Starting phenix.real_space_refine
on Mon Aug 25 07:52:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gd2_51244/08_2025/9gd2_51244.map"
  }
  resolution = 4.2
  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=   0.032 sd=   1.319
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: 8
    Type Number    sf(0)   Gaussians
     P     476      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     Be      1      3.05       5
     C   15283      2.51       5
     N    4916      2.21       5
     O    5910      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 26638
  Number of models: 1
  Model: ""
    Number of chains: 22
    Chain: "A"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 763
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 786
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 763
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 614
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 742
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "H"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 4828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 4828
          Classifications: {'DNA': 237}
          Link IDs: {'rna3p': 236}
    Chain: "J"
      Number of atoms: 4889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 4889
          Classifications: {'DNA': 237}
          Link IDs: {'rna3p': 236}
    Chain: "K"
      Number of atoms: 592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 592
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "L"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 626
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "M"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "N"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "O"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 795
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "P"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "Q"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "R"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 719
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "S"
      Number of atoms: 122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 122
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
    Chain: "T"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 196
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "W"
      Number of atoms: 5274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 5274
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 20, 'TRANS': 620}
          Chain breaks: 3
    Chain: "W"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.04, per 1000 atoms: 0.23
  Number of scatterers: 26638
  At special positions: 0
  Unit cell: (127.602, 134.274, 219.342, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      48     16.00
     P     476     15.00
     Mg      1     11.99
     F       3      9.00
     O    5910      8.00
     N    4916      7.00
     C   15283      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 777.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3974

  Finding SS restraints...
    Secondary structure from input PDB file:
      102 helices and 24 sheets defined
      69.9% alpha, 5.8% beta
      237 base pairs and 470 stacking pairs defined.
    Time for finding SS restraints: 4.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.570A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 115
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 3.663A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 74
      removed outlier: 4.341A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.751A  pdb=" N   THR D  93 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 120
      removed outlier: 3.932A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.568A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.650A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 3.887A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.624A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   HIS H 106 " --> pdb=" O   GLU H 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 63 through 79
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
    Processing helix  chain 'L' and resid 23 through 28
      removed outlier: 3.711A  pdb=" N   GLN L  27 " --> pdb=" O   ARG L  23 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.967A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASP L  68 " --> pdb=" O   ASN L  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 97
    Processing helix  chain 'M' and resid 16 through 22
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.239A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU M  65 " --> pdb=" O   GLU M  61 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 90
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'M' and resid 112 through 116
    Processing helix  chain 'N' and resid 34 through 46
    Processing helix  chain 'N' and resid 52 through 81
    Processing helix  chain 'N' and resid 87 through 99
      removed outlier: 3.668A  pdb=" N   ARG N  96 " --> pdb=" O   GLN N  92 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 100 through 121
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 77
      removed outlier: 3.709A  pdb=" N   ASP O  77 " --> pdb=" O   GLU O  73 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 115
    Processing helix  chain 'O' and resid 120 through 131
    Processing helix  chain 'P' and resid 22 through 29
      removed outlier: 3.767A  pdb=" N   GLN P  27 " --> pdb=" O   ARG P  23 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 3.608A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 94
    Processing helix  chain 'Q' and resid 34 through 46
    Processing helix  chain 'Q' and resid 52 through 81
    Processing helix  chain 'Q' and resid 87 through 99
    Processing helix  chain 'Q' and resid 100 through 121
    Processing helix  chain 'R' and resid 16 through 22
    Processing helix  chain 'R' and resid 26 through 37
      removed outlier: 3.627A  pdb=" N   ARG R  35 " --> pdb=" O   HIS R  31 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 45 through 73
      removed outlier: 3.939A  pdb=" N   VAL R  49 " --> pdb=" O   ALA R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 90
    Processing helix  chain 'R' and resid 90 through 97
    Processing helix  chain 'W' and resid 205 through 211
      removed outlier: 3.846A  pdb=" N   TYR W 211 " --> pdb=" O   CYS W 207 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 221 through 225
    Processing helix  chain 'W' and resid 230 through 234
    Processing helix  chain 'W' and resid 238 through 258
      removed outlier: 4.166A  pdb=" N   LEU W 242 " --> pdb=" O   GLY W 238 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 263 through 285
    Processing helix  chain 'W' and resid 324 through 331
      removed outlier: 4.227A  pdb=" N   LYS W 329 " --> pdb=" O   THR W 325 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 331 through 342
    Processing helix  chain 'W' and resid 347 through 351
    Processing helix  chain 'W' and resid 353 through 357
      removed outlier: 4.210A  pdb=" N   SER W 356 " --> pdb=" O   ASN W 353 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 377 through 394
    Processing helix  chain 'W' and resid 406 through 421
    Processing helix  chain 'W' and resid 433 through 435
      No H-bonds generated for 'chain 'W' and resid 433 through 435'
    Processing helix  chain 'W' and resid 436 through 448
    Processing helix  chain 'W' and resid 459 through 470
    Processing helix  chain 'W' and resid 491 through 497
    Processing helix  chain 'W' and resid 498 through 504
    Processing helix  chain 'W' and resid 514 through 518
    Processing helix  chain 'W' and resid 523 through 532
    Processing helix  chain 'W' and resid 548 through 560
      removed outlier: 3.576A  pdb=" N   LEU W 552 " --> pdb=" O   ASN W 548 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 576 through 591
    Processing helix  chain 'W' and resid 598 through 603
    Processing helix  chain 'W' and resid 619 through 631
    Processing helix  chain 'W' and resid 633 through 639
    Processing helix  chain 'W' and resid 650 through 661
    Processing helix  chain 'W' and resid 662 through 664
      No H-bonds generated for 'chain 'W' and resid 662 through 664'
    Processing helix  chain 'W' and resid 665 through 677
      removed outlier: 4.088A  pdb=" N   GLU W 669 " --> pdb=" O   PHE W 665 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLU W 670 " --> pdb=" O   ASP W 666 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 678 through 681
    Processing helix  chain 'W' and resid 682 through 692
    Processing helix  chain 'W' and resid 694 through 711
    Processing helix  chain 'W' and resid 720 through 734
    Processing helix  chain 'W' and resid 746 through 759
    Processing helix  chain 'W' and resid 794 through 806
      removed outlier: 3.969A  pdb=" N   ASP W 798 " --> pdb=" O   ASN W 794 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA W 805 " --> pdb=" O   ALA W 801 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 825 through 844
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.800A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.132A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.748A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.702A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.665A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 43
      removed outlier: 6.866A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'M' and resid 77 through 78
    Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 101
    Processing sheet with id=AB7, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AB8, first strand: chain 'Q' and resid 50 through 51
      removed outlier: 6.618A  pdb=" N   GLY Q  50 " --> pdb=" O   ILE R  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'Q' and resid 85 through 86
    Processing sheet with id=AC1, first strand: chain 'W' and resid 179 through 180
    Processing sheet with id=AC2, first strand: chain 'W' and resid 179 through 180
      removed outlier: 3.534A  pdb=" N   THR W 226 " --> pdb=" O   ILE W 215 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'W' and resid 287 through 297
      removed outlier: 6.621A  pdb=" N   LEU W 308 " --> pdb=" O   ILE W 291 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   SER W 293 " --> pdb=" O   GLN W 306 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLN W 306 " --> pdb=" O   SER W 293 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ARG W 295 " --> pdb=" O   GLN W 304 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLN W 304 " --> pdb=" O   ARG W 295 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'W' and resid 453 through 456
      removed outlier: 6.599A  pdb=" N   ILE W 454 " --> pdb=" O   LEU W 489 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   MET W 510 " --> pdb=" O   MET W 538 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ILE W 540 " --> pdb=" O   MET W 510 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL W 512 " --> pdb=" O   ILE W 540 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY W 397 " --> pdb=" O   LEU W 539 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ILE W 398 " --> pdb=" O   LEU W 595 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'W' and resid 472 through 473
      removed outlier: 4.003A  pdb=" N   THR W 482 " --> pdb=" O   THR W 473 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'W' and resid 609 through 616
      removed outlier: 6.634A  pdb=" N   VAL W 786 " --> pdb=" O   TYR W 817 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   LEU W 819 " --> pdb=" O   VAL W 786 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE W 788 " --> pdb=" O   LEU W 819 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   SER W 821 " --> pdb=" O   ILE W 788 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU W 715 " --> pdb=" O   VAL W 787 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN W 739 " --> pdb=" O   LEU W 768 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   SER W 770 " --> pdb=" O   GLN W 739 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LEU W 741 " --> pdb=" O   SER W 770 " (cutoff:3.500A)

    1085 hydrogen bonds defined for protein.
    3198 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      608 hydrogen bonds
      1216 hydrogen bond angles
      0 basepair planarities
      237 basepair parallelities
      470 stacking parallelities
  Total time for adding SS restraints: 8.98

  Time building geometry restraints manager: 3.28 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: 6981
        1.34 -     1.45: 7343
        1.45 -     1.57: 12711
        1.57 -     1.69: 949
        1.69 -     1.81: 88
  Bond restraints: 28072
  Sorted by residual:
  bond pdb=" N   LYS L  91 "
       pdb=" CA  LYS L  91 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.45e+00
  bond pdb=" N   GLY W 178 "
       pdb=" CA  GLY W 178 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.34e+00
  bond pdb=" N   ARG P  78 "
       pdb=" CA  ARG P  78 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.27e-02 6.20e+03 6.32e+00
  bond pdb=" N   ARG L  92 "
       pdb=" CA  ARG L  92 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.19e-02 7.06e+03 6.13e+00
  bond pdb=" N   THR L  96 "
       pdb=" CA  THR L  96 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.12e+00
  ... (remaining 28067 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.86: 39389
        2.86 -     5.71: 543
        5.71 -     8.57: 9
        8.57 -    11.42: 2
       11.42 -    14.28: 3
  Bond angle restraints: 39946
  Sorted by residual:
  angle pdb=" O3'  DG J 130 "
        pdb=" C3'  DG J 130 "
        pdb=" C2'  DG J 130 "
      ideal   model   delta    sigma   weight residual
     111.50  102.37    9.13 1.50e+00 4.44e-01 3.70e+01
  angle pdb=" O3'  DG I  25 "
        pdb=" C3'  DG I  25 "
        pdb=" C2'  DG I  25 "
      ideal   model   delta    sigma   weight residual
     111.50  120.25   -8.75 1.50e+00 4.44e-01 3.40e+01
  angle pdb=" O3'  DG I -41 "
        pdb=" C3'  DG I -41 "
        pdb=" C2'  DG I -41 "
      ideal   model   delta    sigma   weight residual
     111.50  119.53   -8.03 1.50e+00 4.44e-01 2.87e+01
  angle pdb=" O3'  DG I -78 "
        pdb=" C3'  DG I -78 "
        pdb=" C2'  DG I -78 "
      ideal   model   delta    sigma   weight residual
     111.50  119.43   -7.93 1.50e+00 4.44e-01 2.79e+01
  angle pdb=" F1  BEF W1502 "
        pdb="BE   BEF W1502 "
        pdb=" F2  BEF W1502 "
      ideal   model   delta    sigma   weight residual
     119.91  105.63   14.28 3.00e+00 1.11e-01 2.26e+01
  ... (remaining 39941 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 13143
       35.91 -    71.82: 2539
       71.82 -   107.73: 21
      107.73 -   143.64: 3
      143.64 -   179.55: 2
  Dihedral angle restraints: 15708
    sinusoidal: 9570
      harmonic: 6138
  Sorted by residual:
  dihedral pdb=" O1B ADP W1501 "
           pdb=" O3A ADP W1501 "
           pdb=" PB  ADP W1501 "
           pdb=" PA  ADP W1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  120.44  179.55     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" C5' ADP W1501 "
           pdb=" O5' ADP W1501 "
           pdb=" PA  ADP W1501 "
           pdb=" O2A ADP W1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  101.33 -161.33     1      2.00e+01 2.50e-03 4.67e+01
  dihedral pdb=" CA  ASP W 180 "
           pdb=" C   ASP W 180 "
           pdb=" N   ILE W 181 "
           pdb=" CA  ILE W 181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.77  -29.23     0      5.00e+00 4.00e-02 3.42e+01
  ... (remaining 15705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 3768
       0.082 -    0.163: 736
       0.163 -    0.245: 26
       0.245 -    0.327: 0
       0.327 -    0.409: 2
  Chirality restraints: 4532
  Sorted by residual:
  chirality pdb=" C3'  DG I -78 "
            pdb=" C4'  DG I -78 "
            pdb=" O3'  DG I -78 "
            pdb=" C2'  DG I -78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.25   -0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" C3'  DG I  25 "
            pdb=" C4'  DG I  25 "
            pdb=" O3'  DG I  25 "
            pdb=" C2'  DG I  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.26   -0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" C3'  DG I -41 "
            pdb=" C4'  DG I -41 "
            pdb=" O3'  DG I -41 "
            pdb=" C2'  DG I -41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 4529 not shown)

  Planarity restraints: 3427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR W 245 "    0.003 2.00e-02 2.50e+03   2.60e-02 1.35e+01
        pdb=" CG  TYR W 245 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR W 245 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR W 245 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR W 245 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR W 245 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR W 245 "    0.031 2.00e-02 2.50e+03
        pdb=" OH  TYR W 245 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR L  51 "   -0.017 2.00e-02 2.50e+03   3.46e-02 1.20e+01
        pdb=" C   TYR L  51 "    0.060 2.00e-02 2.50e+03
        pdb=" O   TYR L  51 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU L  52 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA L  69 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   ALA L  69 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA L  69 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   VAL L  70 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 3424 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 1049
        2.70 -     3.25: 26077
        3.25 -     3.80: 51378
        3.80 -     4.35: 63561
        4.35 -     4.90: 93870
  Nonbonded interactions: 235935
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP W 513 "
            pdb="MG    MG W1503 "
     model   vdw
     2.148 2.170
  nonbonded pdb=" OD2 ASP W 513 "
            pdb="MG    MG W1503 "
     model   vdw
     2.156 2.170
  nonbonded pdb=" OD1 ASN W 486 "
            pdb=" N   VAL W 487 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   LYS K  79 "
            pdb=" OG1 THR K  80 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OE2 GLU O  50 "
            pdb=" NE  ARG P  39 "
     model   vdw
     2.297 3.120
  ... (remaining 235930 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = (chain 'O' and resid 41 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 97)
  selection = (chain 'F' and resid 25 through 97)
  selection = (chain 'L' and resid 25 through 97)
  selection = (chain 'P' and resid 25 through 97)
}
ncs_group {
  reference = (chain 'C' and resid 16 through 107)
  selection = (chain 'G' and resid 16 through 107)
  selection = (chain 'M' and resid 16 through 107)
  selection = (chain 'R' and resid 16 through 107)
}
ncs_group {
  reference = (chain 'D' and resid 32 through 120)
  selection = (chain 'H' and resid 32 through 120)
  selection = (chain 'N' and resid 32 through 120)
  selection = (chain 'Q' and resid 32 through 120)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.900
  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:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     31.460
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
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   0.423  28073  Z= 0.369
  Angle     :  0.864  14.276  39946  Z= 0.542
  Chirality :  0.058   0.409   4532
  Planarity :  0.011   0.104   3427
  Dihedral  : 25.641 179.554  11734
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.53 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.16), residues: 2060
  helix: -0.05 (0.12), residues: 1347
  sheet: -0.30 (0.53), residues: 98
  loop : -0.88 (0.22), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.003   ARG W 807 
 TYR   0.042   0.005   TYR W 245 
 PHE   0.016   0.003   PHE M  25 
 TRP   0.028   0.005   TRP W 311 
 HIS   0.015   0.004   HIS W 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (28072)
  covalent geometry    : angle       0.86350 (39946)
  hydrogen bonds       : bond        0.13584 ( 1691)
  hydrogen bonds       : angle       5.92584 ( 4414)
  Misc. bond           : bond        0.42299 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 243
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9338 (mm-30)
REVERT: B   63 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9029 (mt-10)
REVERT: B   84 MET cc_start: 0.9108 (tpp) cc_final: 0.8839 (tpp)
REVERT: C   56 GLU cc_start: 0.9243 (pt0) cc_final: 0.8252 (pp20)
REVERT: D   65 ASP cc_start: 0.9430 (t70) cc_final: 0.8678 (t70)
REVERT: E   90 MET cc_start: 0.9496 (mmp) cc_final: 0.9080 (mmm)
REVERT: E   94 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9159 (mm-30)
REVERT: E   97 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9057 (mt-10)
REVERT: E  120 MET cc_start: 0.9196 (mmm) cc_final: 0.8726 (mmm)
REVERT: H   65 ASP cc_start: 0.9404 (t70) cc_final: 0.9099 (t0)
REVERT: H   73 GLU cc_start: 0.9695 (mm-30) cc_final: 0.9354 (mm-30)
REVERT: H   97 LEU cc_start: 0.9793 (mt) cc_final: 0.9557 (mt)
REVERT: K   90 MET cc_start: 0.9164 (tmm) cc_final: 0.8962 (tmm)
REVERT: L   44 LYS cc_start: 0.9679 (mmpt) cc_final: 0.9284 (mtmt)
REVERT: M  112 GLN cc_start: 0.9600 (mm110) cc_final: 0.9388 (tm-30)
REVERT: N   59 MET cc_start: 0.9820 (mmt) cc_final: 0.9521 (mmm)
REVERT: N   68 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9410 (mm-30)
REVERT: O   97 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9106 (mt-10)
REVERT: O  130 ILE cc_start: 0.9635 (mm) cc_final: 0.9376 (tp)
REVERT: P   53 GLU cc_start: 0.9637 (tp30) cc_final: 0.9436 (tt0)
REVERT: Q   59 MET cc_start: 0.9888 (mmp) cc_final: 0.9646 (mmm)
REVERT: Q  118 TYR cc_start: 0.9413 (t80) cc_final: 0.9209 (t80)
REVERT: R   56 GLU cc_start: 0.9568 (tt0) cc_final: 0.9123 (tt0)
REVERT: R   95 LYS cc_start: 0.9877 (pptt) cc_final: 0.9588 (pttp)
REVERT: S  127 PHE cc_start: 0.8820 (t80) cc_final: 0.8423 (p90)
REVERT: S  131 GLN cc_start: 0.9152 (mp-120) cc_final: 0.8853 (mm-40)
REVERT: T  132 ASN cc_start: 0.9183 (t0) cc_final: 0.8780 (m-40)
REVERT: W  237 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8569 (tpt170)
REVERT: W  403 MET cc_start: 0.9220 (mpp) cc_final: 0.8476 (mpp)
REVERT: W  493 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9083 (pp20)
REVERT: W  510 MET cc_start: 0.9423 (mtt) cc_final: 0.9120 (mtt)
REVERT: W  697 MET cc_start: 0.7734 (mtm) cc_final: 0.7416 (mtm)
  outliers start: 17
  outliers final: 6
  residues processed: 260
  average time/residue: 0.2190
  time to fit residues: 86.5186
Evaluate side-chains
  138 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 216 optimal weight:    0.0000
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:    9.9990
   chunk 227 optimal weight:    9.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 247 optimal weight:   10.0000
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   overall best weight:    5.7992

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
P  25 ASN
Q  44 GLN
W 210 ASN
W 224 HIS
W 337 HIS
** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 459 ASN
W 574 ASN
** W 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 737 ASN
W 810 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.040701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025378 restraints weight = 298358.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.025975 restraints weight = 179382.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.026093 restraints weight = 134486.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.026106 restraints weight = 120217.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.026106 restraints weight = 119950.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.100  28073  Z= 0.304
  Angle     :  0.701  10.664  39946  Z= 0.415
  Chirality :  0.039   0.167   4532
  Planarity :  0.005   0.095   3427
  Dihedral  : 29.594 153.461   7522
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.38 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.18), residues: 2060
  helix:  1.08 (0.13), residues: 1398
  sheet: -0.62 (0.53), residues: 95
  loop : -0.60 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG P  92 
 TYR   0.018   0.002   TYR R  50 
 PHE   0.018   0.002   PHE K 104 
 TRP   0.012   0.002   TRP W 507 
 HIS   0.016   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 (28072)
  covalent geometry    : angle       0.70115 (39946)
  hydrogen bonds       : bond        0.07083 ( 1691)
  hydrogen bonds       : angle       4.40029 ( 4414)
  Misc. bond           : bond        0.00205 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9149 (mmm) cc_final: 0.8711 (mmm)
REVERT: B   67 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9211 (ttp-110)
REVERT: B   84 MET cc_start: 0.9063 (tpp) cc_final: 0.8830 (tpp)
REVERT: C   56 GLU cc_start: 0.9182 (pt0) cc_final: 0.8222 (pp20)
REVERT: C   90 ASP cc_start: 0.8951 (t0) cc_final: 0.8593 (t70)
REVERT: D   65 ASP cc_start: 0.9215 (t70) cc_final: 0.8612 (t0)
REVERT: E   90 MET cc_start: 0.9372 (mmp) cc_final: 0.9055 (mmp)
REVERT: E   97 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8938 (mt-10)
REVERT: E  120 MET cc_start: 0.9114 (mmm) cc_final: 0.8748 (mmm)
REVERT: F   58 LEU cc_start: 0.9745 (tp) cc_final: 0.9536 (tp)
REVERT: H   65 ASP cc_start: 0.9363 (t70) cc_final: 0.9162 (t0)
REVERT: K  106 ASP cc_start: 0.9391 (m-30) cc_final: 0.9117 (m-30)
REVERT: L   84 MET cc_start: 0.9179 (tpp) cc_final: 0.8786 (tpp)
REVERT: N   59 MET cc_start: 0.9751 (mmt) cc_final: 0.9480 (mmm)
REVERT: N   67 PHE cc_start: 0.9728 (t80) cc_final: 0.9368 (t80)
REVERT: N   69 ARG cc_start: 0.9541 (mtp180) cc_final: 0.9290 (mtp180)
REVERT: O   94 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9204 (tt0)
REVERT: O   97 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8999 (mt-10)
REVERT: O  106 ASP cc_start: 0.9443 (m-30) cc_final: 0.9177 (m-30)
REVERT: O  130 ILE cc_start: 0.9735 (mm) cc_final: 0.9455 (tp)
REVERT: P   25 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8444 (m110)
REVERT: Q   97 LEU cc_start: 0.9738 (tt) cc_final: 0.9505 (tt)
REVERT: R   56 GLU cc_start: 0.9624 (tt0) cc_final: 0.9204 (tt0)
REVERT: S  127 PHE cc_start: 0.8840 (t80) cc_final: 0.8425 (p90)
REVERT: T  132 ASN cc_start: 0.9212 (t0) cc_final: 0.8630 (m-40)
REVERT: W  237 ARG cc_start: 0.8965 (ttm170) cc_final: 0.8685 (tpt170)
REVERT: W  387 MET cc_start: 0.9396 (mtm) cc_final: 0.9156 (mtt)
REVERT: W  403 MET cc_start: 0.9122 (mpp) cc_final: 0.8537 (mpp)
REVERT: W  720 MET cc_start: 0.9126 (tpt) cc_final: 0.8908 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1608
  time to fit residues: 48.2047
Evaluate side-chains
  120 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 209 optimal weight:    5.9990
   chunk 190 optimal weight:    8.9990
   chunk 166 optimal weight:   10.0000
   chunk 192 optimal weight:   30.0000
   chunk 46 optimal weight:    6.9990
   chunk 233 optimal weight:    0.7980
   chunk 160 optimal weight:    6.9990
   chunk 220 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 214 optimal weight:    4.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 113 HIS
O  68 GLN
** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
W 222 HIS
W 315 ASN
W 385 ASN
W 530 ASN
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.041125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.026019 restraints weight = 292335.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026138 restraints weight = 173821.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026274 restraints weight = 132267.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.026550 restraints weight = 118542.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.026553 restraints weight = 106405.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  28073  Z= 0.216
  Angle     :  0.614  10.204  39946  Z= 0.364
  Chirality :  0.036   0.169   4532
  Planarity :  0.004   0.069   3427
  Dihedral  : 29.452 140.478   7522
  Min Nonbonded Distance : 1.818

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.54 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.18), residues: 2060
  helix:  1.52 (0.14), residues: 1396
  sheet: -0.48 (0.54), residues: 88
  loop : -0.55 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG W 807 
 TYR   0.021   0.002   TYR H  80 
 PHE   0.020   0.002   PHE W 379 
 TRP   0.009   0.001   TRP W 507 
 HIS   0.011   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (28072)
  covalent geometry    : angle       0.61399 (39946)
  hydrogen bonds       : bond        0.04811 ( 1691)
  hydrogen bonds       : angle       4.03410 ( 4414)
  Misc. bond           : bond        0.00049 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 177
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.9657 (pt) cc_final: 0.9260 (pt)
REVERT: A  120 MET cc_start: 0.9139 (mmm) cc_final: 0.8693 (mmm)
REVERT: B   67 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9091 (ttp-110)
REVERT: B   84 MET cc_start: 0.9112 (tpp) cc_final: 0.8852 (tpp)
REVERT: C   56 GLU cc_start: 0.9150 (pt0) cc_final: 0.8209 (pp20)
REVERT: C   73 ASN cc_start: 0.9195 (t0) cc_final: 0.8886 (t0)
REVERT: C   90 ASP cc_start: 0.8853 (t0) cc_final: 0.8504 (t70)
REVERT: D   65 ASP cc_start: 0.9135 (t70) cc_final: 0.8534 (t0)
REVERT: E   90 MET cc_start: 0.9306 (mmp) cc_final: 0.8915 (mmp)
REVERT: E   94 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8887 (mm-30)
REVERT: E   97 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8876 (mt-10)
REVERT: E  120 MET cc_start: 0.9107 (mmm) cc_final: 0.8789 (mmm)
REVERT: F   84 MET cc_start: 0.9012 (tpp) cc_final: 0.8781 (tpp)
REVERT: H   73 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9163 (mm-30)
REVERT: L   84 MET cc_start: 0.9125 (tpp) cc_final: 0.8695 (tpp)
REVERT: M   61 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9206 (tp30)
REVERT: N   34 TYR cc_start: 0.9700 (m-80) cc_final: 0.8941 (m-10)
REVERT: N   59 MET cc_start: 0.9737 (mmt) cc_final: 0.9478 (mmm)
REVERT: N   67 PHE cc_start: 0.9685 (t80) cc_final: 0.9408 (t80)
REVERT: N   73 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9426 (mm-30)
REVERT: O   97 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9067 (mt-10)
REVERT: O  106 ASP cc_start: 0.9430 (m-30) cc_final: 0.9149 (m-30)
REVERT: O  120 MET cc_start: 0.9477 (tpt) cc_final: 0.9218 (mmm)
REVERT: Q   59 MET cc_start: 0.9893 (mmp) cc_final: 0.9684 (mmm)
REVERT: Q   73 GLU cc_start: 0.9765 (mm-30) cc_final: 0.9527 (mm-30)
REVERT: R   56 GLU cc_start: 0.9547 (tt0) cc_final: 0.9168 (tt0)
REVERT: S  127 PHE cc_start: 0.8865 (t80) cc_final: 0.8454 (p90)
REVERT: T  132 ASN cc_start: 0.9126 (t0) cc_final: 0.8503 (m-40)
REVERT: W  387 MET cc_start: 0.9411 (mtm) cc_final: 0.9168 (mtt)
REVERT: W  403 MET cc_start: 0.9145 (mpp) cc_final: 0.8319 (mpp)
REVERT: W  697 MET cc_start: 0.8446 (mtm) cc_final: 0.8194 (ptp)
REVERT: W  781 MET cc_start: 0.9201 (mmp) cc_final: 0.8882 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1825
  time to fit residues: 51.7329
Evaluate side-chains
  121 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 163 optimal weight:   10.0000
   chunk 227 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   chunk 120 optimal weight:    0.9990
   chunk 196 optimal weight:   30.0000
   chunk 246 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 147 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  89 ASN
D  92 GLN
O 113 HIS
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 813 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.041576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026146 restraints weight = 289730.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.026776 restraints weight = 171778.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.026934 restraints weight = 130374.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.026934 restraints weight = 116510.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.026934 restraints weight = 116510.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  28073  Z= 0.167
  Angle     :  0.576   7.785  39946  Z= 0.341
  Chirality :  0.034   0.173   4532
  Planarity :  0.004   0.064   3427
  Dihedral  : 29.137 130.151   7522
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.18), residues: 2060
  helix:  1.74 (0.14), residues: 1391
  sheet: -0.12 (0.54), residues: 96
  loop : -0.49 (0.24), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG P  78 
 TYR   0.016   0.001   TYR W 230 
 PHE   0.018   0.001   PHE K 104 
 TRP   0.011   0.001   TRP W 311 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (28072)
  covalent geometry    : angle       0.57583 (39946)
  hydrogen bonds       : bond        0.03952 ( 1691)
  hydrogen bonds       : angle       3.75947 ( 4414)
  Misc. bond           : bond        0.00001 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.9619 (pt) cc_final: 0.9239 (pt)
REVERT: A  120 MET cc_start: 0.9094 (mmm) cc_final: 0.8722 (mmm)
REVERT: B   67 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.9101 (ttp-110)
REVERT: B   84 MET cc_start: 0.9073 (tpp) cc_final: 0.8855 (tpp)
REVERT: C   56 GLU cc_start: 0.8944 (pt0) cc_final: 0.8229 (pp20)
REVERT: C   73 ASN cc_start: 0.9218 (t0) cc_final: 0.8840 (t0)
REVERT: C   95 LYS cc_start: 0.9431 (mtmm) cc_final: 0.9226 (mtmm)
REVERT: D   65 ASP cc_start: 0.9107 (t70) cc_final: 0.8472 (t0)
REVERT: E   90 MET cc_start: 0.9271 (mmp) cc_final: 0.8895 (mmp)
REVERT: E   94 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8861 (mm-30)
REVERT: E   97 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8821 (mt-10)
REVERT: E  120 MET cc_start: 0.9099 (mmm) cc_final: 0.8889 (mmm)
REVERT: F   84 MET cc_start: 0.8962 (tpp) cc_final: 0.8704 (tpp)
REVERT: H   56 MET cc_start: 0.9324 (tpt) cc_final: 0.9062 (tpp)
REVERT: H   65 ASP cc_start: 0.9450 (t0) cc_final: 0.9208 (t0)
REVERT: H   73 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9202 (mm-30)
REVERT: K   97 GLU cc_start: 0.9425 (mt-10) cc_final: 0.8953 (mm-30)
REVERT: L   84 MET cc_start: 0.9032 (tpp) cc_final: 0.8590 (tpp)
REVERT: M   61 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9195 (tp30)
REVERT: M   84 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9241 (tp40)
REVERT: N   34 TYR cc_start: 0.9701 (m-80) cc_final: 0.9315 (m-10)
REVERT: N   59 MET cc_start: 0.9732 (mmt) cc_final: 0.9449 (mmm)
REVERT: N   73 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9420 (mm-30)
REVERT: O   94 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9240 (mm-30)
REVERT: O  106 ASP cc_start: 0.9432 (m-30) cc_final: 0.9147 (m-30)
REVERT: O  120 MET cc_start: 0.9511 (tpt) cc_final: 0.9231 (mmm)
REVERT: R   56 GLU cc_start: 0.9527 (tt0) cc_final: 0.9230 (tt0)
REVERT: S  127 PHE cc_start: 0.8955 (t80) cc_final: 0.8514 (p90)
REVERT: T  132 ASN cc_start: 0.9094 (t0) cc_final: 0.8579 (m110)
REVERT: T  140 ASP cc_start: 0.8939 (t0) cc_final: 0.8464 (p0)
REVERT: W  387 MET cc_start: 0.9416 (mtm) cc_final: 0.9192 (mtt)
REVERT: W  403 MET cc_start: 0.9014 (mpp) cc_final: 0.8189 (mpp)
REVERT: W  697 MET cc_start: 0.8562 (mtm) cc_final: 0.8002 (mtm)
REVERT: W  781 MET cc_start: 0.9271 (mmp) cc_final: 0.8819 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1619
  time to fit residues: 49.5910
Evaluate side-chains
  131 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 195 optimal weight:   20.0000
   chunk 192 optimal weight:   40.0000
   chunk 171 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 180 optimal weight:    8.9990
   chunk 232 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 188 optimal weight:    4.9990
   chunk 187 optimal weight:   50.0000
   chunk 136 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.040296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.025310 restraints weight = 299637.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.025608 restraints weight = 184705.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.025748 restraints weight = 139186.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026146 restraints weight = 124481.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.026297 restraints weight = 112476.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.092  28073  Z= 0.287
  Angle     :  0.632   9.620  39946  Z= 0.373
  Chirality :  0.037   0.186   4532
  Planarity :  0.004   0.064   3427
  Dihedral  : 29.129 129.568   7522
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.55 %
    Favored  : 97.40 %
  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 aren not related in a simple way.
  whole:  1.49 (0.18), residues: 2060
  helix:  1.72 (0.14), residues: 1385
  sheet: -0.25 (0.55), residues: 94
  loop : -0.51 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG W 804 
 TYR   0.018   0.002   TYR W 316 
 PHE   0.020   0.002   PHE W 676 
 TRP   0.008   0.001   TRP W 507 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 (28072)
  covalent geometry    : angle       0.63212 (39946)
  hydrogen bonds       : bond        0.06457 ( 1691)
  hydrogen bonds       : angle       3.99143 ( 4414)
  Misc. bond           : bond        0.00073 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9195 (mmm) cc_final: 0.8717 (mmm)
REVERT: B   67 ARG cc_start: 0.9352 (ttp-110) cc_final: 0.9044 (ttp-110)
REVERT: B   84 MET cc_start: 0.9087 (tpp) cc_final: 0.8883 (tpp)
REVERT: C   56 GLU cc_start: 0.9098 (pt0) cc_final: 0.8305 (pp20)
REVERT: C   73 ASN cc_start: 0.9368 (t0) cc_final: 0.8996 (t0)
REVERT: C   90 ASP cc_start: 0.8816 (t70) cc_final: 0.8566 (t70)
REVERT: E   90 MET cc_start: 0.9242 (mmp) cc_final: 0.8873 (mmp)
REVERT: E   94 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8864 (mm-30)
REVERT: E   97 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8849 (mt-10)
REVERT: E  120 MET cc_start: 0.9243 (mmm) cc_final: 0.8914 (mmm)
REVERT: H   65 ASP cc_start: 0.9440 (t0) cc_final: 0.9155 (t0)
REVERT: L   84 MET cc_start: 0.9033 (tpp) cc_final: 0.8551 (tpp)
REVERT: M   61 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9167 (tp30)
REVERT: N   34 TYR cc_start: 0.9710 (m-80) cc_final: 0.9361 (m-10)
REVERT: N   59 MET cc_start: 0.9713 (mmt) cc_final: 0.9459 (mmm)
REVERT: N   73 GLU cc_start: 0.9642 (mm-30) cc_final: 0.9405 (mm-30)
REVERT: O   94 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8565 (tp30)
REVERT: O   97 GLU cc_start: 0.9098 (pt0) cc_final: 0.8888 (pp20)
REVERT: O  106 ASP cc_start: 0.9455 (m-30) cc_final: 0.9170 (m-30)
REVERT: Q   59 MET cc_start: 0.9876 (mmp) cc_final: 0.9663 (mmm)
REVERT: R   56 GLU cc_start: 0.9563 (tt0) cc_final: 0.9162 (tt0)
REVERT: S  127 PHE cc_start: 0.8861 (t80) cc_final: 0.8372 (p90)
REVERT: T  132 ASN cc_start: 0.9118 (t0) cc_final: 0.8553 (m110)
REVERT: T  140 ASP cc_start: 0.8843 (t0) cc_final: 0.8403 (p0)
REVERT: W  387 MET cc_start: 0.9411 (mtm) cc_final: 0.9146 (mtt)
REVERT: W  403 MET cc_start: 0.9021 (mpp) cc_final: 0.8208 (mpp)
REVERT: W  697 MET cc_start: 0.8555 (mtm) cc_final: 0.8033 (mtm)
REVERT: W  781 MET cc_start: 0.9120 (mmp) cc_final: 0.8644 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1845
  time to fit residues: 47.2352
Evaluate side-chains
  119 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 150 optimal weight:    5.9990
   chunk 239 optimal weight:   20.0000
   chunk 106 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 155 optimal weight:   10.0000
   chunk 247 optimal weight:    5.9990
   chunk 230 optimal weight:   20.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
W 410 GLN
W 424 GLN
W 520 ASN
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.040481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025451 restraints weight = 292428.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.025594 restraints weight = 178479.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.025761 restraints weight = 134392.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026041 restraints weight = 118564.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 64)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.026256 restraints weight = 109257.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  28073  Z= 0.223
  Angle     :  0.598  12.358  39946  Z= 0.352
  Chirality :  0.035   0.197   4532
  Planarity :  0.004   0.063   3427
  Dihedral  : 29.248 129.426   7522
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.18), residues: 2060
  helix:  1.70 (0.14), residues: 1388
  sheet: -0.49 (0.52), residues: 94
  loop : -0.62 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG P  78 
 TYR   0.017   0.001   TYR W 316 
 PHE   0.019   0.002   PHE O 104 
 TRP   0.011   0.001   TRP W 507 
 HIS   0.011   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (28072)
  covalent geometry    : angle       0.59812 (39946)
  hydrogen bonds       : bond        0.04685 ( 1691)
  hydrogen bonds       : angle       3.91365 ( 4414)
  Misc. bond           : bond        0.00056 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.9636 (pt) cc_final: 0.9328 (pt)
REVERT: A  120 MET cc_start: 0.9210 (mmm) cc_final: 0.8697 (mmm)
REVERT: B   31 LYS cc_start: 0.9718 (ttmt) cc_final: 0.9504 (mtpp)
REVERT: B   62 LEU cc_start: 0.9772 (mt) cc_final: 0.9538 (mt)
REVERT: B   67 ARG cc_start: 0.9335 (ttp-110) cc_final: 0.9017 (ttp-110)
REVERT: B   84 MET cc_start: 0.9091 (tpp) cc_final: 0.8872 (tpp)
REVERT: C   56 GLU cc_start: 0.9082 (pt0) cc_final: 0.8292 (pp20)
REVERT: C   73 ASN cc_start: 0.9385 (t0) cc_final: 0.9027 (t0)
REVERT: C   90 ASP cc_start: 0.8847 (t70) cc_final: 0.8599 (t70)
REVERT: C   95 LYS cc_start: 0.9355 (mtmm) cc_final: 0.8961 (mtmt)
REVERT: E   90 MET cc_start: 0.9284 (mmp) cc_final: 0.8913 (mmp)
REVERT: E   94 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8868 (mm-30)
REVERT: E   97 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8895 (mt-10)
REVERT: E  120 MET cc_start: 0.9286 (mmm) cc_final: 0.8828 (mmm)
REVERT: H   65 ASP cc_start: 0.9206 (t0) cc_final: 0.8447 (t0)
REVERT: K  120 MET cc_start: 0.9403 (tpp) cc_final: 0.9191 (mmm)
REVERT: L   84 MET cc_start: 0.8971 (tpp) cc_final: 0.8485 (tpp)
REVERT: M   61 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9164 (tp30)
REVERT: N   34 TYR cc_start: 0.9732 (m-80) cc_final: 0.9418 (m-10)
REVERT: N   59 MET cc_start: 0.9743 (mmt) cc_final: 0.9477 (mmm)
REVERT: N   73 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9427 (mm-30)
REVERT: O   94 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8911 (tp30)
REVERT: O   97 GLU cc_start: 0.9105 (pt0) cc_final: 0.8819 (pp20)
REVERT: O  106 ASP cc_start: 0.9444 (m-30) cc_final: 0.9178 (m-30)
REVERT: O  120 MET cc_start: 0.9516 (tpt) cc_final: 0.9240 (mmm)
REVERT: Q   59 MET cc_start: 0.9877 (mmp) cc_final: 0.9659 (mmm)
REVERT: R   56 GLU cc_start: 0.9533 (tt0) cc_final: 0.9118 (tt0)
REVERT: S  132 ASN cc_start: 0.6962 (p0) cc_final: 0.6256 (m-40)
REVERT: T  132 ASN cc_start: 0.9126 (t0) cc_final: 0.8649 (m110)
REVERT: T  140 ASP cc_start: 0.8831 (t0) cc_final: 0.8432 (p0)
REVERT: W  387 MET cc_start: 0.9425 (mtm) cc_final: 0.9146 (mtt)
REVERT: W  403 MET cc_start: 0.8982 (mpp) cc_final: 0.8494 (mpp)
REVERT: W  697 MET cc_start: 0.8636 (mtm) cc_final: 0.8097 (mtm)
REVERT: W  781 MET cc_start: 0.9133 (mmp) cc_final: 0.8621 (mmp)
REVERT: W  789 PHE cc_start: 0.9229 (m-80) cc_final: 0.8987 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1763
  time to fit residues: 46.5871
Evaluate side-chains
  122 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 120 optimal weight:    7.9990
   chunk 190 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 212 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 166 optimal weight:    6.9990
   chunk 192 optimal weight:    1.9990
   chunk 221 optimal weight:    4.9990
   chunk 189 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.040572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.025415 restraints weight = 296794.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026014 restraints weight = 176896.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026162 restraints weight = 132769.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026162 restraints weight = 116876.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026162 restraints weight = 116876.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  28073  Z= 0.212
  Angle     :  0.592  10.775  39946  Z= 0.349
  Chirality :  0.035   0.204   4532
  Planarity :  0.004   0.061   3427
  Dihedral  : 29.100 127.917   7522
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.18), residues: 2060
  helix:  1.85 (0.14), residues: 1382
  sheet: -0.60 (0.51), residues: 95
  loop : -0.60 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P  78 
 TYR   0.015   0.001   TYR S 137 
 PHE   0.022   0.002   PHE A 104 
 TRP   0.010   0.001   TRP W 507 
 HIS   0.007   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (28072)
  covalent geometry    : angle       0.59233 (39946)
  hydrogen bonds       : bond        0.04860 ( 1691)
  hydrogen bonds       : angle       3.89389 ( 4414)
  Misc. bond           : bond        0.00027 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.9644 (pt) cc_final: 0.9348 (pt)
REVERT: A  120 MET cc_start: 0.9222 (mmm) cc_final: 0.8704 (mmm)
REVERT: B   67 ARG cc_start: 0.9320 (ttp-110) cc_final: 0.9001 (ttp-110)
REVERT: B   84 MET cc_start: 0.9150 (tpp) cc_final: 0.8930 (tpp)
REVERT: C   56 GLU cc_start: 0.9145 (pt0) cc_final: 0.8523 (pp20)
REVERT: C   73 ASN cc_start: 0.9398 (t0) cc_final: 0.9121 (t0)
REVERT: C   90 ASP cc_start: 0.8849 (t70) cc_final: 0.8593 (t70)
REVERT: D   65 ASP cc_start: 0.9135 (t0) cc_final: 0.8627 (t0)
REVERT: E   90 MET cc_start: 0.9294 (mmp) cc_final: 0.8916 (mmp)
REVERT: E   94 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8866 (mm-30)
REVERT: E   97 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8894 (mt-10)
REVERT: E  120 MET cc_start: 0.9296 (mmm) cc_final: 0.8821 (mmm)
REVERT: F   84 MET cc_start: 0.8795 (tpp) cc_final: 0.8539 (tpp)
REVERT: H   65 ASP cc_start: 0.9172 (t0) cc_final: 0.8439 (t0)
REVERT: L   84 MET cc_start: 0.8938 (tpp) cc_final: 0.8442 (tpp)
REVERT: L   85 ASP cc_start: 0.9265 (m-30) cc_final: 0.9064 (m-30)
REVERT: M   61 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9171 (tp30)
REVERT: N   34 TYR cc_start: 0.9736 (m-80) cc_final: 0.9452 (m-10)
REVERT: N   59 MET cc_start: 0.9750 (mmt) cc_final: 0.9503 (mmm)
REVERT: N   68 GLU cc_start: 0.9413 (mp0) cc_final: 0.9207 (mp0)
REVERT: O   94 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8895 (tp30)
REVERT: O   97 GLU cc_start: 0.9161 (pt0) cc_final: 0.8888 (pp20)
REVERT: O  106 ASP cc_start: 0.9446 (m-30) cc_final: 0.9182 (m-30)
REVERT: P   68 ASP cc_start: 0.9528 (m-30) cc_final: 0.9324 (m-30)
REVERT: Q   59 MET cc_start: 0.9873 (mmp) cc_final: 0.9650 (mmm)
REVERT: Q   73 GLU cc_start: 0.9720 (mm-30) cc_final: 0.9311 (tp30)
REVERT: R   56 GLU cc_start: 0.9524 (tt0) cc_final: 0.9110 (tt0)
REVERT: S  127 PHE cc_start: 0.8795 (t80) cc_final: 0.8585 (t80)
REVERT: S  132 ASN cc_start: 0.7068 (p0) cc_final: 0.6283 (m-40)
REVERT: T  132 ASN cc_start: 0.9143 (t0) cc_final: 0.8591 (m110)
REVERT: T  140 ASP cc_start: 0.8845 (t0) cc_final: 0.8449 (p0)
REVERT: W  387 MET cc_start: 0.9455 (mtm) cc_final: 0.9195 (mtt)
REVERT: W  403 MET cc_start: 0.8894 (mpp) cc_final: 0.8410 (mpp)
REVERT: W  697 MET cc_start: 0.8922 (mtm) cc_final: 0.8503 (mtm)
REVERT: W  781 MET cc_start: 0.9182 (mmp) cc_final: 0.8555 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1857
  time to fit residues: 48.7498
Evaluate side-chains
  125 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 250
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 70 optimal weight:   20.0000
   chunk 112 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 175 optimal weight:   20.0000
   chunk 9 optimal weight:    0.8980
   chunk 236 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  93 GLN
P  93 GLN
** W 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.041748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.026540 restraints weight = 284862.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.026723 restraints weight = 172532.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.026862 restraints weight = 128898.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.026862 restraints weight = 114503.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.026862 restraints weight = 114503.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  28073  Z= 0.142
  Angle     :  0.570   8.912  39946  Z= 0.331
  Chirality :  0.034   0.167   4532
  Planarity :  0.004   0.062   3427
  Dihedral  : 28.881 126.890   7522
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.18), residues: 2060
  helix:  1.91 (0.14), residues: 1390
  sheet: -0.36 (0.54), residues: 87
  loop : -0.58 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P  78 
 TYR   0.013   0.001   TYR G  50 
 PHE   0.018   0.001   PHE W 379 
 TRP   0.014   0.001   TRP W 311 
 HIS   0.006   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (28072)
  covalent geometry    : angle       0.56954 (39946)
  hydrogen bonds       : bond        0.03465 ( 1691)
  hydrogen bonds       : angle       3.67141 ( 4414)
  Misc. bond           : bond        0.00024 (    1)

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

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

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4120 Ramachandran restraints generated.
    2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.9623 (pt) cc_final: 0.9331 (pt)
REVERT: A  120 MET cc_start: 0.9265 (mmm) cc_final: 0.8764 (mmm)
REVERT: B   67 ARG cc_start: 0.9304 (ttp-110) cc_final: 0.9054 (ttp-110)
REVERT: C   56 GLU cc_start: 0.8917 (pt0) cc_final: 0.8438 (pp20)
REVERT: C   73 ASN cc_start: 0.9315 (t0) cc_final: 0.9028 (t0)
REVERT: C   90 ASP cc_start: 0.8842 (t70) cc_final: 0.8564 (t70)
REVERT: C   95 LYS cc_start: 0.9410 (mtmm) cc_final: 0.9018 (mtmt)
REVERT: D   65 ASP cc_start: 0.9111 (t0) cc_final: 0.8521 (t0)
REVERT: E   90 MET cc_start: 0.9287 (mmp) cc_final: 0.8898 (mmp)
REVERT: E   94 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8994 (mm-30)
REVERT: E  120 MET cc_start: 0.9266 (mmm) cc_final: 0.8785 (mmm)
REVERT: F   84 MET cc_start: 0.8695 (tpp) cc_final: 0.8424 (tpp)
REVERT: H   65 ASP cc_start: 0.9116 (t0) cc_final: 0.8351 (t0)
REVERT: L   84 MET cc_start: 0.8887 (tpp) cc_final: 0.8586 (tpp)
REVERT: L   85 ASP cc_start: 0.9225 (m-30) cc_final: 0.8999 (p0)
REVERT: M   61 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9162 (tp30)
REVERT: M   84 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9237 (tp40)
REVERT: M   89 ASN cc_start: 0.9456 (m-40) cc_final: 0.9131 (m110)
REVERT: N   34 TYR cc_start: 0.9703 (m-80) cc_final: 0.9478 (m-10)
REVERT: N   59 MET cc_start: 0.9715 (mmt) cc_final: 0.9443 (mmm)
REVERT: O   94 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8900 (mm-30)
REVERT: O  106 ASP cc_start: 0.9382 (m-30) cc_final: 0.9103 (m-30)
REVERT: O  120 MET cc_start: 0.9466 (tpt) cc_final: 0.9260 (mmm)
REVERT: Q   73 GLU cc_start: 0.9720 (mm-30) cc_final: 0.9163 (tp30)
REVERT: Q   77 LEU cc_start: 0.9915 (tt) cc_final: 0.9674 (pp)
REVERT: R   56 GLU cc_start: 0.9519 (tt0) cc_final: 0.9098 (tt0)
REVERT: S  127 PHE cc_start: 0.8934 (t80) cc_final: 0.8351 (p90)
REVERT: S  132 ASN cc_start: 0.7052 (p0) cc_final: 0.6301 (m-40)
REVERT: T  132 ASN cc_start: 0.9198 (t0) cc_final: 0.8776 (m110)
REVERT: T  140 ASP cc_start: 0.8872 (t0) cc_final: 0.8504 (p0)
REVERT: W  387 MET cc_start: 0.9471 (mtm) cc_final: 0.9201 (mtt)
REVERT: W  403 MET cc_start: 0.8793 (mpp) cc_final: 0.8295 (mpp)
REVERT: W  697 MET cc_start: 0.9008 (mtm) cc_final: 0.8614 (mtm)
REVERT: W  781 MET cc_start: 0.9230 (mmp) cc_final: 0.8464 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1843
  time to fit residues: 52.2817
Evaluate side-chains
  137 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7972 > 50:
  distance: 54 - 186:  31.260
  distance: 57 - 183:  35.164
  distance: 68 - 165:  34.198
  distance: 71 - 162:  36.746
  distance: 92 - 101:  23.798
  distance: 101 - 102:   6.767
  distance: 102 - 103:  10.550
  distance: 102 - 105:  18.185
  distance: 103 - 104:  39.692
  distance: 103 - 112:  50.114
  distance: 105 - 106:  40.534
  distance: 106 - 107:  56.160
  distance: 107 - 108:  25.974
  distance: 108 - 109:  33.079
  distance: 109 - 110:   7.066
  distance: 109 - 111:  26.172
  distance: 112 - 113:  32.944
  distance: 113 - 114:  33.200
  distance: 113 - 116:  27.806
  distance: 114 - 115:  38.181
  distance: 114 - 120:  54.843
  distance: 116 - 117:  37.682
  distance: 117 - 119:  53.265
  distance: 120 - 121:  47.527
  distance: 121 - 122:  57.325
  distance: 121 - 124:  25.633
  distance: 122 - 123:  56.953
  distance: 124 - 125:  33.870
  distance: 128 - 129:  28.023
  distance: 129 - 130:  16.269
  distance: 129 - 132:  26.483
  distance: 130 - 131:   7.366
  distance: 130 - 140:  51.171
  distance: 132 - 133:   7.056
  distance: 133 - 135:  39.281
  distance: 134 - 136:  39.164
  distance: 136 - 138:  28.462
  distance: 137 - 138:  40.365
  distance: 138 - 139:  11.097
  distance: 140 - 141:  39.907
  distance: 141 - 142:  51.233
  distance: 141 - 144:  15.767
  distance: 142 - 143:  33.285
  distance: 142 - 148:   7.804
  distance: 144 - 145:  21.782
  distance: 145 - 146:  45.974
  distance: 145 - 147:   6.614
  distance: 148 - 149:  16.499
  distance: 149 - 150:  35.766
  distance: 149 - 152:  25.217
  distance: 150 - 157:  19.998
  distance: 152 - 153:  40.300
  distance: 153 - 154:  41.014
  distance: 154 - 155:  11.317
  distance: 154 - 156:  10.117
  distance: 157 - 158:  37.077
  distance: 158 - 159:  40.730
  distance: 158 - 161:  30.785
  distance: 159 - 160:  40.104
  distance: 159 - 162:  68.879
  distance: 162 - 163:  64.067
  distance: 163 - 164:  16.139
  distance: 163 - 166:   8.133
  distance: 164 - 165:  23.718
  distance: 164 - 169:  15.578
  distance: 166 - 167:  40.799
  distance: 166 - 168:  49.386
  distance: 169 - 170:  40.600
  distance: 170 - 171:  10.230
  distance: 170 - 173:  64.595
  distance: 171 - 172:  28.807
  distance: 171 - 183:  57.911
  distance: 173 - 174:  40.911
  distance: 174 - 175:  22.897
  distance: 174 - 176:  28.818
  distance: 175 - 177:  24.187
  distance: 176 - 178:  23.205
  distance: 176 - 179:  27.335
  distance: 177 - 178:  12.848
  distance: 178 - 180:  21.483
  distance: 179 - 181:  19.478
  distance: 180 - 182:  11.308
  distance: 181 - 182:  20.344
  distance: 183 - 184:  18.883
  distance: 184 - 185:  22.788
  distance: 184 - 187:  43.768
  distance: 185 - 186:  40.222
  distance: 185 - 192:  33.601
  distance: 187 - 188:  59.695
  distance: 188 - 189:  25.428
  distance: 189 - 190:  32.144
  distance: 189 - 191:  45.019