Starting phenix.real_space_refine
on Thu Mar 13 03:18:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ia7_35297/03_2025/8ia7_35297.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5489      2.51       5
     N    1473      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8586
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2159
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 13, 'TRANS': 262}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2471
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 99
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1723
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 1802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1802
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 77
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.34, per 1000 atoms: 0.62
  Number of scatterers: 8586
  At special positions: 0
  Unit cell: (114.582, 114.582, 123.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1565      8.00
     N    1473      7.00
     C    5489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04

  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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.1% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'R' and resid 54 through 82
    Processing helix  chain 'R' and resid 87 through 108
      removed outlier: 3.787A  pdb=" N   ALA R  91 " --> pdb=" O   THR R  87 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE R  92 " --> pdb=" O   VAL R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 108 through 117
      Proline residue:  R 114  - end of helix
    Processing helix  chain 'R' and resid 122 through 158
      removed outlier: 4.370A  pdb=" N   ILE R 126 " --> pdb=" O   PHE R 122 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG R 158 " --> pdb=" O   SER R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 158 through 164
      removed outlier: 3.950A  pdb=" N   VAL R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 186
    Processing helix  chain 'R' and resid 187 through 192
    Processing helix  chain 'R' and resid 214 through 227
    Processing helix  chain 'R' and resid 227 through 248
      removed outlier: 3.920A  pdb=" N   GLY R 248 " --> pdb=" O   GLU R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 325 through 360
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 360 through 367
    Processing helix  chain 'R' and resid 370 through 391
      removed outlier: 3.523A  pdb=" N   PHE R 374 " --> pdb=" O   ALA R 370 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER R 382 " --> pdb=" O   LEU R 378 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ALA R 383 " --> pdb=" O   SER R 379 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS R 384 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      Proline residue:  R 387  - end of helix
    Processing helix  chain 'R' and resid 396 through 403
      removed outlier: 3.694A  pdb=" N   ALA R 400 " --> pdb=" O   ARG R 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.665A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.622A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 24
      removed outlier: 3.554A  pdb=" N   VAL C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.522A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.901A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 3.528A  pdb=" N   ILE A  56 " --> pdb=" O   GLN A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 269 through 277
      removed outlier: 3.587A  pdb=" N   LEU A 273 " --> pdb=" O   LYS A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 309
    Processing helix  chain 'A' and resid 329 through 350
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.817A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.735A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.966A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.583A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.957A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.551A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.049A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.282A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG E  98 " --> pdb=" O   PHE E 110 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.501A  pdb=" N   VAL E 135 " --> pdb=" O   LYS E 232 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148
    Processing sheet with id=AB4, first strand: chain 'A' and resid 183 through 190
      removed outlier: 4.231A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   MET A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   LEU A 223 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 8.685A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE A 220 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   PHE A 266 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   PHE A 222 " --> pdb=" O   PHE A 266 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ASN A 268 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL A 224 " --> pdb=" O   ASN A 268 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1161 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1742
        1.33 -     1.45: 2110
        1.45 -     1.57: 4826
        1.57 -     1.69: 1
        1.69 -     1.82: 87
  Bond restraints: 8766
  Sorted by residual:
  bond pdb=" O2  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.461  1.632 -0.171 2.00e-02 2.50e+03 7.35e+01
  bond pdb=" OH  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.534  0.145 2.00e-02 2.50e+03 5.29e+01
  bond pdb=" C   ALA R 352 "
       pdb=" O   ALA R 352 "
    ideal  model  delta    sigma   weight residual
    1.237  1.207  0.030 1.17e-02 7.31e+03 6.49e+00
  bond pdb=" CA  ASN R 353 "
       pdb=" C   ASN R 353 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 4.97e+00
  bond pdb=" CA  TRP R 355 "
       pdb=" C   TRP R 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.30e-02 5.92e+03 3.76e+00
  ... (remaining 8761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 11653
        2.02 -     4.05: 211
        4.05 -     6.07: 35
        6.07 -     8.10: 8
        8.10 -    10.12: 3
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   THR R 193 "
        pdb=" CA  THR R 193 "
        pdb=" C   THR R 193 "
      ideal   model   delta    sigma   weight residual
     108.56  118.68  -10.12 1.74e+00 3.30e-01 3.38e+01
  angle pdb=" CA  TYR R 189 "
        pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
      ideal   model   delta    sigma   weight residual
     120.58  116.55    4.03 7.40e-01 1.83e+00 2.97e+01
  angle pdb=" N   TYR E 161 "
        pdb=" CA  TYR E 161 "
        pdb=" C   TYR E 161 "
      ideal   model   delta    sigma   weight residual
     108.52  116.46   -7.94 1.74e+00 3.30e-01 2.08e+01
  angle pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
        pdb=" CA  PRO R 190 "
      ideal   model   delta    sigma   weight residual
     119.05  123.92   -4.87 1.11e+00 8.12e-01 1.93e+01
  angle pdb=" N   ASP L   7 "
        pdb=" CA  ASP L   7 "
        pdb=" C   ASP L   7 "
      ideal   model   delta    sigma   weight residual
     110.80  119.96   -9.16 2.13e+00 2.20e-01 1.85e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4728
       17.74 -    35.49: 393
       35.49 -    53.23: 48
       53.23 -    70.97: 4
       70.97 -    88.71: 1
  Dihedral angle restraints: 5174
    sinusoidal: 1924
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  TYR E 223 "
           pdb=" C   TYR E 223 "
           pdb=" N   PRO E 224 "
           pdb=" CA  PRO E 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.63   42.37     0      5.00e+00 4.00e-02 7.18e+01
  dihedral pdb=" CA  LEU R 203 "
           pdb=" C   LEU R 203 "
           pdb=" N   GLN R 204 "
           pdb=" CA  GLN R 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.25   26.75     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 313 "
           pdb=" C   ASP A 313 "
           pdb=" N   SER A 314 "
           pdb=" CA  SER A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5171 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1227
       0.070 -    0.139: 141
       0.139 -    0.209: 5
       0.209 -    0.278: 2
       0.278 -    0.348: 1
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  ASP L   7 "
            pdb=" N   ASP L   7 "
            pdb=" C   ASP L   7 "
            pdb=" CB  ASP L   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  THR R 193 "
            pdb=" N   THR R 193 "
            pdb=" C   THR R 193 "
            pdb=" CB  THR R 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  PHE L   8 "
            pdb=" N   PHE L   8 "
            pdb=" C   PHE L   8 "
            pdb=" CB  PHE L   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 223 "   -0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO E 224 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO E 224 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 224 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 188 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   PRO R 188 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PRO R 188 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR R 189 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 179 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   ARG E 179 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG E 179 "    0.009 2.00e-02 2.50e+03
        pdb=" N   MET E 180 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 797
        2.74 -     3.28: 8289
        3.28 -     3.82: 13600
        3.82 -     4.36: 16186
        4.36 -     4.90: 28937
  Nonbonded interactions: 67809
  Sorted by model distance:
  nonbonded pdb=" O   SER E 194 "
            pdb=" OG1 THR E 201 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER E 106 "
            pdb=" OG  SER E 106 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR R 189 "
            pdb=" OD2 ASP L   7 "
     model   vdw
     2.286 3.040
  ... (remaining 67804 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.200
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
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      :  0.004   0.171   8766  Z= 0.265
  Angle     :  0.727  10.122  11910  Z= 0.434
  Chirality :  0.045   0.348   1376
  Planarity :  0.004   0.062   1500
  Dihedral  : 12.552  88.713   3072
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.00 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.23), residues: 1101
  helix:  0.12 (0.26), residues: 357
  sheet: -1.07 (0.31), residues: 251
  loop : -2.99 (0.24), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 346 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.012   0.001   PHE A  49 
 TYR   0.015   0.001   TYR E  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.951 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7404 (m-80) cc_final: 0.7051 (m-80)
REVERT: R  244 GLU cc_start: 0.6481 (mp0) cc_final: 0.5780 (mp0)
REVERT: B  215 GLU cc_start: 0.7815 (tt0) cc_final: 0.7457 (tt0)
REVERT: B  304 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7867 (ttp-170)
REVERT: C   29 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8459 (mmtt)
REVERT: C   48 ASP cc_start: 0.8917 (t0) cc_final: 0.8705 (t0)
REVERT: E  103 TYR cc_start: 0.8681 (t80) cc_final: 0.8357 (t80)
REVERT: A  230 ASP cc_start: 0.8047 (m-30) cc_final: 0.7838 (m-30)
REVERT: L    6 MET cc_start: 0.7200 (ttt) cc_final: 0.6797 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2087
  time to fit residues: 51.4891
Evaluate side-chains
  143 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 45 optimal weight:    0.2980
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0770
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    0.3980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
R  72 ASN
R 204 GLN
R 353 ASN
B  32 GLN
E 167 GLN
E 174 GLN
A 293 GLN
A 311 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.164868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.124187 restraints weight = 10168.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 2.37
r_work: 0.3360 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8766  Z= 0.218
  Angle     :  0.583   7.774  11910  Z= 0.298
  Chirality :  0.043   0.229   1376
  Planarity :  0.004   0.053   1500
  Dihedral  :  4.704  42.784   1220
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.09 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.49 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.25), residues: 1101
  helix:  1.39 (0.27), residues: 363
  sheet: -0.72 (0.31), residues: 270
  loop : -2.52 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  63 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.015   0.002   TYR R 192 
 ARG   0.003   0.000   ARG E  18 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.867 
Fit side-chains
REVERT: R  189 TYR cc_start: 0.7900 (m-80) cc_final: 0.7402 (m-80)
REVERT: R  333 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6159 (ttp80)
REVERT: R  367 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6653 (pp)
REVERT: B  259 GLN cc_start: 0.8938 (pt0) cc_final: 0.8666 (pt0)
REVERT: C   29 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8373 (mmtt)
REVERT: E  103 TYR cc_start: 0.8918 (t80) cc_final: 0.8594 (t80)
REVERT: L    6 MET cc_start: 0.7146 (ttt) cc_final: 0.6867 (ttp)
  outliers start: 16
  outliers final: 10
  residues processed: 144
  average time/residue: 0.1951
  time to fit residues: 39.4393
Evaluate side-chains
  140 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  337 VAL
Chi-restraints excluded: chain R residue  367 LEU
Chi-restraints excluded: chain R residue  388 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  129 THR
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  198 THR
Chi-restraints excluded: chain E residue  226 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4077 > 50:
  distance: 53 - 58:   5.674
  distance: 58 - 59:   3.663
  distance: 59 - 60:   4.872
  distance: 60 - 61:  13.421
  distance: 61 - 160:  17.892
  distance: 63 - 65:   4.368
  distance: 64 - 66:   3.229
  distance: 65 - 67:   7.716
  distance: 67 - 69:   3.488
  distance: 68 - 70:   3.821
  distance: 69 - 71:   3.175
  distance: 70 - 71:   3.089
  distance: 72 - 224:   6.442
  distance: 73 - 76:   4.104
  distance: 74 - 75:   4.703
  distance: 74 - 83:   5.138
  distance: 75 - 221:   4.535
  distance: 76 - 77:   4.837
  distance: 77 - 78:   3.395
  distance: 83 - 147:   7.868
  distance: 84 - 85:   9.484
  distance: 84 - 87:   6.488
  distance: 85 - 86:  14.407
  distance: 85 - 91:  12.039
  distance: 86 - 144:   3.420
  distance: 87 - 88:   4.929
  distance: 91 - 92:   7.615
  distance: 91 - 206:   5.791
  distance: 92 - 93:  13.907
  distance: 92 - 95:   7.419
  distance: 93 - 100:  10.737
  distance: 94 - 203:  11.101
  distance: 95 - 96:   4.795
  distance: 96 - 97:   4.870
  distance: 97 - 98:   5.917
  distance: 97 - 99:   4.917
  distance: 100 - 101:   9.258
  distance: 101 - 102:   6.235
  distance: 101 - 104:  10.883
  distance: 102 - 103:  10.486
  distance: 102 - 111:  27.460
  distance: 104 - 105:  10.982
  distance: 106 - 107:   4.980
  distance: 107 - 108:   3.001
  distance: 111 - 112:  20.261
  distance: 111 - 117:  21.974
  distance: 112 - 113:   9.799
  distance: 112 - 115:   7.835
  distance: 113 - 114:  42.498
  distance: 113 - 118:   7.259
  distance: 115 - 116:  14.309
  distance: 116 - 117:  13.233
  distance: 118 - 119:  22.423
  distance: 119 - 120:  19.224
  distance: 120 - 121:  31.829
  distance: 120 - 122:  19.850
  distance: 122 - 123:   8.336
  distance: 123 - 124:  19.138
  distance: 123 - 126:   8.460
  distance: 124 - 125:  10.946
  distance: 124 - 131:   9.163
  distance: 126 - 127:   8.695
  distance: 127 - 128:  13.203
  distance: 128 - 129:   3.767
  distance: 128 - 130:   4.737
  distance: 131 - 132:   5.782
  distance: 132 - 133:  13.821
  distance: 132 - 135:  28.200
  distance: 133 - 134:  19.370
  distance: 133 - 137:   5.924
  distance: 135 - 136:  22.717
  distance: 137 - 138:   5.090
  distance: 137 - 143:  17.591
  distance: 138 - 139:   7.704
  distance: 138 - 141:  12.682
  distance: 139 - 140:   6.105
  distance: 139 - 144:   8.064
  distance: 141 - 142:  10.096
  distance: 142 - 143:  15.186