Starting phenix.real_space_refine
on Fri Aug 22 13:26:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x12_21986/08_2025/6x12_21986.map"
  }
  resolution = 3.52
  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=   0.003
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       1      5.49       5
     S      18      5.16       5
     C    2019      2.51       5
     N     486      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  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: 3059
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3017
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 17, 'TRANS': 389}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
  Time building chain proxies: 0.85, per 1000 atoms: 0.28
  Number of scatterers: 3059
  At special positions: 0
  Unit cell: (67.6148, 79.4205, 69.7613, 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      18     16.00
     P       1     15.00
     O     535      8.00
     N     486      7.00
     C    2019      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: 0.16
  Conformation dependent library (CDL) restraints added in 97.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      86.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 12 through 32
      removed outlier: 3.791A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A  18 " --> pdb=" O   GLN A  14 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 43
      removed outlier: 3.518A  pdb=" N   THR A  41 " --> pdb=" O   HIS A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.535A  pdb=" N   LEU A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 71
      removed outlier: 3.784A  pdb=" N   ILE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 107
      removed outlier: 3.557A  pdb=" N   LEU A  90 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.635A  pdb=" N   LEU A 134 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 148
    Processing helix  chain 'A' and resid 150 through 170
      removed outlier: 3.526A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 220
      removed outlier: 3.631A  pdb=" N   VAL A 198 " --> pdb=" O   MET A 194 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY A 200 " --> pdb=" O   LYS A 196 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 222 through 254
      removed outlier: 3.827A  pdb=" N   LYS A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   THR A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 241 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   PHE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.617A  pdb=" N   PHE A 261 " --> pdb=" O   ASP A 257 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ALA A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 292
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.523A  pdb=" N   TYR A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      Proline residue:  A 304  - end of helix
      removed outlier: 3.725A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 328
      removed outlier: 4.277A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 322 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 349
      removed outlier: 4.078A  pdb=" N   THR A 340 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ILE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   THR A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 371
      removed outlier: 3.708A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL A 366 " --> pdb=" O   MET A 362 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   HIS A 368 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
    Processing helix  chain 'A' and resid 382 through 389
      removed outlier: 3.850A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 417
      removed outlier: 4.021A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    633 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.39

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 469
        1.31 -     1.43: 763
        1.43 -     1.56: 1835
        1.56 -     1.68: 14
        1.68 -     1.81: 34
  Bond restraints: 3115
  Sorted by residual:
  bond pdb=" C16 6OU A 501 "
       pdb=" O18 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.415 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C31 6OU A 501 "
       pdb=" O30 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.409 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" C39 6OU A 501 "
       pdb=" C40 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.497  1.569 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C15 6OU A 501 "
       pdb=" C16 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.501  1.563 -0.062 2.00e-02 2.50e+03 9.64e+00
  bond pdb=" C38 6OU A 501 "
       pdb=" C39 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.530  1.582 -0.052 2.00e-02 2.50e+03 6.85e+00
  ... (remaining 3110 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 4145
        2.96 -     5.93: 75
        5.93 -     8.89: 11
        8.89 -    11.86: 5
       11.86 -    14.82: 1
  Bond angle restraints: 4237
  Sorted by residual:
  angle pdb=" O22 6OU A 501 "
        pdb=" P23 6OU A 501 "
        pdb=" O26 6OU A 501 "
      ideal   model   delta    sigma   weight residual
      93.95  108.77  -14.82 3.00e+00 1.11e-01 2.44e+01
  angle pdb=" N   THR A 375 "
        pdb=" CA  THR A 375 "
        pdb=" C   THR A 375 "
      ideal   model   delta    sigma   weight residual
     114.04  108.42    5.62 1.24e+00 6.50e-01 2.05e+01
  angle pdb=" N   ALA A 205 "
        pdb=" CA  ALA A 205 "
        pdb=" C   ALA A 205 "
      ideal   model   delta    sigma   weight residual
     109.81  119.02   -9.21 2.21e+00 2.05e-01 1.74e+01
  angle pdb=" C   THR A 308 "
        pdb=" N   ILE A 309 "
        pdb=" CA  ILE A 309 "
      ideal   model   delta    sigma   weight residual
     122.95  118.55    4.40 1.24e+00 6.50e-01 1.26e+01
  angle pdb=" C   THR A 281 "
        pdb=" N   LEU A 282 "
        pdb=" CA  LEU A 282 "
      ideal   model   delta    sigma   weight residual
     120.09  124.47   -4.38 1.25e+00 6.40e-01 1.23e+01
  ... (remaining 4232 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.79: 1748
       27.79 -    55.58: 82
       55.58 -    83.38: 10
       83.38 -   111.17: 3
      111.17 -   138.96: 1
  Dihedral angle restraints: 1844
    sinusoidal: 689
      harmonic: 1155
  Sorted by residual:
  dihedral pdb=" C43 6OU A 501 "
           pdb=" C44 6OU A 501 "
           pdb=" C45 6OU A 501 "
           pdb=" C46 6OU A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.62  -39.66 -138.96     1      3.00e+01 1.11e-03 1.87e+01
  dihedral pdb=" C19 6OU A 501 "
           pdb=" C20 6OU A 501 "
           pdb=" C21 6OU A 501 "
           pdb=" O22 6OU A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00   35.22  -94.22     1      3.00e+01 1.11e-03 1.15e+01
  dihedral pdb=" CA  THR A 154 "
           pdb=" C   THR A 154 "
           pdb=" N   ILE A 155 "
           pdb=" CA  ILE A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.30   16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 1841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 413
       0.061 -    0.121: 96
       0.121 -    0.182: 17
       0.182 -    0.242: 2
       0.242 -    0.302: 2
  Chirality restraints: 530
  Sorted by residual:
  chirality pdb=" CB  ILE A 113 "
            pdb=" CA  ILE A 113 "
            pdb=" CG1 ILE A 113 "
            pdb=" CG2 ILE A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  ILE A 309 "
            pdb=" CA  ILE A 309 "
            pdb=" CG1 ILE A 309 "
            pdb=" CG2 ILE A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" C20 6OU A 501 "
            pdb=" C19 6OU A 501 "
            pdb=" C21 6OU A 501 "
            pdb=" O30 6OU A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.55   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 527 not shown)

  Planarity restraints: 516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 355 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 356 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 152 "    0.041 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO A 153 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 153 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 153 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 205 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 206 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "    0.034 5.00e-02 4.00e+02
  ... (remaining 513 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 966
        2.84 -     3.35: 2885
        3.35 -     3.87: 4958
        3.87 -     4.38: 5530
        4.38 -     4.90: 9590
  Nonbonded interactions: 23929
  Sorted by model distance:
  nonbonded pdb=" O   SER A 349 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   ILE A 392 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" NZ  LYS A  84 "
            pdb=" OE2 GLU A 416 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" OE1 GLU A 296 "
            pdb=" OH  TYR A 299 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OD2 ASP A 267 "
            pdb=" NH2 ARG A 287 "
     model   vdw
     2.424 3.120
  ... (remaining 23924 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.770
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.200
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
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      :  0.008   0.088   3115  Z= 0.355
  Angle     :  1.079  14.824   4237  Z= 0.580
  Chirality :  0.056   0.302    530
  Planarity :  0.008   0.063    516
  Dihedral  : 16.636 138.961   1112
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.29 (0.27), residues: 403
  helix: -3.21 (0.17), residues: 348
  sheet:  None (None), residues: 0
  loop : -3.27 (0.66), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.026   0.002   TYR A 299 
 PHE   0.010   0.002   PHE A 210 
 HIS   0.005   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00799 ( 3115)
  covalent geometry    : angle       1.07876 ( 4237)
  hydrogen bonds       : bond        0.18326 (  211)
  hydrogen bonds       : angle       6.52977 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7616 (mtt-85)
REVERT: A   37 HIS cc_start: 0.7841 (t70) cc_final: 0.7585 (p90)
REVERT: A  136 ASP cc_start: 0.8232 (m-30) cc_final: 0.7670 (m-30)
REVERT: A  316 LEU cc_start: 0.9196 (mt) cc_final: 0.8985 (mm)
REVERT: A  347 LEU cc_start: 0.9059 (tp) cc_final: 0.8818 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0657
  time to fit residues: 4.7391
Evaluate side-chains
  51 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 203 GLN
A 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.085815 restraints weight = 4607.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.088734 restraints weight = 2352.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.090673 restraints weight = 1577.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.091829 restraints weight = 1239.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.092592 restraints weight = 1073.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3115  Z= 0.177
  Angle     :  0.602   6.283   4237  Z= 0.310
  Chirality :  0.041   0.119    530
  Planarity :  0.005   0.039    516
  Dihedral  : 11.184  90.785    470
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.30 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.37), residues: 403
  helix: -1.37 (0.25), residues: 350
  sheet:  None (None), residues: 0
  loop : -2.29 (0.79), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 324 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 3115)
  covalent geometry    : angle       0.60203 ( 4237)
  hydrogen bonds       : bond        0.04681 (  211)
  hydrogen bonds       : angle       4.25706 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8243 (m-30) cc_final: 0.7725 (m-30)
REVERT: A  251 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7023 (mm)
REVERT: A  269 MET cc_start: 0.8301 (ttm) cc_final: 0.7822 (ttp)
REVERT: A  347 LEU cc_start: 0.9018 (tp) cc_final: 0.8817 (tt)
  outliers start: 10
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0584
  time to fit residues: 4.4170
Evaluate side-chains
  51 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.090686 restraints weight = 4457.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.093583 restraints weight = 2313.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.095676 restraints weight = 1584.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.096848 restraints weight = 1244.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.097610 restraints weight = 1081.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3115  Z= 0.146
  Angle     :  0.581   6.161   4237  Z= 0.296
  Chirality :  0.041   0.137    530
  Planarity :  0.004   0.033    516
  Dihedral  :  9.582  88.505    470
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 14.20 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.41), residues: 403
  helix: -0.46 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.09 (0.85), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A   5 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.003   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3115)
  covalent geometry    : angle       0.58121 ( 4237)
  hydrogen bonds       : bond        0.04207 (  211)
  hydrogen bonds       : angle       4.00486 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8210 (m-30) cc_final: 0.7690 (m-30)
REVERT: A  251 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7323 (mm)
REVERT: A  269 MET cc_start: 0.8285 (ttm) cc_final: 0.7815 (ttp)
  outliers start: 15
  outliers final: 11
  residues processed: 53
  average time/residue: 0.0378
  time to fit residues: 2.6409
Evaluate side-chains
  50 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
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: 62.5868 > 50:
  distance: 1 - 23:  30.031
  distance: 5 - 30:  37.072
  distance: 9 - 41:  20.615
  distance: 14 - 23:  27.593
  distance: 15 - 49:  21.532
  distance: 23 - 24:  25.707
  distance: 24 - 25:  41.713
  distance: 24 - 27:  30.967
  distance: 25 - 26:  62.587
  distance: 25 - 30:  51.601
  distance: 26 - 57:  47.505
  distance: 27 - 28:  17.489
  distance: 27 - 29:  45.859
  distance: 30 - 31:  25.038
  distance: 31 - 32:  39.390
  distance: 31 - 34:  35.853
  distance: 32 - 33:  21.364
  distance: 32 - 41:  21.262
  distance: 33 - 63:  26.698
  distance: 34 - 35:  29.350
  distance: 35 - 36:  19.578
  distance: 36 - 37:   7.561
  distance: 37 - 38:   3.626
  distance: 38 - 39:   3.875
  distance: 41 - 42:  32.861
  distance: 42 - 43:  49.188
  distance: 42 - 45:  21.711
  distance: 43 - 44:  30.318
  distance: 43 - 49:  43.956
  distance: 45 - 46:  19.679
  distance: 46 - 47:  10.568
  distance: 46 - 48:  13.124
  distance: 49 - 50:  22.175
  distance: 50 - 51:  30.008
  distance: 50 - 53:  26.622
  distance: 51 - 52:  18.556
  distance: 51 - 57:  20.865
  distance: 53 - 54:  18.017
  distance: 54 - 55:  25.620
  distance: 54 - 56:  25.045
  distance: 57 - 58:  38.332
  distance: 58 - 59:  41.480
  distance: 58 - 61:  27.088
  distance: 59 - 60:  11.431
  distance: 59 - 63:  15.501
  distance: 61 - 62:  39.243
  distance: 63 - 64:  25.188
  distance: 64 - 65:  39.828
  distance: 64 - 67:  20.770
  distance: 65 - 66:  31.483
  distance: 65 - 71:  35.674
  distance: 67 - 68:  38.099
  distance: 68 - 69:  15.512
  distance: 69 - 70:   8.667
  distance: 71 - 72:  44.996
  distance: 72 - 73:  47.775
  distance: 72 - 75:  22.109
  distance: 73 - 74:  19.139
  distance: 73 - 79:  40.215
  distance: 75 - 76:  43.516
  distance: 76 - 77:  35.342
  distance: 76 - 78:  44.859
  distance: 79 - 80:  31.992
  distance: 80 - 81:  24.758
  distance: 80 - 83:  18.379
  distance: 81 - 82:  42.298
  distance: 81 - 86:   8.456
  distance: 82 - 109:  33.143
  distance: 83 - 84:  34.945
  distance: 83 - 85:  31.751
  distance: 86 - 87:  28.425
  distance: 87 - 88:  26.534
  distance: 87 - 90:  28.027
  distance: 88 - 89:  29.191
  distance: 88 - 94:  27.288
  distance: 89 - 115:  27.283
  distance: 90 - 91:  54.663
  distance: 91 - 92:  46.066
  distance: 92 - 93:  54.075
  distance: 94 - 95:  18.749
  distance: 94 - 100:  41.958
  distance: 95 - 96:  38.144
  distance: 95 - 98:  39.491
  distance: 96 - 97:  38.837
  distance: 96 - 101:  13.666
  distance: 97 - 119:  27.458
  distance: 98 - 99:  12.508
  distance: 99 - 100:  24.976