Starting phenix.real_space_refine
on Fri Sep 11 12:58:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mix_48304/09_2026/9mix_48304.map"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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      68      5.16       5
     C    6134      2.51       5
     N    1402      2.21       5
     O    1516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9120
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 4406
          Classifications: {'peptide': 567}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 27, 'TRANS': 539}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 62
    Chain: "A"
      Number of atoms: 154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 154
          Unusual residues: {'CLR': 5, 'NAG': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.75, per 1000 atoms: 0.41
  Number of scatterers: 9120
  At special positions: 0
  Unit cell: (92.463, 127.449, 104.958, 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      68     16.00
     O    1516      8.00
     N    1402      7.00
     C    6134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 667 " - pdb=" SG  CYS A 715 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 669 " - pdb=" SG  CYS A 703 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B 667 " - pdb=" SG  CYS B 715 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 669 " - pdb=" SG  CYS B 703 " distance=2.10

  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
  Links applied
    NAG-ASN
      " NAG A1206 " - " ASN A 697 "
      " NAG B1206 " - " ASN B 697 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 355.7 milliseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 6 sheets defined
      72.0% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 473 through 477
      removed outlier: 3.831A  pdb=" N   GLN A 477 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.636A  pdb=" N   ARG A 502 " --> pdb=" O   TRP A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 535
      removed outlier: 3.725A  pdb=" N   LEU A 510 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 519 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   SER A 522 " --> pdb=" O   CYS A 518 " (cutoff:3.500A)
      Proline residue:  A 523  - end of helix
    Processing helix  chain 'A' and resid 540 through 558
    Processing helix  chain 'A' and resid 570 through 586
    Processing helix  chain 'A' and resid 590 through 611
    Processing helix  chain 'A' and resid 612 through 620
      removed outlier: 4.040A  pdb=" N   SER A 615 " --> pdb=" O   ASP A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 651
      removed outlier: 3.660A  pdb=" N   GLU A 625 " --> pdb=" O   THR A 621 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 627 " --> pdb=" O   PHE A 623 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA A 640 " --> pdb=" O   PHE A 636 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 641 " --> pdb=" O   ILE A 637 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER A 648 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 649 " --> pdb=" O   PHE A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 665
      removed outlier: 3.604A  pdb=" N   LEU A 661 " --> pdb=" O   ASP A 658 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU A 662 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   THR A 663 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR A 665 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 687
      removed outlier: 3.684A  pdb=" N   GLU A 685 " --> pdb=" O   LYS A 681 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   SER A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 698
      removed outlier: 3.513A  pdb=" N   ASN A 697 " --> pdb=" O   ILE A 694 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 698 " --> pdb=" O   TRP A 695 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 694 through 698'
    Processing helix  chain 'A' and resid 699 through 706
    Processing helix  chain 'A' and resid 725 through 745
      removed outlier: 3.522A  pdb=" N   SER A 729 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 763
    Processing helix  chain 'A' and resid 763 through 780
    Processing helix  chain 'A' and resid 811 through 817
      removed outlier: 4.175A  pdb=" N   ILE A 815 " --> pdb=" O   TRP A 811 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA A 816 " --> pdb=" O   TRP A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 840
      removed outlier: 3.899A  pdb=" N   LEU A 822 " --> pdb=" O   ILE A 818 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LEU A 823 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP A 831 " --> pdb=" O   LEU A 827 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 834 " --> pdb=" O   MET A 830 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   THR A 835 " --> pdb=" O   ASP A 831 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN A 840 " --> pdb=" O   ALA A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 845
      removed outlier: 3.503A  pdb=" N   HIS A 844 " --> pdb=" O   ARG A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 870
    Processing helix  chain 'A' and resid 878 through 888
    Processing helix  chain 'A' and resid 911 through 923
    Processing helix  chain 'A' and resid 926 through 931
    Processing helix  chain 'A' and resid 934 through 949
      removed outlier: 4.015A  pdb=" N   LEU A 938 " --> pdb=" O   PRO A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 961
    Processing helix  chain 'A' and resid 972 through 976
    Processing helix  chain 'A' and resid 979 through 1003
      removed outlier: 3.821A  pdb=" N   VAL A 983 " --> pdb=" O   PRO A 979 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   HIS A 984 " --> pdb=" O   LEU A 980 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU A 985 " --> pdb=" O   ARG A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1009
      removed outlier: 3.849A  pdb=" N   VAL A1008 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A1009 " --> pdb=" O   ALA A1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1005 through 1009'
    Processing helix  chain 'A' and resid 1012 through 1024
      removed outlier: 3.835A  pdb=" N   ASP A1024 " --> pdb=" O   ARG A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1036
      removed outlier: 3.896A  pdb=" N   TRP A1034 " --> pdb=" O   ARG A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1048
    Processing helix  chain 'B' and resid 473 through 477
      removed outlier: 3.830A  pdb=" N   GLN B 477 " --> pdb=" O   PRO B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 494
    Processing helix  chain 'B' and resid 498 through 503
      removed outlier: 3.636A  pdb=" N   ARG B 502 " --> pdb=" O   TRP B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 535
      removed outlier: 3.725A  pdb=" N   LEU B 510 " --> pdb=" O   SER B 506 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS B 518 " --> pdb=" O   LEU B 514 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B 519 " --> pdb=" O   PHE B 515 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   SER B 522 " --> pdb=" O   CYS B 518 " (cutoff:3.500A)
      Proline residue:  B 523  - end of helix
    Processing helix  chain 'B' and resid 540 through 558
    Processing helix  chain 'B' and resid 570 through 586
    Processing helix  chain 'B' and resid 590 through 611
    Processing helix  chain 'B' and resid 613 through 620
    Processing helix  chain 'B' and resid 621 through 651
      removed outlier: 3.660A  pdb=" N   GLU B 625 " --> pdb=" O   THR B 621 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 627 " --> pdb=" O   PHE B 623 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA B 640 " --> pdb=" O   PHE B 636 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU B 641 " --> pdb=" O   ILE B 637 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER B 648 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU B 649 " --> pdb=" O   PHE B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 665
      removed outlier: 3.604A  pdb=" N   LEU B 661 " --> pdb=" O   ASP B 658 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU B 662 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   THR B 663 " --> pdb=" O   GLU B 660 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TYR B 665 " --> pdb=" O   LEU B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 676 through 687
      removed outlier: 3.684A  pdb=" N   GLU B 685 " --> pdb=" O   LYS B 681 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   SER B 686 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 694 through 698
      removed outlier: 3.513A  pdb=" N   ASN B 697 " --> pdb=" O   ILE B 694 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 698 " --> pdb=" O   TRP B 695 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 694 through 698'
    Processing helix  chain 'B' and resid 699 through 706
    Processing helix  chain 'B' and resid 725 through 745
      removed outlier: 3.522A  pdb=" N   SER B 729 " --> pdb=" O   VAL B 725 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 753 through 763
    Processing helix  chain 'B' and resid 763 through 780
    Processing helix  chain 'B' and resid 811 through 817
      removed outlier: 4.175A  pdb=" N   ILE B 815 " --> pdb=" O   TRP B 811 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA B 816 " --> pdb=" O   TRP B 812 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 840
      removed outlier: 3.899A  pdb=" N   LEU B 822 " --> pdb=" O   ILE B 818 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LEU B 823 " --> pdb=" O   ILE B 819 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP B 831 " --> pdb=" O   LEU B 827 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 834 " --> pdb=" O   MET B 830 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   THR B 835 " --> pdb=" O   ASP B 831 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN B 840 " --> pdb=" O   ALA B 836 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 845
      removed outlier: 3.503A  pdb=" N   HIS B 844 " --> pdb=" O   ARG B 841 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 853 through 870
    Processing helix  chain 'B' and resid 878 through 888
    Processing helix  chain 'B' and resid 911 through 923
    Processing helix  chain 'B' and resid 926 through 931
    Processing helix  chain 'B' and resid 934 through 949
      removed outlier: 4.015A  pdb=" N   LEU B 938 " --> pdb=" O   PRO B 934 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 953 through 961
    Processing helix  chain 'B' and resid 972 through 976
    Processing helix  chain 'B' and resid 979 through 1003
      removed outlier: 3.821A  pdb=" N   VAL B 983 " --> pdb=" O   PRO B 979 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   HIS B 984 " --> pdb=" O   LEU B 980 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU B 985 " --> pdb=" O   ARG B 981 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1005 through 1009
      removed outlier: 3.849A  pdb=" N   VAL B1008 " --> pdb=" O   ALA B1005 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE B1009 " --> pdb=" O   ALA B1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1005 through 1009'
    Processing helix  chain 'B' and resid 1012 through 1024
      removed outlier: 3.835A  pdb=" N   ASP B1024 " --> pdb=" O   ARG B1020 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1028 through 1036
      removed outlier: 3.896A  pdb=" N   TRP B1034 " --> pdb=" O   ARG B1030 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1040 through 1048
    Processing sheet with id=AA1, first strand: chain 'A' and resid 566 through 567
    Processing sheet with id=AA2, first strand: chain 'A' and resid 667 through 670
    Processing sheet with id=AA3, first strand: chain 'A' and resid 889 through 890
      removed outlier: 3.780A  pdb=" N   GLY A 905 " --> pdb=" O   LEU A 890 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 566 through 567
    Processing sheet with id=AA5, first strand: chain 'B' and resid 667 through 670
    Processing sheet with id=AA6, first strand: chain 'B' and resid 889 through 890
      removed outlier: 3.780A  pdb=" N   GLY B 905 " --> pdb=" O   LEU B 890 " (cutoff:3.500A)

    514 hydrogen bonds defined for protein.
    1470 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: 0.93

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2429
        1.34 -     1.46: 1628
        1.46 -     1.58: 5215
        1.58 -     1.70: 0
        1.70 -     1.82: 106
  Bond restraints: 9378
  Sorted by residual:
  bond pdb=" N   LEU A1026 "
       pdb=" CA  LEU A1026 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 1.03e+01
  bond pdb=" N   LEU B1026 "
       pdb=" CA  LEU B1026 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.29e-02 6.01e+03 1.03e+01
  bond pdb=" CA  SER A 568 "
       pdb=" CB  SER A 568 "
    ideal  model  delta    sigma   weight residual
    1.536  1.473  0.062 2.08e-02 2.31e+03 8.95e+00
  bond pdb=" CA  SER B 568 "
       pdb=" CB  SER B 568 "
    ideal  model  delta    sigma   weight residual
    1.536  1.474  0.062 2.08e-02 2.31e+03 8.93e+00
  bond pdb=" N   ILE A1000 "
       pdb=" CA  ILE A1000 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.73e+00
  ... (remaining 9373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 11631
        1.31 -     2.63: 871
        2.63 -     3.94: 254
        3.94 -     5.26: 42
        5.26 -     6.57: 6
  Bond angle restraints: 12804
  Sorted by residual:
  angle pdb=" C   LYS B1001 "
        pdb=" CA  LYS B1001 "
        pdb=" CB  LYS B1001 "
      ideal   model   delta    sigma   weight residual
     110.85  104.28    6.57 1.70e+00 3.46e-01 1.49e+01
  angle pdb=" C   LYS A1001 "
        pdb=" CA  LYS A1001 "
        pdb=" CB  LYS A1001 "
      ideal   model   delta    sigma   weight residual
     110.85  104.29    6.56 1.70e+00 3.46e-01 1.49e+01
  angle pdb=" C   ASN B 668 "
        pdb=" N   CYS B 669 "
        pdb=" CA  CYS B 669 "
      ideal   model   delta    sigma   weight residual
     122.73  116.63    6.10 1.62e+00 3.81e-01 1.42e+01
  angle pdb=" C   ASN A 668 "
        pdb=" N   CYS A 669 "
        pdb=" CA  CYS A 669 "
      ideal   model   delta    sigma   weight residual
     122.73  116.67    6.06 1.62e+00 3.81e-01 1.40e+01
  angle pdb=" O   GLY B 532 "
        pdb=" C   GLY B 532 "
        pdb=" N   GLU B 533 "
      ideal   model   delta    sigma   weight residual
     122.19  118.73    3.46 9.60e-01 1.09e+00 1.30e+01
  ... (remaining 12799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.14: 5381
       15.14 -    30.28: 491
       30.28 -    45.41: 120
       45.41 -    60.55: 16
       60.55 -    75.69: 8
  Dihedral angle restraints: 6016
    sinusoidal: 2722
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" CB  CYS B 669 "
           pdb=" SG  CYS B 669 "
           pdb=" SG  CYS B 703 "
           pdb=" CB  CYS B 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.01  -36.01     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CB  CYS A 669 "
           pdb=" SG  CYS A 669 "
           pdb=" SG  CYS A 703 "
           pdb=" CB  CYS A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.98  -35.98     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CG  ARG B 492 "
           pdb=" CD  ARG B 492 "
           pdb=" NE  ARG B 492 "
           pdb=" CZ  ARG B 492 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.04   44.96     2      1.50e+01 4.44e-03 1.07e+01
  ... (remaining 6013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1081
       0.047 -    0.094: 297
       0.094 -    0.141: 111
       0.141 -    0.188: 41
       0.188 -    0.235: 14
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" CA  ARG B 478 "
            pdb=" N   ARG B 478 "
            pdb=" C   ARG B 478 "
            pdb=" CB  ARG B 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  ARG A 478 "
            pdb=" N   ARG A 478 "
            pdb=" C   ARG A 478 "
            pdb=" CB  ARG A 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  ILE A 693 "
            pdb=" N   ILE A 693 "
            pdb=" C   ILE A 693 "
            pdb=" CB  ILE A 693 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1541 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1206 "   -0.300 2.00e-02 2.50e+03   2.56e-01 8.18e+02
        pdb=" C7  NAG A1206 "    0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG A1206 "   -0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG A1206 "    0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG A1206 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1206 "    0.300 2.00e-02 2.50e+03   2.56e-01 8.17e+02
        pdb=" C7  NAG B1206 "   -0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG B1206 "    0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG B1206 "   -0.445 2.00e-02 2.50e+03
        pdb=" O7  NAG B1206 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 565 "    0.022 2.00e-02 2.50e+03   4.41e-02 1.94e+01
        pdb=" C   ILE B 565 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   ILE B 565 "    0.029 2.00e-02 2.50e+03
        pdb=" N   LEU B 566 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.04: 5600
        3.04 -     3.50: 8953
        3.50 -     3.97: 13138
        3.97 -     4.43: 15382
        4.43 -     4.90: 24705
  Nonbonded interactions: 67778
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 532 "
            pdb=" CA  GLU B 533 "
     model   vdw
     2.575 2.776
  nonbonded pdb=" O   GLY A 532 "
            pdb=" CA  GLU A 533 "
     model   vdw
     2.575 2.776
  nonbonded pdb=" CB  GLU A 536 "
            pdb=" OE1 GLU A 536 "
     model   vdw
     2.586 2.752
  nonbonded pdb=" CB  GLU B 536 "
            pdb=" OE1 GLU B 536 "
     model   vdw
     2.587 2.752
  nonbonded pdb=" O   TRP A 683 "
            pdb=" C   ARG A 684 "
     model   vdw
     2.623 3.270
  ... (remaining 67773 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.040
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
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      :  0.006   0.066   9384  Z= 0.415
  Angle     :  0.812   6.572  12818  Z= 0.558
  Chirality :  0.056   0.235   1544
  Planarity :  0.011   0.256   1484
  Dihedral  : 11.770  75.691   3872
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.25), residues: 1122
  helix:  1.08 (0.20), residues: 702
  sheet: -2.13 (0.92), residues: 20
  loop : -1.18 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 799 
 TYR   0.006   0.001   TYR B 852 
 PHE   0.016   0.001   PHE B 645 
 TRP   0.017   0.001   TRP B 695 
 HIS   0.010   0.001   HIS B 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00587 /  0.41 ( 9378)
  covalent geometry    : angle       0.80982 /  0.56 (12804)
  SS BOND              : bond        0.04697 /  2.29 (    4)
  SS BOND              : angle       2.31749 /  1.92 (    8)
  hydrogen bonds       : bond        0.15590 / 10.43 (  514)
  hydrogen bonds       : angle       4.99714 /  3.69 ( 1470)
  link_NAG-ASN         : bond        0.00149 /  0.08 (    2)
  link_NAG-ASN         : angle       1.09826 /  0.85 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  787 GLN cc_start: 0.8621 (mt0) cc_final: 0.8084 (mm110)
REVERT: A  935 MET cc_start: 0.7966 (mmt) cc_final: 0.7708 (mmt)
REVERT: A  974 TYR cc_start: 0.8139 (p90) cc_final: 0.7621 (p90)
REVERT: B  787 GLN cc_start: 0.8635 (mt0) cc_final: 0.8081 (mm110)
REVERT: B  974 TYR cc_start: 0.8140 (p90) cc_final: 0.7608 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.5427
  time to fit residues: 96.1119
Evaluate side-chains
  116 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0470
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6880

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.144932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107424 restraints weight = 9806.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.53
r_work: 0.3152 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9384  Z= 0.140
  Angle     :  0.511   4.939  12818  Z= 0.260
  Chirality :  0.040   0.139   1544
  Planarity :  0.005   0.045   1484
  Dihedral  :  5.544  46.403   1894
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  8.82 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.26), residues: 1122
  helix:  1.62 (0.20), residues: 710
  sheet: -1.85 (1.03), residues: 20
  loop : -0.82 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 502 
 TYR   0.011   0.001   TYR B 665 
 PHE   0.019   0.001   PHE A 733 
 TRP   0.009   0.001   TRP A 498 
 HIS   0.003   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 9378)
  covalent geometry    : angle       0.50727 /  0.26 (12804)
  SS BOND              : bond        0.00244 /  0.12 (    4)
  SS BOND              : angle       1.60114 /  1.20 (    8)
  hydrogen bonds       : bond        0.05853 /  3.83 (  514)
  hydrogen bonds       : angle       3.67468 /  2.70 ( 1470)
  link_NAG-ASN         : bond        0.00371 /  0.19 (    2)
  link_NAG-ASN         : angle       2.29147 /  1.83 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  500 ASP cc_start: 0.8142 (m-30) cc_final: 0.7819 (m-30)
REVERT: A  787 GLN cc_start: 0.8510 (mt0) cc_final: 0.8024 (mm110)
REVERT: A  935 MET cc_start: 0.7586 (mmt) cc_final: 0.7265 (mmt)
REVERT: B  500 ASP cc_start: 0.8167 (m-30) cc_final: 0.7814 (m-30)
REVERT: B  750 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6899 (ptp90)
REVERT: B  787 GLN cc_start: 0.8484 (mt0) cc_final: 0.8026 (mm110)
  outliers start: 25
  outliers final: 14
  residues processed: 138
  average time/residue: 0.5333
  time to fit residues: 79.1581
Evaluate side-chains
  130 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  959 ILE
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  607 ILE
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  929 ILE
Chi-restraints excluded: chain B residue  959 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.1784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.096430 restraints weight = 10630.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.44
r_work: 0.2970 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9384  Z= 0.198
  Angle     :  0.573   5.657  12818  Z= 0.292
  Chirality :  0.042   0.131   1544
  Planarity :  0.005   0.044   1484
  Dihedral  :  6.040  54.750   1894
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.87 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.26), residues: 1122
  helix:  1.63 (0.20), residues: 724
  sheet: -2.09 (1.00), residues: 20
  loop : -1.05 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 502 
 TYR   0.012   0.001   TYR A 665 
 PHE   0.024   0.002   PHE B 733 
 TRP   0.009   0.001   TRP B 498 
 HIS   0.005   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00497 /  0.20 ( 9378)
  covalent geometry    : angle       0.56924 /  0.29 (12804)
  SS BOND              : bond        0.00200 /  0.10 (    4)
  SS BOND              : angle       2.01868 /  1.50 (    8)
  hydrogen bonds       : bond        0.07301 /  4.78 (  514)
  hydrogen bonds       : angle       3.70452 /  2.71 ( 1470)
  link_NAG-ASN         : bond        0.00447 /  0.23 (    2)
  link_NAG-ASN         : angle       1.89310 /  1.54 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  498 TRP cc_start: 0.8331 (t60) cc_final: 0.7905 (t60)
REVERT: A  502 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7547 (ttp80)
REVERT: A  787 GLN cc_start: 0.8296 (mt0) cc_final: 0.7766 (mm110)
REVERT: A  935 MET cc_start: 0.7236 (mmt) cc_final: 0.6990 (mmt)
REVERT: B  498 TRP cc_start: 0.8299 (t60) cc_final: 0.7960 (t60)
REVERT: B  502 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7452 (ttp80)
REVERT: B  787 GLN cc_start: 0.8339 (mt0) cc_final: 0.7839 (mm110)
REVERT: B  815 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6511 (mp)
  outliers start: 26
  outliers final: 10
  residues processed: 148
  average time/residue: 0.4983
  time to fit residues: 79.7445
Evaluate side-chains
  138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  959 ILE
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  607 ILE
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  959 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100735 restraints weight = 10577.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.44
r_work: 0.2951 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9384  Z= 0.132
  Angle     :  0.512  10.143  12818  Z= 0.257
  Chirality :  0.039   0.125   1544
  Planarity :  0.005   0.043   1484
  Dihedral  :  5.916  57.126   1894
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.60 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.26), residues: 1122
  helix:  2.01 (0.20), residues: 706
  sheet: -2.07 (1.00), residues: 20
  loop : -0.92 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 502 
 TYR   0.008   0.001   TYR B 665 
 PHE   0.017   0.001   PHE A 733 
 TRP   0.005   0.001   TRP B 728 
 HIS   0.004   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 ( 9378)
  covalent geometry    : angle       0.50852 /  0.26 (12804)
  SS BOND              : bond        0.00121 /  0.06 (    4)
  SS BOND              : angle       1.74637 /  1.28 (    8)
  hydrogen bonds       : bond        0.05677 /  3.68 (  514)
  hydrogen bonds       : angle       3.54852 /  2.60 ( 1470)
  link_NAG-ASN         : bond        0.00345 /  0.17 (    2)
  link_NAG-ASN         : angle       1.85864 /  1.52 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  498 TRP cc_start: 0.8298 (t60) cc_final: 0.7920 (t60)
REVERT: A  750 ARG cc_start: 0.6920 (ptp90) cc_final: 0.6421 (ptp90)
REVERT: A  787 GLN cc_start: 0.8259 (mt0) cc_final: 0.7744 (mm110)
REVERT: A  868 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6549 (tt)
REVERT: B  498 TRP cc_start: 0.8303 (t60) cc_final: 0.7951 (t60)
REVERT: B  502 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7415 (ttp80)
REVERT: B  709 GLU cc_start: 0.6276 (mm-30) cc_final: 0.6068 (mm-30)
REVERT: B  787 GLN cc_start: 0.8261 (mt0) cc_final: 0.7756 (mm110)
REVERT: B  815 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6481 (mp)
REVERT: B  868 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6541 (tt)
  outliers start: 19
  outliers final: 8
  residues processed: 136
  average time/residue: 0.5179
  time to fit residues: 76.0900
Evaluate side-chains
  136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  868 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 108 optimal weight:    0.1980
   overall best weight:    0.8184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.133973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.097182 restraints weight = 10592.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.36
r_work: 0.2927 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9384  Z= 0.150
  Angle     :  0.522   8.534  12818  Z= 0.264
  Chirality :  0.040   0.124   1544
  Planarity :  0.005   0.044   1484
  Dihedral  :  6.038  58.002   1894
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.55 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.26), residues: 1122
  helix:  2.09 (0.20), residues: 706
  sheet: -2.25 (0.97), residues: 20
  loop : -0.98 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 502 
 TYR   0.010   0.001   TYR B 665 
 PHE   0.019   0.001   PHE B 733 
 TRP   0.004   0.001   TRP A 498 
 HIS   0.004   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.15 ( 9378)
  covalent geometry    : angle       0.51898 /  0.26 (12804)
  SS BOND              : bond        0.00250 /  0.13 (    4)
  SS BOND              : angle       1.90765 /  1.40 (    8)
  hydrogen bonds       : bond        0.06113 /  3.98 (  514)
  hydrogen bonds       : angle       3.53580 /  2.59 ( 1470)
  link_NAG-ASN         : bond        0.00347 /  0.17 (    2)
  link_NAG-ASN         : angle       1.82605 /  1.50 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  481 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7434 (mtm-85)
REVERT: A  498 TRP cc_start: 0.8449 (t60) cc_final: 0.8038 (t60)
REVERT: A  502 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7599 (ttp80)
REVERT: A  750 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6573 (ptp90)
REVERT: A  787 GLN cc_start: 0.8324 (mt0) cc_final: 0.7804 (mm110)
REVERT: A  991 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6917 (mtt)
REVERT: B  481 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7394 (mtm-85)
REVERT: B  498 TRP cc_start: 0.8429 (t60) cc_final: 0.8060 (t60)
REVERT: B  709 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6299 (mm-30)
REVERT: B  750 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6616 (ptp90)
REVERT: B  787 GLN cc_start: 0.8372 (mt0) cc_final: 0.7874 (mm110)
REVERT: B  815 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6681 (mp)
  outliers start: 21
  outliers final: 10
  residues processed: 141
  average time/residue: 0.4567
  time to fit residues: 69.8496
Evaluate side-chains
  141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue 1019 VAL
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  959 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0010
   chunk 27 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.5186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.138876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.102039 restraints weight = 10540.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.43
r_work: 0.3043 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9384  Z= 0.116
  Angle     :  0.479   7.798  12818  Z= 0.243
  Chirality :  0.038   0.142   1544
  Planarity :  0.005   0.045   1484
  Dihedral  :  5.863  56.127   1894
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.39 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.26), residues: 1122
  helix:  2.27 (0.20), residues: 706
  sheet: -2.07 (1.00), residues: 20
  loop : -0.87 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.007   0.001   TYR A 665 
 PHE   0.015   0.001   PHE B 733 
 TRP   0.005   0.001   TRP B 728 
 HIS   0.003   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 9378)
  covalent geometry    : angle       0.47627 /  0.24 (12804)
  SS BOND              : bond        0.00103 /  0.05 (    4)
  SS BOND              : angle       1.53937 /  1.15 (    8)
  hydrogen bonds       : bond        0.05022 /  3.26 (  514)
  hydrogen bonds       : angle       3.42240 /  2.51 ( 1470)
  link_NAG-ASN         : bond        0.00316 /  0.16 (    2)
  link_NAG-ASN         : angle       1.76629 /  1.47 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  498 TRP cc_start: 0.8370 (t60) cc_final: 0.8012 (t60)
REVERT: A  750 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6513 (ptp90)
REVERT: A  787 GLN cc_start: 0.8258 (mt0) cc_final: 0.7748 (mm110)
REVERT: A  815 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6584 (mp)
REVERT: A  868 ILE cc_start: 0.6842 (tt) cc_final: 0.6577 (tt)
REVERT: A  991 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6835 (mtt)
REVERT: B  481 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.7229 (mtm-85)
REVERT: B  498 TRP cc_start: 0.8375 (t60) cc_final: 0.8007 (t60)
REVERT: B  750 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6457 (ptp90)
REVERT: B  787 GLN cc_start: 0.8264 (mt0) cc_final: 0.7771 (mm110)
REVERT: B  815 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6565 (mp)
REVERT: B  868 ILE cc_start: 0.6857 (tt) cc_final: 0.6596 (tt)
  outliers start: 16
  outliers final: 6
  residues processed: 131
  average time/residue: 0.4627
  time to fit residues: 65.5644
Evaluate side-chains
  126 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.0984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.133720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.097210 restraints weight = 10724.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.35
r_work: 0.2967 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9384  Z= 0.186
  Angle     :  0.559   7.026  12818  Z= 0.285
  Chirality :  0.041   0.134   1544
  Planarity :  0.005   0.045   1484
  Dihedral  :  6.244  59.457   1894
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.28 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.26), residues: 1122
  helix:  2.07 (0.20), residues: 708
  sheet: -2.28 (0.95), residues: 20
  loop : -1.07 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 502 
 TYR   0.011   0.001   TYR B 665 
 PHE   0.023   0.002   PHE A 733 
 TRP   0.004   0.001   TRP B 812 
 HIS   0.004   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.19 ( 9378)
  covalent geometry    : angle       0.55513 /  0.28 (12804)
  SS BOND              : bond        0.00193 /  0.10 (    4)
  SS BOND              : angle       2.34997 /  1.72 (    8)
  hydrogen bonds       : bond        0.06845 /  4.46 (  514)
  hydrogen bonds       : angle       3.58817 /  2.63 ( 1470)
  link_NAG-ASN         : bond        0.00354 /  0.18 (    2)
  link_NAG-ASN         : angle       1.76150 /  1.46 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7504 (mtm-85)
REVERT: A  498 TRP cc_start: 0.8538 (t60) cc_final: 0.8159 (t60)
REVERT: A  750 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6680 (ptp90)
REVERT: A  787 GLN cc_start: 0.8425 (mt0) cc_final: 0.7582 (mm110)
REVERT: A  815 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6880 (mp)
REVERT: A  991 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7098 (mtt)
REVERT: B  498 TRP cc_start: 0.8565 (t60) cc_final: 0.8174 (t60)
REVERT: B  750 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6654 (ptp90)
REVERT: B  787 GLN cc_start: 0.8489 (mt0) cc_final: 0.7990 (mm110)
REVERT: B  815 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6854 (mp)
  outliers start: 23
  outliers final: 13
  residues processed: 152
  average time/residue: 0.4411
  time to fit residues: 72.4795
Evaluate side-chains
  151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain A residue 1024 ASP
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  607 ILE
Chi-restraints excluded: chain B residue  669 CYS
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  959 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 37 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.099129 restraints weight = 10478.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.31
r_work: 0.2851 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9384  Z= 0.130
  Angle     :  0.507   6.882  12818  Z= 0.258
  Chirality :  0.039   0.134   1544
  Planarity :  0.005   0.045   1484
  Dihedral  :  6.126  59.882   1894
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.49 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.26), residues: 1122
  helix:  2.18 (0.20), residues: 706
  sheet: -2.25 (0.94), residues: 20
  loop : -0.89 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 502 
 TYR   0.008   0.001   TYR B 665 
 PHE   0.016   0.001   PHE A 733 
 TRP   0.005   0.001   TRP B 728 
 HIS   0.003   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 9378)
  covalent geometry    : angle       0.50377 /  0.26 (12804)
  SS BOND              : bond        0.00159 /  0.08 (    4)
  SS BOND              : angle       1.76752 /  1.32 (    8)
  hydrogen bonds       : bond        0.05472 /  3.55 (  514)
  hydrogen bonds       : angle       3.49216 /  2.56 ( 1470)
  link_NAG-ASN         : bond        0.00317 /  0.16 (    2)
  link_NAG-ASN         : angle       1.75601 /  1.45 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7359 (mtm-85)
REVERT: A  498 TRP cc_start: 0.8366 (t60) cc_final: 0.7919 (t60)
REVERT: A  750 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6568 (ptp90)
REVERT: A  787 GLN cc_start: 0.8266 (mt0) cc_final: 0.7416 (mm110)
REVERT: A  868 ILE cc_start: 0.6981 (tt) cc_final: 0.6655 (tt)
REVERT: A  991 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6911 (OUTLIER)
REVERT: A 1022 LEU cc_start: 0.6909 (tp) cc_final: 0.6554 (tt)
REVERT: B  498 TRP cc_start: 0.8409 (t60) cc_final: 0.8004 (t60)
REVERT: B  750 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6588 (ptp90)
REVERT: B  787 GLN cc_start: 0.8338 (mt0) cc_final: 0.7830 (mm110)
REVERT: B  815 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6673 (mp)
REVERT: B  868 ILE cc_start: 0.6991 (tt) cc_final: 0.6661 (tt)
REVERT: B 1022 LEU cc_start: 0.6872 (tp) cc_final: 0.6527 (tt)
  outliers start: 23
  outliers final: 12
  residues processed: 136
  average time/residue: 0.4714
  time to fit residues: 69.2195
Evaluate side-chains
  143 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  550 MET
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0020
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.100223 restraints weight = 10480.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.41
r_work: 0.2975 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9384  Z= 0.134
  Angle     :  0.512   6.601  12818  Z= 0.261
  Chirality :  0.039   0.133   1544
  Planarity :  0.005   0.044   1484
  Dihedral  :  6.098  59.665   1894
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.28 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.26), residues: 1122
  helix:  2.16 (0.20), residues: 710
  sheet: -2.23 (0.94), residues: 20
  loop : -0.99 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 502 
 TYR   0.008   0.001   TYR A 638 
 PHE   0.017   0.001   PHE A 733 
 TRP   0.005   0.001   TRP B 728 
 HIS   0.004   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.13 ( 9378)
  covalent geometry    : angle       0.50927 /  0.26 (12804)
  SS BOND              : bond        0.00226 /  0.11 (    4)
  SS BOND              : angle       1.67774 /  1.19 (    8)
  hydrogen bonds       : bond        0.05616 /  3.65 (  514)
  hydrogen bonds       : angle       3.48891 /  2.56 ( 1470)
  link_NAG-ASN         : bond        0.00315 /  0.16 (    2)
  link_NAG-ASN         : angle       1.70358 /  1.41 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.7286 (mtm-85)
REVERT: A  498 TRP cc_start: 0.8302 (t60) cc_final: 0.7860 (t60)
REVERT: A  750 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6443 (ptp90)
REVERT: A  787 GLN cc_start: 0.8205 (mt0) cc_final: 0.7680 (mm110)
REVERT: A  868 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6521 (tt)
REVERT: A  991 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6800 (OUTLIER)
REVERT: A 1022 LEU cc_start: 0.6837 (tp) cc_final: 0.6517 (tt)
REVERT: B  498 TRP cc_start: 0.8325 (t60) cc_final: 0.7912 (t60)
REVERT: B  750 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6484 (ptp90)
REVERT: B  787 GLN cc_start: 0.8272 (mt0) cc_final: 0.7762 (mm110)
REVERT: B  815 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6605 (mp)
REVERT: B  868 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6541 (tt)
REVERT: B 1022 LEU cc_start: 0.6825 (tp) cc_final: 0.6508 (tt)
  outliers start: 23
  outliers final: 14
  residues processed: 143
  average time/residue: 0.5016
  time to fit residues: 77.3120
Evaluate side-chains
  150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  550 MET
Chi-restraints excluded: chain B residue  669 CYS
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  815 ILE
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  868 ILE
Chi-restraints excluded: chain B residue  959 ILE
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 90 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.8580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.135474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.098595 restraints weight = 10573.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.43
r_work: 0.3041 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9384  Z= 0.155
  Angle     :  0.539   6.535  12818  Z= 0.275
  Chirality :  0.040   0.131   1544
  Planarity :  0.005   0.044   1484
  Dihedral  :  6.079  58.527   1894
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.02 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.26), residues: 1122
  helix:  2.08 (0.20), residues: 712
  sheet: -2.37 (0.89), residues: 20
  loop : -1.09 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.010   0.001   TYR A 665 
 PHE   0.020   0.001   PHE A 733 
 TRP   0.004   0.001   TRP A 812 
 HIS   0.004   0.001   HIS A 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 9378)
  covalent geometry    : angle       0.53520 /  0.27 (12804)
  SS BOND              : bond        0.00207 /  0.10 (    4)
  SS BOND              : angle       2.00236 /  1.47 (    8)
  hydrogen bonds       : bond        0.06154 /  4.00 (  514)
  hydrogen bonds       : angle       3.53524 /  2.60 ( 1470)
  link_NAG-ASN         : bond        0.00321 /  0.16 (    2)
  link_NAG-ASN         : angle       1.73111 /  1.43 (    6)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.7206 (mtm-85)
REVERT: A  498 TRP cc_start: 0.8213 (t60) cc_final: 0.7842 (t60)
REVERT: A  750 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6424 (ptp90)
REVERT: A  787 GLN cc_start: 0.8175 (mt0) cc_final: 0.7319 (mm110)
REVERT: A  991 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6676 (OUTLIER)
REVERT: B  498 TRP cc_start: 0.8314 (t60) cc_final: 0.7833 (t60)
REVERT: B  750 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6402 (ptp90)
REVERT: B  787 GLN cc_start: 0.8251 (mt0) cc_final: 0.7733 (mm110)
REVERT: B 1022 LEU cc_start: 0.6742 (tp) cc_final: 0.6418 (tt)
  outliers start: 19
  outliers final: 13
  residues processed: 146
  average time/residue: 0.4924
  time to fit residues: 77.6192
Evaluate side-chains
  152 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain A residue  513 PHE
Chi-restraints excluded: chain A residue  550 MET
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  991 MET
Chi-restraints excluded: chain A residue  992 SER
Chi-restraints excluded: chain B residue  482 ILE
Chi-restraints excluded: chain B residue  513 PHE
Chi-restraints excluded: chain B residue  550 MET
Chi-restraints excluded: chain B residue  669 CYS
Chi-restraints excluded: chain B residue  750 ARG
Chi-restraints excluded: chain B residue  837 VAL
Chi-restraints excluded: chain B residue  992 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 96 optimal weight:    0.1980
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0570
   chunk 97 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0170
   overall best weight:    0.3336

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.141231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.104966 restraints weight = 10288.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.39
r_work: 0.3130 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9384  Z= 0.104
  Angle     :  0.479   6.458  12818  Z= 0.245
  Chirality :  0.037   0.134   1544
  Planarity :  0.005   0.045   1484
  Dihedral  :  5.895  59.448   1894
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 17.65 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.26), residues: 1122
  helix:  2.30 (0.20), residues: 710
  sheet: -2.28 (0.95), residues: 20
  loop : -0.84 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 502 
 TYR   0.008   0.001   TYR B 665 
 PHE   0.013   0.001   PHE B 733 
 TRP   0.006   0.001   TRP B 728 
 HIS   0.003   0.001   HIS B 719 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 9378)
  covalent geometry    : angle       0.47709 /  0.24 (12804)
  SS BOND              : bond        0.00146 /  0.07 (    4)
  SS BOND              : angle       1.35491 /  1.05 (    8)
  hydrogen bonds       : bond        0.04324 /  2.79 (  514)
  hydrogen bonds       : angle       3.39462 /  2.50 ( 1470)
  link_NAG-ASN         : bond        0.00304 /  0.15 (    2)
  link_NAG-ASN         : angle       1.64534 /  1.36 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3309.32 seconds
wall clock time: 57 minutes 11.81 seconds (3431.81 seconds total)