (m-80)
REVERT: B  761 PHE cc_start: 0.6531 (t80) cc_final: 0.6322 (t80)
REVERT: B  793 CYS cc_start: 0.8047 (t) cc_final: 0.7791 (t)
REVERT: B  895 MET cc_start: 0.6964 (ttm) cc_final: 0.6760 (ttm)
REVERT: B  931 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6971 (m-10)
REVERT: B 1012 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7501 (mmmm)
  outliers start: 32
  outliers final: 23
  residues processed: 164
  average time/residue: 0.1833
  time to fit residues: 47.0616
Evaluate side-chains
  160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 132
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  859 LEU
Chi-restraints excluded: chain A residue  891 CYS
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain B residue  478 CYS
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  739 PHE
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  930 LEU
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  955 PHE
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 67 optimal weight:    0.6980
   chunk 105 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 49 optimal weight:    0.2980
   chunk 82 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 923 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.118526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.099849 restraints weight = 27923.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 3.53
r_work: 0.3605 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.8895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9411  Z= 0.195
  Angle     :  0.758  11.843  12795  Z= 0.359
  Chirality :  0.045   0.262   1504
  Planarity :  0.005   0.055   1548
  Dihedral  :  8.198  76.058   1382
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.48 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.58 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.03 (0.24), residues: 1138
  helix:  0.78 (0.19), residues: 721
  sheet:  None (None), residues: 0
  loop : -1.29 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 569 
 HIS   0.004   0.001   HIS A 630 
 PHE   0.032   0.002   PHE A 496 
 TYR   0.031   0.001   TYR B 486 
 ARG   0.004   0.000   ARG B 945 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  542 LEU cc_start: 0.8767 (pp) cc_final: 0.8534 (tt)
REVERT: A  701 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9054 (mt)
REVERT: A  969 ILE cc_start: 0.9113 (mm) cc_final: 0.8841 (mp)
REVERT: A  987 PHE cc_start: 0.6803 (m-80) cc_final: 0.6457 (m-80)
REVERT: A  990 LYS cc_start: 0.6684 (tmtt) cc_final: 0.5971 (mmtm)
REVERT: A 1008 MET cc_start: 0.8185 (ttp) cc_final: 0.7855 (ttp)
REVERT: B  478 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8012 (p)
REVERT: B  615 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7977 (t70)
REVERT: B  735 PHE cc_start: 0.6136 (t80) cc_final: 0.5908 (t80)
REVERT: B  739 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6028 (m-80)
REVERT: B  793 CYS cc_start: 0.7997 (t) cc_final: 0.7717 (t)
REVERT: B  931 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7086 (m-10)
REVERT: B 1012 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7639 (mmmm)
  outliers start: 31
  outliers final: 22
  residues processed: 159
  average time/residue: 0.1660
  time to fit residues: 40.2384
Evaluate side-chains
  154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 CYS
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  859 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain B residue  478 CYS
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  739 PHE
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  930 LEU
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  955 PHE
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0030
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 65 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0000
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 923 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.118226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.099718 restraints weight = 28330.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.48
r_work: 0.3604 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.9056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9411  Z= 0.197
  Angle     :  0.786  15.316  12795  Z= 0.370
  Chirality :  0.045   0.256   1504
  Planarity :  0.005   0.055   1548
  Dihedral  :  7.873  75.309   1382
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.39 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 25.07 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1138
  helix:  0.62 (0.19), residues: 738
  sheet:  None (None), residues: 0
  loop : -1.45 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1003 
 HIS   0.004   0.001   HIS B 853 
 PHE   0.031   0.002   PHE B 544 
 TYR   0.024   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 876 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 LEU cc_start: 0.8707 (mt) cc_final: 0.8366 (mt)
REVERT: A  542 LEU cc_start: 0.8774 (pp) cc_final: 0.8545 (tt)
REVERT: A  701 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9141 (mt)
REVERT: A  969 ILE cc_start: 0.9090 (mm) cc_final: 0.8811 (mp)
REVERT: A  987 PHE cc_start: 0.6711 (m-80) cc_final: 0.6413 (m-80)
REVERT: A  990 LYS cc_start: 0.6750 (tmtt) cc_final: 0.6040 (mmtm)
REVERT: A 1008 MET cc_start: 0.8126 (ttp) cc_final: 0.7809 (ttp)
REVERT: B  478 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (p)
REVERT: B  486 TYR cc_start: 0.7807 (t80) cc_final: 0.7532 (t80)
REVERT: B  615 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7886 (t70)
REVERT: B  761 PHE cc_start: 0.6554 (t80) cc_final: 0.6353 (t80)
REVERT: B  799 MET cc_start: 0.7497 (ptp) cc_final: 0.7245 (ptp)
REVERT: B  931 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6977 (m-10)
REVERT: B 1012 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7635 (mmmm)
  outliers start: 26
  outliers final: 21
  residues processed: 150
  average time/residue: 0.1627
  time to fit residues: 37.2136
Evaluate side-chains
  152 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  594 GLU
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  624 MET
Chi-restraints excluded: chain A residue  664 TRP
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain A residue  720 TYR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  859 LEU
Chi-restraints excluded: chain A residue  906 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  947 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1006 ASP
Chi-restraints excluded: chain B residue  478 CYS
Chi-restraints excluded: chain B residue  533 THR
Chi-restraints excluded: chain B residue  615 HIS
Chi-restraints excluded: chain B residue  668 THR
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  844 VAL
Chi-restraints excluded: chain B residue  930 LEU
Chi-restraints excluded: chain B residue  931 PHE
Chi-restraints excluded: chain B residue  955 PHE
Chi-restraints excluded: chain B residue  977 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 923 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.115904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.096781 restraints weight = 28348.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 3.51
r_work: 0.3554 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.9415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9411  Z= 0.214
  Angle     :  0.773  13.155  12795  Z= 0.363
  Chirality :  0.045   0.221   1504
  Planarity :  0.005   0.055   1548
  Dihedral  :  7.334  73.952   1382
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.57 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 25.37 %
    Favored  : 71.93 %
  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: -0.15 (0.24), residues: 1138
  helix:  0.62 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.39 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 781 
 HIS   0.004   0.001   HIS A 813 
 PHE   0.045   0.002   PHE A 496 
 TYR   0.015   0.001   TYR B 486 
 ARG   0.003   0.000   ARG B 989 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4524.47 seconds
wall clock time: 81 minutes 1.61 seconds (4861.61 seconds total)