Starting phenix.real_space_refine
on Sun Aug 24 00:58:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qay_52979/08_2025/9qay_52979.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     P     260      5.49       5
     S      42      5.16       5
     C    8819      2.51       5
     N    2812      2.21       5
     O    3538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s

  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: 15471
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 954, 7649
          Classifications: {'peptide': 954}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 55, 'TRANS': 895}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 5371
          Classifications: {'RNA': 253}
          Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 18, 'rna3p_pur': 100, 'rna3p_pyr': 119}
          Link IDs: {'rna2p': 34, 'rna3p': 218}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 632
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 3, 'TRANS': 77}
    Chain: "M"
      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: "N"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 149
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "O"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 971
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
          Chain breaks: 3
  Time building chain proxies: 3.91, per 1000 atoms: 0.25
  Number of scatterers: 15471
  At special positions: 0
  Unit cell: (167.322, 124.962, 144.024, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P     260     15.00
     O    3538      8.00
     N    2812      7.00
     C    8819      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 506.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2346

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      54.3% alpha, 12.7% beta
      71 base pairs and 125 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
      removed outlier: 3.899A  pdb=" N   ARG A  11 " --> pdb=" O   CYS A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 18
      No H-bonds generated for 'chain 'A' and resid 16 through 18'
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
      removed outlier: 3.584A  pdb=" N   VAL A  51 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 92
      removed outlier: 3.579A  pdb=" N   VAL A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 133
      removed outlier: 3.853A  pdb=" N   GLY A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.797A  pdb=" N   ARG A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.732A  pdb=" N   LEU A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.657A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.504A  pdb=" N   LEU A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 454
      removed outlier: 3.516A  pdb=" N   ARG A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.923A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.692A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 497
      removed outlier: 3.504A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.676A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.508A  pdb=" N   LYS A 543 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.611A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 597
      removed outlier: 3.711A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.665A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 672
      removed outlier: 4.097A  pdb=" N   LYS A 659 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.854A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 734
      removed outlier: 3.665A  pdb=" N   GLU A 727 " --> pdb=" O   ASP A 723 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 733 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.581A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 837 through 854
      removed outlier: 3.640A  pdb=" N   CYS A 842 " --> pdb=" O   SER A 838 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER A 843 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS A 852 " --> pdb=" O   ASP A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 859
    Processing helix  chain 'A' and resid 876 through 890
      removed outlier: 3.693A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.619A  pdb=" N   TYR A 949 " --> pdb=" O   TYR A 946 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 946 through 950'
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.557A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
      removed outlier: 3.562A  pdb=" N   LEU A1007 " --> pdb=" O   LYS A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1028
      removed outlier: 3.538A  pdb=" N   LYS A1027 " --> pdb=" O   GLN A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1051
      removed outlier: 3.546A  pdb=" N   ASP A1038 " --> pdb=" O   ARG A1034 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS A1043 " --> pdb=" O   THR A1039 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1085
      removed outlier: 3.902A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   HIS A1075 " --> pdb=" O   GLN A1071 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A1083 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG A1084 " --> pdb=" O   LEU A1080 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   HIS A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.606A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.090A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1119
      removed outlier: 3.879A  pdb=" N   THR A1113 " --> pdb=" O   GLY A1109 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 38
      removed outlier: 4.411A  pdb=" N   LEU L  34 " --> pdb=" O   ARG L  30 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  31 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLY L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 73
      removed outlier: 4.507A  pdb=" N   VAL L  50 " --> pdb=" O   ALA L  46 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   TYR L  51 " --> pdb=" O   GLY L  47 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU L  57 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR L  60 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE L  63 " --> pdb=" O   LEU L  59 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU L  66 " --> pdb=" O   GLU L  62 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 91
      removed outlier: 3.965A  pdb=" N   LEU L  84 " --> pdb=" O   ILE L  80 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP L  91 " --> pdb=" O   ALA L  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 91 through 99
      removed outlier: 3.636A  pdb=" N   ASN L  95 " --> pdb=" O   ASP L  91 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LYS L  96 " --> pdb=" O   GLU L  92 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 40 through 50
      removed outlier: 3.629A  pdb=" N   VAL M  45 " --> pdb=" O   TYR M  41 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS M  47 " --> pdb=" O   TYR M  43 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLN M  48 " --> pdb=" O   LYS M  44 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL M  49 " --> pdb=" O   VAL M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 56 through 86
      removed outlier: 4.001A  pdb=" N   SER M  65 " --> pdb=" O   GLY M  61 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE M  66 " --> pdb=" O   ILE M  62 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE M  70 " --> pdb=" O   PHE M  66 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   SER M  79 " --> pdb=" O   ALA M  75 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   HIS M  83 " --> pdb=" O   SER M  79 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR M  84 " --> pdb=" O   ARG M  80 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 91 through 103
      removed outlier: 3.781A  pdb=" N   ILE M  95 " --> pdb=" O   THR M  91 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN M  96 " --> pdb=" O   SER M  92 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   THR M  97 " --> pdb=" O   ARG M  93 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ALA M  98 " --> pdb=" O   GLU M  94 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG M 100 " --> pdb=" O   GLN M  96 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU M 102 " --> pdb=" O   ALA M  98 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU M 103 " --> pdb=" O   VAL M  99 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 107 through 125
      removed outlier: 3.757A  pdb=" N   SER M 113 " --> pdb=" O   LYS M 109 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU M 114 " --> pdb=" O   HIS M 110 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY M 115 " --> pdb=" O   ALA M 111 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR M 120 " --> pdb=" O   THR M 116 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER M 125 " --> pdb=" O   LYS M 121 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 98 through 104
      removed outlier: 3.842A  pdb=" N   ILE O 103 " --> pdb=" O   ILE O  99 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 158 through 164
      removed outlier: 3.622A  pdb=" N   LEU O 162 " --> pdb=" O   THR O 158 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 227 through 238
      removed outlier: 3.505A  pdb=" N   LYS O 232 " --> pdb=" O   LEU O 228 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LYS O 233 " --> pdb=" O   ASP O 229 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR O 235 " --> pdb=" O   GLN O 231 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ASP O 236 " --> pdb=" O   LYS O 232 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS O 237 " --> pdb=" O   LYS O 233 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU O 238 " --> pdb=" O   LEU O 234 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.771A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.349A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 3.771A  pdb=" N   ALA A 157 " --> pdb=" O   CYS A  57 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 11.349A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 739 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600
      removed outlier: 7.355A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680
      removed outlier: 3.717A  pdb=" N   LEU A 866 " --> pdb=" O   ASP A 869 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP A 869 " --> pdb=" O   LEU A 866 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   VAL A 709 " --> pdb=" O   LEU A 872 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 905 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA9, first strand: chain 'O' and resid 181 through 184
      removed outlier: 7.216A  pdb=" N   LEU O 145 " --> pdb=" O   LEU O 118 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   VAL O 120 " --> pdb=" O   THR O 143 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   THR O 143 " --> pdb=" O   VAL O 120 " (cutoff:3.500A)
      removed outlier: 9.521A  pdb=" N   LEU O 204 " --> pdb=" O   SER O 152 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   ARG O 154 " --> pdb=" O   LEU O 204 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   VAL O 206 " --> pdb=" O   ARG O 154 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU O 156 " --> pdb=" O   VAL O 206 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1326 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      187 hydrogen bonds
      346 hydrogen bond angles
      0 basepair planarities
      71 basepair parallelities
      125 stacking parallelities
  Total time for adding SS restraints: 3.99

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1962
        1.32 -     1.45: 5806
        1.45 -     1.57: 7985
        1.57 -     1.70: 515
        1.70 -     1.83: 55
  Bond restraints: 16323
  Sorted by residual:
  bond pdb=" C   GLN A 454 "
       pdb=" O   GLN A 454 "
    ideal  model  delta    sigma   weight residual
    1.233  1.191  0.043 1.06e-02 8.90e+03 1.64e+01
  bond pdb=" C   VAL A 563 "
       pdb=" O   VAL A 563 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.20e-02 6.94e+03 1.32e+01
  bond pdb=" CZ  ARG L  33 "
       pdb=" NH2 ARG L  33 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.14e+01
  bond pdb=" CG  ARG A 378 "
       pdb=" CD  ARG A 378 "
    ideal  model  delta    sigma   weight residual
    1.520  1.429  0.091 3.00e-02 1.11e+03 9.26e+00
  bond pdb=" CE1 HIS A 482 "
       pdb=" NE2 HIS A 482 "
    ideal  model  delta    sigma   weight residual
    1.321  1.292  0.029 1.00e-02 1.00e+04 8.21e+00
  ... (remaining 16318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 22184
        2.57 -     5.14: 1113
        5.14 -     7.71: 41
        7.71 -    10.29: 4
       10.29 -    12.86: 4
  Bond angle restraints: 23346
  Sorted by residual:
  angle pdb=" O3'   C B 119 "
        pdb=" P     G B 120 "
        pdb=" O5'   G B 120 "
      ideal   model   delta    sigma   weight residual
     104.00   91.14   12.86 1.50e+00 4.44e-01 7.35e+01
  angle pdb=" C   LYS A 338 "
        pdb=" CA  LYS A 338 "
        pdb=" CB  LYS A 338 "
      ideal   model   delta    sigma   weight residual
     109.84  101.62    8.22 1.50e+00 4.44e-01 3.00e+01
  angle pdb=" C   HIS A1022 "
        pdb=" CA  HIS A1022 "
        pdb=" CB  HIS A1022 "
      ideal   model   delta    sigma   weight residual
     110.42  121.08  -10.66 1.99e+00 2.53e-01 2.87e+01
  angle pdb=" P    DG N  28 "
        pdb=" O5'  DG N  28 "
        pdb=" C5'  DG N  28 "
      ideal   model   delta    sigma   weight residual
     120.00  127.18   -7.18 1.50e+00 4.44e-01 2.29e+01
  angle pdb=" N   PRO A 530 "
        pdb=" CA  PRO A 530 "
        pdb=" C   PRO A 530 "
      ideal   model   delta    sigma   weight residual
     110.40  117.67   -7.27 1.61e+00 3.86e-01 2.04e+01
  ... (remaining 23341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 9448
       35.74 -    71.48: 707
       71.48 -   107.22: 110
      107.22 -   142.96: 7
      142.96 -   178.70: 12
  Dihedral angle restraints: 10284
    sinusoidal: 6663
      harmonic: 3621
  Sorted by residual:
  dihedral pdb=" C5'   A B 176 "
           pdb=" C4'   A B 176 "
           pdb=" C3'   A B 176 "
           pdb=" O3'   A B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   74.41   72.59     1      8.00e+00 1.56e-02 1.05e+02
  dihedral pdb=" C4'   U B 307 "
           pdb=" C3'   U B 307 "
           pdb=" C2'   U B 307 "
           pdb=" C1'   U B 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.36  -70.36     1      8.00e+00 1.56e-02 9.96e+01
  dihedral pdb=" C4'   A B 176 "
           pdb=" C3'   A B 176 "
           pdb=" C2'   A B 176 "
           pdb=" C1'   A B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   33.60  -68.60     1      8.00e+00 1.56e-02 9.53e+01
  ... (remaining 10281 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 2482
       0.117 -    0.234: 348
       0.234 -    0.351: 15
       0.351 -    0.468: 1
       0.468 -    0.585: 4
  Chirality restraints: 2850
  Sorted by residual:
  chirality pdb=" P    DG N  24 "
            pdb=" OP1  DG N  24 "
            pdb=" OP2  DG N  24 "
            pdb=" O5'  DG N  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.93   -0.58 2.00e-01 2.50e+01 8.54e+00
  chirality pdb=" P     C B 238 "
            pdb=" OP1   C B 238 "
            pdb=" OP2   C B 238 "
            pdb=" O5'   C B 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.93   -0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" P     G B 163 "
            pdb=" OP1   G B 163 "
            pdb=" OP2   G B 163 "
            pdb=" O5'   G B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.34e+00
  ... (remaining 2847 not shown)

  Planarity restraints: 2013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 142 "   -0.208 2.00e-02 2.50e+03   1.05e-01 2.50e+02
        pdb=" N1    C B 142 "    0.051 2.00e-02 2.50e+03
        pdb=" C2    C B 142 "    0.057 2.00e-02 2.50e+03
        pdb=" O2    C B 142 "    0.055 2.00e-02 2.50e+03
        pdb=" N3    C B 142 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    C B 142 "    0.055 2.00e-02 2.50e+03
        pdb=" N4    C B 142 "   -0.176 2.00e-02 2.50e+03
        pdb=" C5    C B 142 "    0.067 2.00e-02 2.50e+03
        pdb=" C6    C B 142 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 307 "   -0.105 2.00e-02 2.50e+03   5.73e-02 7.38e+01
        pdb=" N1    U B 307 "    0.091 2.00e-02 2.50e+03
        pdb=" C2    U B 307 "    0.010 2.00e-02 2.50e+03
        pdb=" O2    U B 307 "    0.052 2.00e-02 2.50e+03
        pdb=" N3    U B 307 "   -0.053 2.00e-02 2.50e+03
        pdb=" C4    U B 307 "   -0.022 2.00e-02 2.50e+03
        pdb=" O4    U B 307 "   -0.027 2.00e-02 2.50e+03
        pdb=" C5    U B 307 "    0.059 2.00e-02 2.50e+03
        pdb=" C6    U B 307 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 690 "   -0.086 2.00e-02 2.50e+03   4.81e-02 5.78e+01
        pdb=" CG  TRP A 690 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 690 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 690 "    0.076 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 690 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 690 "    0.032 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 690 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 690 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 690 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 690 "   -0.065 2.00e-02 2.50e+03
  ... (remaining 2010 not shown)

  Histogram of nonbonded interaction distances:
        1.28 -     2.00: 3
        2.00 -     2.73: 882
        2.73 -     3.45: 20308
        3.45 -     4.18: 39930
        4.18 -     4.90: 61174
  Nonbonded interactions: 122297
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 510 "
            pdb=" O2'   C B 313 "
     model   vdw
     1.280 3.040
  nonbonded pdb=" CA  HIS A 752 "
            pdb=" O6    G B  58 "
     model   vdw
     1.833 3.470
  nonbonded pdb=" OG  SER A  12 "
            pdb=" O2'   A B  61 "
     model   vdw
     1.833 3.040
  nonbonded pdb=" C   HIS A 752 "
            pdb=" O6    G B  58 "
     model   vdw
     2.006 3.270
  nonbonded pdb=" O   PHE A1021 "
            pdb=" O2'   U B 312 "
     model   vdw
     2.033 3.040
  ... (remaining 122292 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.940
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     16.250
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
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      :  0.009   0.091  16323  Z= 0.547
  Angle     :  1.227  12.857  23346  Z= 0.782
  Chirality :  0.082   0.585   2850
  Planarity :  0.012   0.166   2013
  Dihedral  : 21.975 178.697   7938
  Min Nonbonded Distance : 1.280

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.19 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.96 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -3.03 (0.19), residues: 1227
  helix: -1.77 (0.17), residues: 535
  sheet: -1.92 (0.43), residues: 106
  loop : -2.20 (0.22), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.043   0.003   ARG A 470 
 TYR   0.041   0.008   TYR A 946 
 PHE   0.043   0.008   PHE A 986 
 TRP   0.086   0.011   TRP A 690 
 HIS   0.019   0.004   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00872 (16323)
  covalent geometry    : angle       1.22658 (23346)
  hydrogen bonds       : bond        0.27776 (  632)
  hydrogen bonds       : angle       8.37247 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.307 
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  178 LEU cc_start: 0.7258 (mt) cc_final: 0.7046 (mp)
REVERT: A  337 ASP cc_start: 0.8904 (m-30) cc_final: 0.8091 (t0)
REVERT: A  512 MET cc_start: 0.7802 (mmt) cc_final: 0.7568 (mmm)
REVERT: A  709 VAL cc_start: 0.7825 (t) cc_final: 0.7211 (p)
REVERT: A  718 ASP cc_start: 0.8359 (t70) cc_final: 0.8126 (t0)
REVERT: A  739 TYR cc_start: 0.6747 (m-80) cc_final: 0.6541 (m-80)
REVERT: A  782 GLU cc_start: 0.9286 (tt0) cc_final: 0.9077 (pt0)
REVERT: A  799 ASN cc_start: 0.7797 (t0) cc_final: 0.7434 (m110)
REVERT: A  824 SER cc_start: 0.8934 (m) cc_final: 0.8709 (p)
REVERT: A  860 ASP cc_start: 0.7974 (m-30) cc_final: 0.7220 (p0)
REVERT: A  942 VAL cc_start: 0.8171 (t) cc_final: 0.7967 (p)
REVERT: A 1054 MET cc_start: 0.6568 (mtt) cc_final: 0.6301 (mtt)
REVERT: L   52 LEU cc_start: 0.8141 (tt) cc_final: 0.7721 (pp)
REVERT: L   63 ILE cc_start: 0.7011 (tt) cc_final: 0.6653 (tp)
REVERT: L   74 ASN cc_start: 0.7583 (t0) cc_final: 0.7197 (m110)
REVERT: M   62 ILE cc_start: 0.8092 (mm) cc_final: 0.7629 (mm)
REVERT: O  148 ASP cc_start: 0.4296 (p0) cc_final: 0.3792 (p0)
REVERT: O  174 PHE cc_start: 0.6027 (m-80) cc_final: 0.5725 (m-10)
REVERT: O  209 PHE cc_start: 0.8176 (p90) cc_final: 0.7769 (p90)
REVERT: O  218 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7729 (mtm-85)
  outliers start: 1
  outliers final: 1
  residues processed: 177
  average time/residue: 0.1540
  time to fit residues: 36.5834
Evaluate side-chains
  104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   40 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 460 GLN
** L  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  50 HIS
M  96 GLN
O 151 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.113129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.088586 restraints weight = 82761.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.090422 restraints weight = 41308.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.091579 restraints weight = 28080.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.091831 restraints weight = 22868.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 72)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.092491 restraints weight = 21271.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16323  Z= 0.153
  Angle     :  0.690  10.566  23346  Z= 0.345
  Chirality :  0.039   0.261   2850
  Planarity :  0.005   0.081   2013
  Dihedral  : 23.875 177.601   5520
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.02 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.89 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -1.12 (0.22), residues: 1227
  helix:  0.21 (0.20), residues: 574
  sheet: -1.41 (0.41), residues: 128
  loop : -1.60 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG O  92 
 TYR   0.009   0.001   TYR A 562 
 PHE   0.022   0.002   PHE M  66 
 TRP   0.021   0.002   TRP A 547 
 HIS   0.004   0.001   HIS A 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (16323)
  covalent geometry    : angle       0.68957 (23346)
  hydrogen bonds       : bond        0.05787 (  632)
  hydrogen bonds       : angle       4.45059 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.8820 (mt) cc_final: 0.8485 (mt)
REVERT: A  178 LEU cc_start: 0.7539 (mt) cc_final: 0.7332 (mp)
REVERT: A  363 THR cc_start: 0.7419 (m) cc_final: 0.6726 (p)
REVERT: A  739 TYR cc_start: 0.4879 (m-80) cc_final: 0.4631 (m-80)
REVERT: A  824 SER cc_start: 0.7305 (m) cc_final: 0.6984 (p)
REVERT: A  870 PHE cc_start: 0.7230 (m-80) cc_final: 0.6918 (m-80)
REVERT: A 1038 ASP cc_start: 0.8007 (m-30) cc_final: 0.7686 (m-30)
REVERT: L   74 ASN cc_start: 0.7198 (t0) cc_final: 0.6765 (m110)
REVERT: M   62 ILE cc_start: 0.7684 (mm) cc_final: 0.7414 (mm)
REVERT: M   63 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9132 (mpp)
REVERT: M   66 PHE cc_start: 0.8580 (m-80) cc_final: 0.8196 (m-80)
REVERT: M  100 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7547 (mtm110)
REVERT: O   97 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7469 (Cg_exo)
REVERT: O   98 TRP cc_start: 0.4306 (p-90) cc_final: 0.3785 (p-90)
REVERT: O  148 ASP cc_start: 0.1743 (p0) cc_final: 0.1142 (p0)
REVERT: O  209 PHE cc_start: 0.7617 (p90) cc_final: 0.7127 (p90)
  outliers start: 17
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1149
  time to fit residues: 22.8108
Evaluate side-chains
  103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   63 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 146 optimal weight:    9.9990
   chunk 78 optimal weight:    0.0870
   chunk 148 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 101 optimal weight:   10.0000
   chunk 135 optimal weight:   30.0000
   chunk 60 optimal weight:    5.9990
   overall best weight:    2.5564

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

Flipped N/Q/H residues before XYZ refinement:
A 399 ASN
A 762 HIS
A 983 HIS
M  85 ASN
O 151 HIS
O 216 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.106676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.082271 restraints weight = 80547.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.083082 restraints weight = 45335.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.083144 restraints weight = 34179.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.083214 restraints weight = 29717.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.083461 restraints weight = 26087.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  16323  Z= 0.207
  Angle     :  0.723   9.638  23346  Z= 0.362
  Chirality :  0.040   0.231   2850
  Planarity :  0.006   0.046   2013
  Dihedral  : 24.031 177.180   5520
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.42 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.22 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.71 (0.22), residues: 1227
  helix:  0.35 (0.20), residues: 578
  sheet: -0.80 (0.45), residues: 116
  loop : -1.27 (0.24), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 901 
 TYR   0.015   0.002   TYR O 203 
 PHE   0.017   0.002   PHE A 928 
 TRP   0.016   0.002   TRP A 930 
 HIS   0.009   0.001   HIS A 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (16323)
  covalent geometry    : angle       0.72323 (23346)
  hydrogen bonds       : bond        0.06564 (  632)
  hydrogen bonds       : angle       4.50066 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LEU cc_start: 0.7740 (mt) cc_final: 0.7509 (mp)
REVERT: A 1038 ASP cc_start: 0.8070 (m-30) cc_final: 0.7684 (m-30)
REVERT: M   62 ILE cc_start: 0.7887 (mm) cc_final: 0.7534 (mm)
REVERT: M   63 MET cc_start: 0.9365 (mpp) cc_final: 0.8838 (mpp)
REVERT: M   66 PHE cc_start: 0.8774 (m-80) cc_final: 0.8240 (m-80)
REVERT: M  100 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7611 (mtm110)
REVERT: O   98 TRP cc_start: 0.5089 (p-90) cc_final: 0.4074 (p-90)
REVERT: O  203 TYR cc_start: 0.7799 (p90) cc_final: 0.7562 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1047
  time to fit residues: 17.2371
Evaluate side-chains
  95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 CYS
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain L residue   88 ILE
Chi-restraints excluded: chain M residue   40 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 140 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 96 optimal weight:   20.0000
   chunk 90 optimal weight:    1.9990
   chunk 123 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 609 HIS
A 762 HIS
A 969 ASN
A 983 HIS
O 151 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.105984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.079253 restraints weight = 80577.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.080898 restraints weight = 42449.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.081937 restraints weight = 30129.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.082313 restraints weight = 25228.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.082582 restraints weight = 23442.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.5376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115  16323  Z= 0.175
  Angle     :  0.641   8.975  23346  Z= 0.321
  Chirality :  0.037   0.208   2850
  Planarity :  0.005   0.057   2013
  Dihedral  : 24.110 176.109   5520
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.93 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.59 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.37 (0.23), residues: 1227
  helix:  0.66 (0.21), residues: 575
  sheet: -0.74 (0.45), residues: 125
  loop : -1.08 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 447 
 TYR   0.011   0.001   TYR A 562 
 PHE   0.016   0.002   PHE A 870 
 TRP   0.009   0.001   TRP A 547 
 HIS   0.006   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (16323)
  covalent geometry    : angle       0.64105 (23346)
  hydrogen bonds       : bond        0.05238 (  632)
  hydrogen bonds       : angle       4.23931 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.8736 (mt) cc_final: 0.8527 (mt)
REVERT: A  409 LEU cc_start: 0.7704 (mt) cc_final: 0.7316 (mt)
REVERT: A  536 LEU cc_start: 0.9485 (tp) cc_final: 0.9198 (tt)
REVERT: A 1038 ASP cc_start: 0.8059 (m-30) cc_final: 0.7678 (m-30)
REVERT: M   62 ILE cc_start: 0.7609 (mm) cc_final: 0.7184 (mm)
REVERT: M   63 MET cc_start: 0.9392 (mpp) cc_final: 0.9014 (mpp)
REVERT: M   66 PHE cc_start: 0.8579 (m-80) cc_final: 0.8035 (m-80)
REVERT: M   73 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.7818 (mmm160)
REVERT: O  151 HIS cc_start: 0.7507 (m-70) cc_final: 0.7277 (m170)
REVERT: O  209 PHE cc_start: 0.8435 (p90) cc_final: 0.7261 (p90)
  outliers start: 29
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1031
  time to fit residues: 17.4543
Evaluate side-chains
  96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  399 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  496 SER
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   67 VAL
Chi-restraints excluded: chain O residue  221 VAL
Chi-restraints excluded: chain O residue  233 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 52 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 114 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 134 optimal weight:   30.0000
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.105611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.079087 restraints weight = 80453.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.080603 restraints weight = 42201.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.081646 restraints weight = 29831.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.082096 restraints weight = 25034.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.082455 restraints weight = 23135.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.5893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16323  Z= 0.144
  Angle     :  0.606  10.382  23346  Z= 0.303
  Chirality :  0.036   0.219   2850
  Planarity :  0.004   0.047   2013
  Dihedral  : 24.051 178.235   5520
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.26 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.29 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.04 (0.23), residues: 1227
  helix:  0.93 (0.21), residues: 580
  sheet: -0.61 (0.46), residues: 126
  loop : -0.91 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  32 
 TYR   0.014   0.001   TYR A 168 
 PHE   0.015   0.001   PHE O 209 
 TRP   0.010   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16323)
  covalent geometry    : angle       0.60634 (23346)
  hydrogen bonds       : bond        0.04975 (  632)
  hydrogen bonds       : angle       4.14831 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.8722 (mt) cc_final: 0.8418 (mt)
REVERT: A 1038 ASP cc_start: 0.8057 (m-30) cc_final: 0.7654 (m-30)
REVERT: M   62 ILE cc_start: 0.7689 (mm) cc_final: 0.6918 (mt)
REVERT: M   63 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8896 (mpp)
REVERT: M   66 PHE cc_start: 0.8699 (m-80) cc_final: 0.8085 (m-80)
  outliers start: 17
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1060
  time to fit residues: 15.2233
Evaluate side-chains
  93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1033 LEU
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   63 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 54 optimal weight:    8.9990
   chunk 58 optimal weight:    8.9990
   chunk 83 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 137 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 104 optimal weight:    8.9990
   chunk 135 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 546 HIS
A 794 GLN
** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.099663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.075175 restraints weight = 79483.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.075260 restraints weight = 48174.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.075831 restraints weight = 36299.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.076531 restraints weight = 28057.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.076439 restraints weight = 26423.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.7209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072  16323  Z= 0.316
  Angle     :  0.859  10.319  23346  Z= 0.426
  Chirality :  0.045   0.262   2850
  Planarity :  0.006   0.060   2013
  Dihedral  : 24.663 178.556   5520
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.01 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.68 (0.23), residues: 1227
  helix:  0.20 (0.20), residues: 586
  sheet: -0.54 (0.53), residues: 103
  loop : -1.08 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG M  73 
 TYR   0.019   0.003   TYR A 846 
 PHE   0.023   0.003   PHE A 544 
 TRP   0.032   0.003   TRP O  98 
 HIS   0.009   0.002   HIS A 546 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 (16323)
  covalent geometry    : angle       0.85868 (23346)
  hydrogen bonds       : bond        0.08213 (  632)
  hydrogen bonds       : angle       5.10536 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 76
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.8771 (mt) cc_final: 0.8554 (mt)
REVERT: A  131 LEU cc_start: 0.8758 (tt) cc_final: 0.8278 (tp)
REVERT: A  873 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7519 (t)
REVERT: A 1038 ASP cc_start: 0.8166 (m-30) cc_final: 0.7737 (m-30)
REVERT: L   89 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7896 (mmp80)
REVERT: M   62 ILE cc_start: 0.7950 (mm) cc_final: 0.7145 (mm)
REVERT: M   63 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8699 (mpp)
REVERT: M   66 PHE cc_start: 0.8780 (m-80) cc_final: 0.7981 (m-80)
REVERT: O  233 LYS cc_start: 0.6077 (pttm) cc_final: 0.5668 (pptt)
  outliers start: 37
  outliers final: 25
  residues processed: 106
  average time/residue: 0.1265
  time to fit residues: 20.6220
Evaluate side-chains
  99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 ASN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  496 SER
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  664 VAL
Chi-restraints excluded: chain A residue  666 ASN
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  937 THR
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   63 MET
Chi-restraints excluded: chain O residue  121 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 143 optimal weight:   50.0000
   chunk 30 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A1023 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.103312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.078784 restraints weight = 79194.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.079244 restraints weight = 44960.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.079739 restraints weight = 33393.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.079937 restraints weight = 26998.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.079896 restraints weight = 24530.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.7191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16323  Z= 0.139
  Angle     :  0.626   9.741  23346  Z= 0.312
  Chirality :  0.036   0.255   2850
  Planarity :  0.004   0.043   2013
  Dihedral  : 24.277 172.586   5520
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.10 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.76 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.10 (0.23), residues: 1227
  helix:  0.71 (0.21), residues: 581
  sheet: -0.38 (0.50), residues: 118
  loop : -0.79 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  32 
 TYR   0.018   0.001   TYR A 168 
 PHE   0.011   0.001   PHE O 174 
 TRP   0.035   0.002   TRP A 137 
 HIS   0.003   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (16323)
  covalent geometry    : angle       0.62589 (23346)
  hydrogen bonds       : bond        0.05268 (  632)
  hydrogen bonds       : angle       4.40822 ( 1672)

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

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

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2454 Ramachandran restraints generated.
    1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.8846 (mt) cc_final: 0.8563 (mt)
REVERT: A  985 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8468 (mp)
REVERT: A 1038 ASP cc_start: 0.8076 (m-30) cc_final: 0.7653 (m-30)
REVERT: M   62 ILE cc_start: 0.7875 (mm) cc_final: 0.7036 (mm)
REVERT: M   63 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8630 (mpp)
REVERT: M   66 PHE cc_start: 0.8747 (m-80) cc_final: 0.7935 (m-80)
REVERT: O  233 LYS cc_start: 0.6431 (pttm) cc_final: 0.6043 (pptt)
  outliers start: 30
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0936
  time to fit residues: 15.0958
Evaluate side-chains
  97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  496 SER
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  566 THR
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  666 ASN
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  815 HIS
Chi-restraints excluded: chain A residue  835 SER
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1035 VAL
Chi-restraints excluded: chain A residue 1037 SER
Chi-restraints excluded: chain A residue 1088 THR
Chi-restraints excluded: chain A residue 1123 LEU
Chi-restraints excluded: chain M residue   40 VAL
Chi-restraints excluded: chain M residue   63 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
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: 61.9708 > 50:
  distance: 2 - 19:   5.062
  distance: 6 - 28:  17.479
  distance: 10 - 38:  18.755
  distance: 14 - 19:   4.643
  distance: 19 - 20:   3.201
  distance: 20 - 21:   6.961
  distance: 20 - 23:   3.945
  distance: 21 - 22:   7.901
  distance: 21 - 28:  15.196
  distance: 22 - 58:  16.732
  distance: 23 - 24:   5.337
  distance: 24 - 25:   6.213
  distance: 25 - 26:   5.127
  distance: 25 - 27:  14.069
  distance: 28 - 29:   5.877
  distance: 29 - 30:  14.372
  distance: 29 - 32:  12.589
  distance: 30 - 31:  18.083
  distance: 30 - 38:  13.409
  distance: 32 - 33:  10.988
  distance: 33 - 34:  12.784
  distance: 33 - 35:   7.884
  distance: 34 - 36:   6.348
  distance: 35 - 37:   9.608
  distance: 36 - 37:  11.902
  distance: 38 - 39:   6.219
  distance: 39 - 40:  10.728
  distance: 39 - 42:   3.333
  distance: 40 - 41:  12.654
  distance: 40 - 49:  16.942
  distance: 42 - 43:  12.431
  distance: 44 - 45:   9.386
  distance: 46 - 47:   3.125
  distance: 49 - 50:  21.298
  distance: 50 - 51:  27.325
  distance: 50 - 53:  29.599
  distance: 51 - 52:   6.058
  distance: 51 - 58:  23.550
  distance: 53 - 54:   8.116
  distance: 54 - 55:  17.859
  distance: 55 - 56:   6.946
  distance: 55 - 57:  10.162
  distance: 58 - 59:  12.053
  distance: 59 - 60:   4.091
  distance: 59 - 62:   3.210
  distance: 60 - 61:   9.789
  distance: 60 - 63:  15.635
  distance: 63 - 64:  27.080
  distance: 64 - 65:  29.382
  distance: 64 - 67:  23.643
  distance: 65 - 66:  11.858
  distance: 65 - 74:  13.068
  distance: 67 - 68:  22.284
  distance: 68 - 69:  25.780
  distance: 69 - 70:  22.528
  distance: 70 - 71:  20.166
  distance: 71 - 72:  23.412
  distance: 71 - 73:  17.814
  distance: 74 - 75:  19.353
  distance: 74 - 80:  40.548
  distance: 75 - 76:  18.125
  distance: 75 - 78:  26.849
  distance: 76 - 77:   9.678
  distance: 76 - 81:  15.209
  distance: 78 - 79:  41.224
  distance: 79 - 80:  40.274
  distance: 81 - 82:   7.809
  distance: 82 - 83:  11.925
  distance: 82 - 85:  25.034
  distance: 83 - 84:  28.991
  distance: 83 - 86:  16.212
  distance: 86 - 87:  16.992
  distance: 87 - 88:  19.685
  distance: 87 - 90:  27.550
  distance: 88 - 89:  10.793
  distance: 88 - 94:  25.003
  distance: 90 - 91:   6.256
  distance: 91 - 92:  30.967
  distance: 91 - 93:  23.354
  distance: 94 - 95:   8.082
  distance: 95 - 96:  13.708
  distance: 95 - 98:   7.767
  distance: 96 - 97:  14.300
  distance: 96 - 102:  22.755
  distance: 98 - 99:   9.215
  distance: 99 - 100:  11.107
  distance: 99 - 101:  18.125