Starting phenix.real_space_refine
on Mon May 12 14:25:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uue_42580/05_2025/8uue_42580_neut.cif"
  }
  resolution = 3.96
  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=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     C    5724      2.51       5
     N    1517      2.21       5
     O    1682      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8984
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2239
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "B"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2255
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2268
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 2222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2222
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 16, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
  Time building chain proxies: 3.34, per 1000 atoms: 0.37
  Number of scatterers: 8984
  At special positions: 0
  Unit cell: (137.816, 128.4, 73.616, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      61     16.00
     O    1682      8.00
     N    1517      7.00
     C    5724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 420 " - pdb=" SG  CYS A 454 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 436 " - pdb=" SG  CYS A 455 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 575 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 543 " - pdb=" SG  CYS B 576 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 859 " - pdb=" SG  CYS B 913 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 420 " - pdb=" SG  CYS C 454 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 436 " - pdb=" SG  CYS C 455 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 537 " - pdb=" SG  CYS D 575 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 859 " - pdb=" SG  CYS D 913 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 16 sheets defined
      38.3% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 458 through 469
      removed outlier: 3.539A  pdb=" N   THR A 469 " --> pdb=" O   LYS A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 507
    Processing helix  chain 'A' and resid 520 through 527
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 3.629A  pdb=" N   ARG A 673 " --> pdb=" O   ASP A 669 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ASN A 674 " --> pdb=" O   PRO A 670 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 669 through 674'
    Processing helix  chain 'A' and resid 687 through 696
    Processing helix  chain 'A' and resid 699 through 708
      removed outlier: 3.649A  pdb=" N   TYR A 703 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 708 " --> pdb=" O   ARG A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 724
    Processing helix  chain 'A' and resid 732 through 742
    Processing helix  chain 'A' and resid 768 through 783
      removed outlier: 3.583A  pdb=" N   VAL A 772 " --> pdb=" O   TRP A 768 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 774 " --> pdb=" O   GLN A 770 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY A 783 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 793
    Processing helix  chain 'B' and resid 550 through 562
    Processing helix  chain 'B' and resid 569 through 571
      No H-bonds generated for 'chain 'B' and resid 569 through 571'
    Processing helix  chain 'B' and resid 578 through 592
    Processing helix  chain 'B' and resid 614 through 622
    Processing helix  chain 'B' and resid 635 through 640
    Processing helix  chain 'B' and resid 782 through 786
    Processing helix  chain 'B' and resid 800 through 810
      removed outlier: 3.587A  pdb=" N   TYR B 805 " --> pdb=" O   SER B 801 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   VAL B 806 " --> pdb=" O   ALA B 802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 820
      removed outlier: 3.876A  pdb=" N   MET B 817 " --> pdb=" O   MET B 813 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR B 820 " --> pdb=" O   TYR B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 824 through 833
    Processing helix  chain 'B' and resid 846 through 854
      removed outlier: 3.710A  pdb=" N   SER B 854 " --> pdb=" O   ASP B 850 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 881 through 884
    Processing helix  chain 'B' and resid 885 through 897
      removed outlier: 3.584A  pdb=" N   GLU B 889 " --> pdb=" O   ALA B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 898 through 906
      removed outlier: 3.840A  pdb=" N   MET B 902 " --> pdb=" O   GLY B 898 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 471
    Processing helix  chain 'C' and resid 499 through 508
      removed outlier: 3.542A  pdb=" N   GLY C 503 " --> pdb=" O   ASN C 499 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY C 508 " --> pdb=" O   GLU C 504 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 669 through 674
    Processing helix  chain 'C' and resid 687 through 696
      removed outlier: 3.659A  pdb=" N   ILE C 691 " --> pdb=" O   SER C 687 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN C 696 " --> pdb=" O   TYR C 692 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 700 through 707
      removed outlier: 4.377A  pdb=" N   ARG C 704 " --> pdb=" O   SER C 700 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   HIS C 705 " --> pdb=" O   THR C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 713 through 723
      removed outlier: 3.761A  pdb=" N   ALA C 717 " --> pdb=" O   SER C 713 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 732 through 743
    Processing helix  chain 'C' and resid 769 through 781
      removed outlier: 3.559A  pdb=" N   GLU C 781 " --> pdb=" O   LEU C 777 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 783 through 793
    Processing helix  chain 'D' and resid 550 through 562
      removed outlier: 3.775A  pdb=" N   LEU D 554 " --> pdb=" O   ASP D 550 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 569 through 573
    Processing helix  chain 'D' and resid 578 through 592
    Processing helix  chain 'D' and resid 614 through 622
    Processing helix  chain 'D' and resid 635 through 642
      removed outlier: 4.066A  pdb=" N   VAL D 641 " --> pdb=" O   ALA D 637 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 782 through 787
      removed outlier: 3.825A  pdb=" N   HIS D 787 " --> pdb=" O   PRO D 783 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 800 through 810
    Processing helix  chain 'D' and resid 810 through 821
      removed outlier: 3.519A  pdb=" N   HIS D 814 " --> pdb=" O   PHE D 810 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR D 820 " --> pdb=" O   TYR D 816 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 824 through 826
      No H-bonds generated for 'chain 'D' and resid 824 through 826'
    Processing helix  chain 'D' and resid 827 through 833
      removed outlier: 3.568A  pdb=" N   TYR D 831 " --> pdb=" O   ASP D 827 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 846 through 856
    Processing helix  chain 'D' and resid 883 through 898
      removed outlier: 3.601A  pdb=" N   ILE D 887 " --> pdb=" O   LEU D 883 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 898 through 908
    Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399
      removed outlier: 7.255A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 475 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 412
    Processing sheet with id=AA3, first strand: chain 'A' and resid 729 through 731
      removed outlier: 3.723A  pdb=" N   PHE A 729 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 541 " --> pdb=" O   PHE A 729 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 729 through 731
      removed outlier: 3.723A  pdb=" N   PHE A 729 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A 541 " --> pdb=" O   PHE A 729 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LYS A 534 " --> pdb=" O   PHE A 758 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A 538 " --> pdb=" O   PHE A 754 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   PHE A 754 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 573 through 576
      removed outlier: 6.892A  pdb=" N   LEU B 542 " --> pdb=" O   LEU B 597 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   ILE B 599 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   LEU B 544 " --> pdb=" O   ILE B 599 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET B 627 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 643 through 644
      removed outlier: 3.503A  pdb=" N   ASP B 643 " --> pdb=" O   LEU B 877 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 844 through 845
      removed outlier: 3.650A  pdb=" N   ILE B 655 " --> pdb=" O   VAL B 864 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 657 " --> pdb=" O   LEU B 862 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU B 862 " --> pdb=" O   VAL B 657 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 402
      removed outlier: 6.999A  pdb=" N   LEU C 398 " --> pdb=" O   GLU C 475 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   HIS C 477 " --> pdb=" O   LEU C 398 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ILE C 400 " --> pdb=" O   HIS C 477 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 434 through 436
    Processing sheet with id=AB1, first strand: chain 'C' and resid 488 through 489
    Processing sheet with id=AB2, first strand: chain 'C' and resid 528 through 529
    Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 536
    Processing sheet with id=AB4, first strand: chain 'C' and resid 710 through 711
      removed outlier: 8.936A  pdb=" N   TYR C 711 " --> pdb=" O   TYR C 681 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   THR C 683 " --> pdb=" O   TYR C 711 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   ALA C 682 " --> pdb=" O   ILE C 730 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE C 540 " --> pdb=" O   THR C 749 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL C 542 " --> pdb=" O   VAL C 747 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL C 747 " --> pdb=" O   VAL C 542 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 543 through 544
      removed outlier: 4.186A  pdb=" N   LEU D 515 " --> pdb=" O   ASP D 594 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP D 596 " --> pdb=" O   LEU D 515 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR D 598 " --> pdb=" O   VAL D 517 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 643 through 644
      removed outlier: 4.203A  pdb=" N   ASP D 643 " --> pdb=" O   LEU D 877 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LEU D 877 " --> pdb=" O   ASP D 643 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 844 through 845
      removed outlier: 3.616A  pdb=" N   MET D 844 " --> pdb=" O   GLY D 654 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   LEU D 653 " --> pdb=" O   ALA D 869 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA D 869 " --> pdb=" O   LEU D 653 " (cutoff:3.500A)
      removed outlier: 9.733A  pdb=" N   ILE D 655 " --> pdb=" O   PRO D 867 " (cutoff:3.500A)
      removed outlier: 10.755A  pdb=" N   VAL D 657 " --> pdb=" O   GLY D 865 " (cutoff:3.500A)
      removed outlier: 10.150A  pdb=" N   GLY D 865 " --> pdb=" O   VAL D 657 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    813 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: 2.39

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        0.79 -     1.03: 1
        1.03 -     1.27: 1494
        1.27 -     1.51: 4271
        1.51 -     1.75: 3337
        1.75 -     1.99: 95
  Bond restraints: 9198
  Sorted by residual:
  bond pdb=" CG  PRO C 675 "
       pdb=" CD  PRO C 675 "
    ideal  model  delta    sigma   weight residual
    1.503  0.795  0.708 3.40e-02 8.65e+02 4.34e+02
  bond pdb=" CA  PRO C 675 "
       pdb=" CB  PRO C 675 "
    ideal  model  delta    sigma   weight residual
    1.531  1.323  0.208 1.67e-02 3.59e+03 1.55e+02
  bond pdb=" N   PRO C 675 "
       pdb=" CD  PRO C 675 "
    ideal  model  delta    sigma   weight residual
    1.473  1.646 -0.173 1.40e-02 5.10e+03 1.53e+02
  bond pdb=" C   ASN C 674 "
       pdb=" N   PRO C 675 "
    ideal  model  delta    sigma   weight residual
    1.326  1.474 -0.148 1.44e-02 4.82e+03 1.06e+02
  bond pdb=" CB  PRO C 675 "
       pdb=" CG  PRO C 675 "
    ideal  model  delta    sigma   weight residual
    1.492  1.992 -0.500 5.00e-02 4.00e+02 1.00e+02
  ... (remaining 9193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.21: 12458
       21.21 -    42.42: 1
       42.42 -    63.63: 1
       63.63 -    84.84: 0
       84.84 -   106.05: 1
  Bond angle restraints: 12461
  Sorted by residual:
  angle pdb=" CB  PRO C 675 "
        pdb=" CG  PRO C 675 "
        pdb=" CD  PRO C 675 "
      ideal   model   delta    sigma   weight residual
     106.10    0.05  106.05 3.20e+00 9.77e-02 1.10e+03
  angle pdb=" CA  PRO C 675 "
        pdb=" N   PRO C 675 "
        pdb=" CD  PRO C 675 "
      ideal   model   delta    sigma   weight residual
     112.00   76.53   35.47 1.40e+00 5.10e-01 6.42e+02
  angle pdb=" CA  ASN C 674 "
        pdb=" C   ASN C 674 "
        pdb=" O   ASN C 674 "
      ideal   model   delta    sigma   weight residual
     120.08  106.91   13.17 1.14e+00 7.69e-01 1.33e+02
  angle pdb=" C   ASN C 674 "
        pdb=" N   PRO C 675 "
        pdb=" CD  PRO C 675 "
      ideal   model   delta    sigma   weight residual
     125.00  170.58  -45.58 4.10e+00 5.95e-02 1.24e+02
  angle pdb=" CA  ASN C 674 "
        pdb=" C   ASN C 674 "
        pdb=" N   PRO C 675 "
      ideal   model   delta    sigma   weight residual
     118.34  128.80  -10.46 1.03e+00 9.43e-01 1.03e+02
  ... (remaining 12456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.52: 4844
       23.52 -    47.05: 580
       47.05 -    70.57: 62
       70.57 -    94.09: 21
       94.09 -   117.62: 1
  Dihedral angle restraints: 5508
    sinusoidal: 2171
      harmonic: 3337
  Sorted by residual:
  dihedral pdb=" CB  CYS A 420 "
           pdb=" SG  CYS A 420 "
           pdb=" SG  CYS A 454 "
           pdb=" CB  CYS A 454 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.59  -83.59     1      1.00e+01 1.00e-02 8.53e+01
  dihedral pdb=" CB  CYS A 436 "
           pdb=" SG  CYS A 436 "
           pdb=" SG  CYS A 455 "
           pdb=" CB  CYS A 455 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.94  -81.94     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" N   PRO C 675 "
           pdb=" CG  PRO C 675 "
           pdb=" CD  PRO C 675 "
           pdb=" CB  PRO C 675 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  147.62 -117.62     1      1.50e+01 4.44e-03 6.24e+01
  ... (remaining 5505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1275
       0.088 -    0.177: 86
       0.177 -    0.265: 6
       0.265 -    0.353: 3
       0.353 -    0.441: 2
  Chirality restraints: 1372
  Sorted by residual:
  chirality pdb=" CA  GLU D 830 "
            pdb=" N   GLU D 830 "
            pdb=" C   GLU D 830 "
            pdb=" CB  GLU D 830 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" CA  PRO C 675 "
            pdb=" N   PRO C 675 "
            pdb=" C   PRO C 675 "
            pdb=" CB  PRO C 675 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.30    0.42 2.00e-01 2.50e+01 4.43e+00
  chirality pdb=" CA  MET B 902 "
            pdb=" N   MET B 902 "
            pdb=" C   MET B 902 "
            pdb=" CB  MET B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 1369 not shown)

  Planarity restraints: 1606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 523 "   -0.088 5.00e-02 4.00e+02   1.33e-01 2.84e+01
        pdb=" N   PRO D 524 "    0.231 5.00e-02 4.00e+02
        pdb=" CA  PRO D 524 "   -0.072 5.00e-02 4.00e+02
        pdb=" CD  PRO D 524 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 908 "   -0.024 2.00e-02 2.50e+03   4.78e-02 2.28e+01
        pdb=" C   TYR B 908 "    0.083 2.00e-02 2.50e+03
        pdb=" O   TYR B 908 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   ARG B 909 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 446 "   -0.059 5.00e-02 4.00e+02   8.35e-02 1.11e+01
        pdb=" N   PRO A 447 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 447 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 447 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1603 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 299
        2.68 -     3.24: 8874
        3.24 -     3.79: 13271
        3.79 -     4.35: 16274
        4.35 -     4.90: 27326
  Nonbonded interactions: 66044
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 901 "
            pdb=" OD1 ASP D 905 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" O   GLY B 618 "
            pdb=" NH1 ARG B 622 "
     model   vdw
     2.142 3.120
  nonbonded pdb=" O   LEU C 517 "
            pdb=" OG1 THR C 518 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" NE1 TRP C 498 "
            pdb=" OH  TYR C 526 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" OG  SER C 507 "
            pdb=" OE1 GLN C 509 "
     model   vdw
     2.180 3.040
  ... (remaining 66039 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 395 through 443 or (resid 444 and (name N or name CA or na \ 
me C or name O or name CB )) or (resid 445 through 448 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 449 through 544 or resid 663 through 73 \ 
1 or (resid 732 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 733 through 745 or (resid 746 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 747 through 798))
  selection = (chain 'C' and (resid 395 through 397 or (resid 398 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 399 through 431 or (resid 432 through 433  \ 
and (name N or name CA or name C or name O or name CB )) or resid 434 through 48 \ 
7 or (resid 488 through 489 and (name N or name CA or name C or name O or name C \ 
B )) or resid 490 or (resid 491 through 496 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 497 through 510 or (resid 511 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 512 through 543 or (resid 544 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 663 through 693 or \ 
 (resid 694 through 695 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 696 through 708 or (resid 709 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 710 through 787 or (resid 788 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 789 through 798))
}
ncs_group {
  reference = (chain 'B' and (resid 511 through 541 or (resid 542 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 543 or (resid 544 through 545 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 546 through 596 or (resid  \ 
597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ 
h 657 or (resid 658 through 777 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 778 through 784 or (resid 785 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 786 through 855 or (resid 856 through 857 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 858 through 888 or \ 
 (resid 889 and (name N or name CA or name C or name O or name CB )) or resid 89 \ 
0 through 891 or (resid 892 through 894 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 895 through 901 or (resid 902 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 903 through 913))
  selection = (chain 'D' and (resid 511 through 565 or (resid 566 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 567 through 642 or (resid 643 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 644 through 829 or (resid  \ 
830 and (name N or name CA or name C or name O or name CB )) or resid 831 throug \ 
h 844 or (resid 845 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 846 through 908 or (resid 909 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 910 through 913))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.310
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
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      :  0.011   0.708   9207  Z= 0.411
  Angle     :  1.338 106.049  12479  Z= 0.609
  Chirality :  0.051   0.441   1372
  Planarity :  0.006   0.133   1606
  Dihedral  : 18.947 117.617   3329
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 10.76 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 39.26 %
    Favored  : 59.30 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.24), residues: 1134
  helix:  0.07 (0.27), residues: 373
  sheet: -1.13 (0.52), residues: 97
  loop : -2.96 (0.22), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 498 
 HIS   0.031   0.001   HIS D 626 
 PHE   0.020   0.001   PHE B 794 
 TYR   0.017   0.001   TYR C 703 
 ARG   0.004   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18507 (  284)
  hydrogen bonds       : angle       7.82023 (  813)
  SS BOND              : bond        0.00847 (    9)
  SS BOND              : angle       0.68896 (   18)
  covalent geometry    : bond        0.01096 ( 9198)
  covalent geometry    : angle       1.33889 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 12
  residues processed: 123
  average time/residue: 0.2087
  time to fit residues: 36.4494
Evaluate side-chains
  125 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain B residue  553 THR
Chi-restraints excluded: chain B residue  586 LYS
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  902 MET
Chi-restraints excluded: chain D residue  586 LYS
Chi-restraints excluded: chain D residue  587 ILE
Chi-restraints excluded: chain D residue  622 ARG
Chi-restraints excluded: chain D residue  626 HIS
Chi-restraints excluded: chain D residue  830 GLU
Chi-restraints excluded: chain D residue  844 MET
Chi-restraints excluded: chain D residue  909 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0060
   chunk 84 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:
B 786 HIS
C 440 ASN
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.133701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.110112 restraints weight = 19903.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.109987 restraints weight = 18648.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.110988 restraints weight = 16813.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.0907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.084   9207  Z= 0.152
  Angle     :  0.659   9.789  12479  Z= 0.347
  Chirality :  0.044   0.239   1372
  Planarity :  0.006   0.135   1606
  Dihedral  :  6.647  57.470   1267
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 10.76 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 35.33 %
    Favored  : 58.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.25), residues: 1134
  helix:  0.52 (0.27), residues: 379
  sheet: -1.63 (0.44), residues: 139
  loop : -2.86 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 498 
 HIS   0.003   0.001   HIS C 404 
 PHE   0.020   0.001   PHE B 794 
 TYR   0.018   0.001   TYR C 526 
 ARG   0.003   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03910 (  284)
  hydrogen bonds       : angle       5.75460 (  813)
  SS BOND              : bond        0.00158 (    9)
  SS BOND              : angle       0.50143 (   18)
  covalent geometry    : bond        0.00366 ( 9198)
  covalent geometry    : angle       0.65962 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 126
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  475 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: A  536 GLN cc_start: 0.8335 (pp30) cc_final: 0.8083 (pp30)
REVERT: B  622 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7735 (mpp80)
REVERT: B  850 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7794 (t0)
REVERT: C  440 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6892 (t0)
REVERT: C  755 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8361 (mtt90)
REVERT: D  636 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8204 (t)
REVERT: D  640 GLN cc_start: 0.8374 (mm110) cc_final: 0.8140 (mm110)
  outliers start: 61
  outliers final: 31
  residues processed: 173
  average time/residue: 0.1807
  time to fit residues: 45.0028
Evaluate side-chains
  150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  810 PHE
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  866 LYS
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  484 PHE
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  691 ILE
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  721 VAL
Chi-restraints excluded: chain C residue  755 ARG
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  564 SER
Chi-restraints excluded: chain D residue  636 THR
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  830 GLU
Chi-restraints excluded: chain D residue  861 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    0.0970
   chunk 51 optimal weight:    0.6980
   chunk 107 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0970
   chunk 10 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   chunk 81 optimal weight:    0.0170
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.2214

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

Flipped N/Q/H residues before XYZ refinement:
B 786 HIS
C 440 ASN
C 686 GLN
C 710 ASN
** D 612 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 = 0.3915 r_free = 0.3915 target = 0.137914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.114533 restraints weight = 20302.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.115105 restraints weight = 17074.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.116395 restraints weight = 14865.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9207  Z= 0.111
  Angle     :  0.611   8.875  12479  Z= 0.319
  Chirality :  0.042   0.242   1372
  Planarity :  0.005   0.134   1606
  Dihedral  :  5.357  48.617   1238
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.64 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 35.64 %
    Favored  : 58.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.95 (0.24), residues: 1134
  helix:  0.77 (0.27), residues: 381
  sheet: -0.87 (0.50), residues: 104
  loop : -2.84 (0.22), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 498 
 HIS   0.005   0.001   HIS C 404 
 PHE   0.022   0.001   PHE B 794 
 TYR   0.013   0.001   TYR C 526 
 ARG   0.003   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  284)
  hydrogen bonds       : angle       5.39784 (  813)
  SS BOND              : bond        0.00179 (    9)
  SS BOND              : angle       0.33088 (   18)
  covalent geometry    : bond        0.00255 ( 9198)
  covalent geometry    : angle       0.61129 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 137
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  475 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7155 (tt0)
REVERT: A  754 PHE cc_start: 0.7858 (t80) cc_final: 0.7577 (t80)
REVERT: B  571 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (mttm)
REVERT: B  622 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7764 (mpp80)
REVERT: C  399 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8234 (mtmt)
REVERT: C  424 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5789 (t80)
  outliers start: 55
  outliers final: 24
  residues processed: 176
  average time/residue: 0.1849
  time to fit residues: 46.6552
Evaluate side-chains
  153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  571 LYS
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain C residue  399 LYS
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  486 THR
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  686 GLN
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  564 SER
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  844 MET
Chi-restraints excluded: chain D residue  864 VAL
Chi-restraints excluded: chain D residue  890 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 440 ASN
C 796 GLN
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.134868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.110140 restraints weight = 20078.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.110703 restraints weight = 16339.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.111548 restraints weight = 13760.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9207  Z= 0.128
  Angle     :  0.633   9.181  12479  Z= 0.331
  Chirality :  0.043   0.236   1372
  Planarity :  0.005   0.137   1606
  Dihedral  :  5.038  46.136   1235
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  9.70 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 35.64 %
    Favored  : 58.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.84 (0.25), residues: 1134
  helix:  0.85 (0.27), residues: 383
  sheet: -1.09 (0.51), residues: 107
  loop : -2.72 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 731 
 HIS   0.003   0.001   HIS C 404 
 PHE   0.022   0.001   PHE B 794 
 TYR   0.026   0.001   TYR C 692 
 ARG   0.002   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  284)
  hydrogen bonds       : angle       5.27638 (  813)
  SS BOND              : bond        0.00284 (    9)
  SS BOND              : angle       1.61212 (   18)
  covalent geometry    : bond        0.00304 ( 9198)
  covalent geometry    : angle       0.63028 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 126
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7318 (tt0)
REVERT: A  701 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7076 (p)
REVERT: A  754 PHE cc_start: 0.7930 (t80) cc_final: 0.7612 (t80)
REVERT: B  850 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7948 (t0)
REVERT: C  424 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6252 (t80)
REVERT: D  541 GLN cc_start: 0.7768 (mp10) cc_final: 0.7549 (mp10)
REVERT: D  595 PHE cc_start: 0.8360 (p90) cc_final: 0.7924 (p90)
  outliers start: 55
  outliers final: 40
  residues processed: 163
  average time/residue: 0.1618
  time to fit residues: 39.1448
Evaluate side-chains
  164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 120
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  810 PHE
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  866 LYS
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  484 PHE
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  526 VAL
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  564 SER
Chi-restraints excluded: chain D residue  629 VAL
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  844 MET
Chi-restraints excluded: chain D residue  854 SER
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0570
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
C 440 ASN
C 686 GLN
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.103448 restraints weight = 19314.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104612 restraints weight = 14024.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.106050 restraints weight = 11447.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9207  Z= 0.119
  Angle     :  0.624   9.119  12479  Z= 0.325
  Chirality :  0.043   0.235   1372
  Planarity :  0.005   0.138   1606
  Dihedral  :  4.959  42.641   1235
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.99 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 35.12 %
    Favored  : 58.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.78 (0.25), residues: 1134
  helix:  0.90 (0.27), residues: 383
  sheet: -1.08 (0.51), residues: 107
  loop : -2.68 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 731 
 HIS   0.004   0.001   HIS C 404 
 PHE   0.022   0.001   PHE B 794 
 TYR   0.031   0.001   TYR C 692 
 ARG   0.002   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (  284)
  hydrogen bonds       : angle       5.18452 (  813)
  SS BOND              : bond        0.00076 (    9)
  SS BOND              : angle       0.83760 (   18)
  covalent geometry    : bond        0.00280 ( 9198)
  covalent geometry    : angle       0.62406 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 127
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7277 (tt0)
REVERT: A  536 GLN cc_start: 0.8120 (pp30) cc_final: 0.7877 (pp30)
REVERT: A  701 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7099 (p)
REVERT: A  754 PHE cc_start: 0.8073 (t80) cc_final: 0.7604 (t80)
REVERT: B  571 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8331 (mttm)
REVERT: B  622 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7276 (mpt-90)
REVERT: B  850 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8138 (t0)
REVERT: C  424 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6482 (t80)
REVERT: D  547 MET cc_start: 0.7175 (pmm) cc_final: 0.6693 (pmm)
REVERT: D  595 PHE cc_start: 0.8389 (p90) cc_final: 0.8144 (p90)
  outliers start: 62
  outliers final: 41
  residues processed: 173
  average time/residue: 0.1761
  time to fit residues: 44.6985
Evaluate side-chains
  164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 117
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  749 THR
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  571 LYS
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  440 ASN
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  526 VAL
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  629 VAL
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  844 MET
Chi-restraints excluded: chain D residue  854 SER
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
C 405 GLN
C 440 ASN
C 686 GLN
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.101118 restraints weight = 19120.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101484 restraints weight = 16239.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102511 restraints weight = 15661.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9207  Z= 0.270
  Angle     :  0.776  10.677  12479  Z= 0.409
  Chirality :  0.048   0.222   1372
  Planarity :  0.006   0.145   1606
  Dihedral  :  5.772  45.727   1235
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  : 11.46 %
    Favored  : 87.57 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 35.43 %
    Favored  : 57.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.24), residues: 1134
  helix:  0.50 (0.26), residues: 382
  sheet: -1.62 (0.47), residues: 122
  loop : -2.85 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 792 
 HIS   0.005   0.001   HIS C 477 
 PHE   0.025   0.002   PHE C 533 
 TYR   0.036   0.002   TYR B 579 
 ARG   0.003   0.000   ARG D 818 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  284)
  hydrogen bonds       : angle       5.53187 (  813)
  SS BOND              : bond        0.00207 (    9)
  SS BOND              : angle       1.03741 (   18)
  covalent geometry    : bond        0.00645 ( 9198)
  covalent geometry    : angle       0.77584 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 111
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A  475 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7525 (pt0)
REVERT: A  701 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7080 (p)
REVERT: A  710 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7944 (m-40)
REVERT: A  754 PHE cc_start: 0.8103 (t80) cc_final: 0.7766 (t80)
REVERT: B  850 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8105 (t0)
REVERT: C  424 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6282 (t80)
REVERT: C  692 TYR cc_start: 0.8283 (t80) cc_final: 0.7897 (t80)
REVERT: D  595 PHE cc_start: 0.8427 (p90) cc_final: 0.8005 (p90)
  outliers start: 71
  outliers final: 47
  residues processed: 168
  average time/residue: 0.1646
  time to fit residues: 41.3706
Evaluate side-chains
  156 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 104
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  710 ASN
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  622 ARG
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  863 THR
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  436 CYS
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  484 PHE
Chi-restraints excluded: chain C residue  507 SER
Chi-restraints excluded: chain C residue  518 THR
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  684 VAL
Chi-restraints excluded: chain C residue  699 LEU
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  718 ILE
Chi-restraints excluded: chain C residue  748 THR
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  631 SER
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  844 MET
Chi-restraints excluded: chain D residue  854 SER
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Chi-restraints excluded: chain D residue  908 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0980
   chunk 18 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 110 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
C 440 ASN
C 453 GLN
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 626 HIS
D 640 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.134065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.108700 restraints weight = 20380.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.110199 restraints weight = 15224.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.111621 restraints weight = 11924.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9207  Z= 0.122
  Angle     :  0.665   9.311  12479  Z= 0.345
  Chirality :  0.043   0.229   1372
  Planarity :  0.005   0.143   1606
  Dihedral  :  5.207  39.771   1235
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.91 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 38.22 %
    Favored  : 56.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.87 (0.25), residues: 1134
  helix:  0.79 (0.27), residues: 382
  sheet: -1.33 (0.47), residues: 119
  loop : -2.67 (0.23), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 498 
 HIS   0.005   0.001   HIS C 404 
 PHE   0.022   0.001   PHE B 794 
 TYR   0.016   0.001   TYR B 579 
 ARG   0.003   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03136 (  284)
  hydrogen bonds       : angle       5.15836 (  813)
  SS BOND              : bond        0.00242 (    9)
  SS BOND              : angle       0.85611 (   18)
  covalent geometry    : bond        0.00279 ( 9198)
  covalent geometry    : angle       0.66427 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 120
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7434 (tt0)
REVERT: A  701 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7069 (p)
REVERT: A  754 PHE cc_start: 0.8110 (t80) cc_final: 0.7686 (t80)
REVERT: B  850 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8067 (t0)
REVERT: C  424 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6281 (t80)
REVERT: C  692 TYR cc_start: 0.8153 (t80) cc_final: 0.7802 (t80)
REVERT: D  547 MET cc_start: 0.7050 (pmm) cc_final: 0.6559 (pmm)
REVERT: D  636 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8166 (t)
REVERT: D  640 GLN cc_start: 0.8520 (mm110) cc_final: 0.8236 (mm110)
REVERT: D  818 ARG cc_start: 0.7606 (ptt90) cc_final: 0.7140 (tmm160)
  outliers start: 53
  outliers final: 38
  residues processed: 159
  average time/residue: 0.1647
  time to fit residues: 39.2348
Evaluate side-chains
  157 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 114
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  475 GLU
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  749 THR
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  506 LEU
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  684 VAL
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  721 VAL
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  568 VAL
Chi-restraints excluded: chain D residue  584 LEU
Chi-restraints excluded: chain D residue  636 THR
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0170
   chunk 15 optimal weight:    8.9990
   overall best weight:    0.9220

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

Flipped N/Q/H residues before XYZ refinement:
** D 612 HIS ** 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 = 0.3764 r_free = 0.3764 target = 0.129857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.105994 restraints weight = 19135.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.106737 restraints weight = 15891.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.108061 restraints weight = 12924.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9207  Z= 0.140
  Angle     :  0.672   9.646  12479  Z= 0.349
  Chirality :  0.044   0.226   1372
  Planarity :  0.005   0.144   1606
  Dihedral  :  4.968  36.144   1231
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 10.23 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 38.12 %
    Favored  : 56.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.81 (0.25), residues: 1134
  helix:  0.82 (0.27), residues: 383
  sheet: -1.30 (0.47), residues: 119
  loop : -2.64 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 792 
 HIS   0.006   0.001   HIS A 449 
 PHE   0.022   0.001   PHE B 794 
 TYR   0.018   0.001   TYR C 703 
 ARG   0.002   0.000   ARG D 818 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  284)
  hydrogen bonds       : angle       5.16429 (  813)
  SS BOND              : bond        0.00146 (    9)
  SS BOND              : angle       0.83098 (   18)
  covalent geometry    : bond        0.00333 ( 9198)
  covalent geometry    : angle       0.67131 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 114
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  701 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7031 (p)
REVERT: A  754 PHE cc_start: 0.8128 (t80) cc_final: 0.7739 (t80)
REVERT: B  580 CYS cc_start: 0.8137 (t) cc_final: 0.7916 (t)
REVERT: B  850 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8126 (t0)
REVERT: C  424 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6087 (t80)
REVERT: C  692 TYR cc_start: 0.8205 (t80) cc_final: 0.7875 (t80)
REVERT: D  595 PHE cc_start: 0.8404 (p90) cc_final: 0.7921 (p90)
REVERT: D  636 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8335 (t)
REVERT: D  818 ARG cc_start: 0.7646 (ptt90) cc_final: 0.7433 (tmm160)
  outliers start: 50
  outliers final: 40
  residues processed: 150
  average time/residue: 0.1676
  time to fit residues: 37.6773
Evaluate side-chains
  154 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 110
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  749 THR
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  507 SER
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  684 VAL
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  721 VAL
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  555 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  636 THR
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Chi-restraints excluded: chain D residue  884 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 9 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.134674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.109213 restraints weight = 20301.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.111255 restraints weight = 15677.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.112392 restraints weight = 11915.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9207  Z= 0.121
  Angle     :  0.647   9.218  12479  Z= 0.335
  Chirality :  0.043   0.228   1372
  Planarity :  0.005   0.143   1606
  Dihedral  :  4.812  35.653   1231
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.99 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 37.81 %
    Favored  : 57.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.76 (0.25), residues: 1134
  helix:  0.85 (0.27), residues: 386
  sheet: -1.29 (0.46), residues: 119
  loop : -2.60 (0.23), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 498 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.023   0.001   PHE B 794 
 TYR   0.015   0.001   TYR B 579 
 ARG   0.002   0.000   ARG C 704 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02996 (  284)
  hydrogen bonds       : angle       5.05584 (  813)
  SS BOND              : bond        0.00125 (    9)
  SS BOND              : angle       0.63081 (   18)
  covalent geometry    : bond        0.00286 ( 9198)
  covalent geometry    : angle       0.64702 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 116
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A  399 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6856 (mtmt)
REVERT: A  701 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7043 (p)
REVERT: A  754 PHE cc_start: 0.8126 (t80) cc_final: 0.7764 (t80)
REVERT: B  850 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8074 (t0)
REVERT: C  424 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6248 (t80)
REVERT: C  692 TYR cc_start: 0.8132 (t80) cc_final: 0.7879 (t80)
REVERT: D  547 MET cc_start: 0.7027 (pmm) cc_final: 0.6409 (pmm)
REVERT: D  636 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8209 (t)
REVERT: D  640 GLN cc_start: 0.8540 (mm110) cc_final: 0.8292 (mm110)
REVERT: D  905 ASP cc_start: 0.7961 (t0) cc_final: 0.7623 (p0)
  outliers start: 49
  outliers final: 36
  residues processed: 151
  average time/residue: 0.1610
  time to fit residues: 36.4730
Evaluate side-chains
  151 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 110
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  749 THR
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  507 SER
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  684 VAL
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  721 VAL
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  636 THR
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Chi-restraints excluded: chain D residue  884 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** D 612 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.127269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.103013 restraints weight = 19367.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.103603 restraints weight = 14906.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.104572 restraints weight = 14323.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9207  Z= 0.164
  Angle     :  0.695   9.432  12479  Z= 0.362
  Chirality :  0.044   0.221   1372
  Planarity :  0.006   0.144   1606
  Dihedral  :  4.972  36.737   1231
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.32 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 38.02 %
    Favored  : 57.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.81 (0.25), residues: 1134
  helix:  0.80 (0.27), residues: 384
  sheet: -1.27 (0.47), residues: 119
  loop : -2.63 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 731 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.022   0.002   PHE B 794 
 TYR   0.021   0.002   TYR B 579 
 ARG   0.003   0.000   ARG D 818 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  284)
  hydrogen bonds       : angle       5.10561 (  813)
  SS BOND              : bond        0.00149 (    9)
  SS BOND              : angle       0.76248 (   18)
  covalent geometry    : bond        0.00393 ( 9198)
  covalent geometry    : angle       0.69459 (12461)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 112
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  701 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7066 (p)
REVERT: A  754 PHE cc_start: 0.8184 (t80) cc_final: 0.7849 (t80)
REVERT: B  850 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8166 (t0)
REVERT: C  424 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6350 (t80)
REVERT: C  692 TYR cc_start: 0.8228 (t80) cc_final: 0.8022 (t80)
REVERT: D  547 MET cc_start: 0.7082 (pmm) cc_final: 0.6532 (pmm)
REVERT: D  595 PHE cc_start: 0.8374 (p90) cc_final: 0.7882 (p90)
REVERT: D  636 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8364 (t)
REVERT: D  905 ASP cc_start: 0.7899 (t0) cc_final: 0.7670 (p0)
  outliers start: 46
  outliers final: 39
  residues processed: 146
  average time/residue: 0.1569
  time to fit residues: 34.6069
Evaluate side-chains
  150 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 107
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  419 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue  519 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  641 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  796 THR
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  850 ASP
Chi-restraints excluded: chain B residue  881 SER
Chi-restraints excluded: chain C residue  396 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 THR
Chi-restraints excluded: chain C residue  424 PHE
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  459 CYS
Chi-restraints excluded: chain C residue  476 VAL
Chi-restraints excluded: chain C residue  507 SER
Chi-restraints excluded: chain C residue  540 ILE
Chi-restraints excluded: chain C residue  684 VAL
Chi-restraints excluded: chain C residue  701 THR
Chi-restraints excluded: chain C residue  721 VAL
Chi-restraints excluded: chain C residue  780 HIS
Chi-restraints excluded: chain D residue  514 HIS
Chi-restraints excluded: chain D residue  561 LEU
Chi-restraints excluded: chain D residue  596 ASP
Chi-restraints excluded: chain D residue  636 THR
Chi-restraints excluded: chain D residue  657 VAL
Chi-restraints excluded: chain D residue  786 HIS
Chi-restraints excluded: chain D residue  810 PHE
Chi-restraints excluded: chain D residue  834 ASN
Chi-restraints excluded: chain D residue  861 LEU
Chi-restraints excluded: chain D residue  864 VAL
Chi-restraints excluded: chain D residue  884 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** D 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 640 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.126422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101127 restraints weight = 19491.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.102966 restraints weight = 14806.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103727 restraints weight = 12280.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9207  Z= 0.175
  Angle     :  0.706   9.323  12479  Z= 0.368
  Chirality :  0.045   0.219   1372
  Planarity :  0.006   0.145   1606
  Dihedral  :  5.111  36.866   1231
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.41 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 37.71 %
    Favored  : 57.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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: -1.90 (0.24), residues: 1134
  helix:  0.69 (0.26), residues: 385
  sheet: -1.20 (0.47), residues: 119
  loop : -2.69 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 792 
 HIS   0.005   0.001   HIS A 449 
 PHE   0.022   0.002   PHE B 794 
 TYR   0.023   0.002   TYR B 579 
 ARG   0.003   0.000   ARG D 818 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  284)
  hydrogen bonds       : angle       5.16809 (  813)
  SS BOND              : bond        0.00160 (    9)
  SS BOND              : angle       0.78007 (   18)
  covalent geometry    : bond        0.00418 ( 9198)
  covalent geometry    : angle       0.70560 (12461)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2611.91 seconds
wall clock time: 47 minutes 7.35 seconds (2827.35 seconds total)