Starting phenix.real_space_refine on Fri Dec 19 21:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.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 { model { file = "/net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm3_13511/12_2025/7pm3_13511.map" } resolution = 3.1 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= 0.001 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: 7 Type Number sf(0) Gaussians Br 3 7.06 5 P 9 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 5649 2.51 5 N 1494 2.21 5 O 1719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MG': 1, '9UE': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 8940 At special positions: 0 Unit cell: (89.1, 90.2, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 3 34.99 S 63 16.00 P 9 15.00 Mg 3 11.99 O 1719 8.00 N 1494 7.00 C 5649 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: 0.92 Conformation dependent library (CDL) restraints added in 351.0 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 49.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.770A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.671A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.509A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.695A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.208A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.026A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.577A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.340A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.500A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.770A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.648A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 263 Proline residue: C 258 - end of helix removed outlier: 4.758A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.175A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.065A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.572A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.372A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.648A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.556A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 263 Proline residue: D 258 - end of helix removed outlier: 4.727A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.270A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.072A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.533A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.355A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.092A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.446A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.199A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.576A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.126A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.504A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 432 hydrogen bonds defined for protein. 1113 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: 1.62 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2371 1.33 - 1.47: 2623 1.47 - 1.60: 4021 1.60 - 1.73: 9 1.73 - 1.86: 114 Bond restraints: 9138 Sorted by residual: bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" O3 PO4 B 402 " pdb=" P PO4 B 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" O3 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.19e+00 ... (remaining 9133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12013 2.45 - 4.90: 331 4.90 - 7.35: 51 7.35 - 9.80: 13 9.80 - 12.25: 6 Bond angle restraints: 12414 Sorted by residual: angle pdb=" CA MET D 44 " pdb=" CB MET D 44 " pdb=" CG MET D 44 " ideal model delta sigma weight residual 114.10 103.58 10.52 2.00e+00 2.50e-01 2.77e+01 angle pdb=" CB MET D 44 " pdb=" CG MET D 44 " pdb=" SD MET D 44 " ideal model delta sigma weight residual 112.70 124.95 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C20 9UE C 401 " pdb=" C8 9UE C 401 " pdb=" C7 9UE C 401 " ideal model delta sigma weight residual 118.25 106.55 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C20 9UE D 405 " pdb=" C8 9UE D 405 " pdb=" C7 9UE D 405 " ideal model delta sigma weight residual 118.25 106.97 11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N PHE B 127 " pdb=" CA PHE B 127 " pdb=" C PHE B 127 " ideal model delta sigma weight residual 109.50 103.74 5.76 1.58e+00 4.01e-01 1.33e+01 ... (remaining 12409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 5361 35.92 - 71.84: 87 71.84 - 107.76: 30 107.76 - 143.68: 21 143.68 - 179.61: 36 Dihedral angle restraints: 5535 sinusoidal: 2319 harmonic: 3216 Sorted by residual: dihedral pdb=" O1B ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " pdb=" PA ADP D 402 " ideal model delta sinusoidal sigma weight residual 300.00 168.79 131.21 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual 300.00 168.84 131.16 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.95 131.05 1 2.00e+01 2.50e-03 3.98e+01 ... (remaining 5532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1179 0.083 - 0.166: 173 0.166 - 0.250: 10 0.250 - 0.333: 3 0.333 - 0.416: 6 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C3 9UE D 405 " pdb=" O 9UE D 405 " pdb=" C2 9UE D 405 " pdb=" C35 9UE D 405 " both_signs ideal model delta sigma weight residual False 2.21 2.62 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C3 9UE C 401 " pdb=" O 9UE C 401 " pdb=" C2 9UE C 401 " pdb=" C35 9UE C 401 " both_signs ideal model delta sigma weight residual False 2.21 2.62 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C3 9UE D 401 " pdb=" O 9UE D 401 " pdb=" C2 9UE D 401 " pdb=" C35 9UE D 401 " both_signs ideal model delta sigma weight residual False 2.21 2.61 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1368 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 335 " 0.134 9.50e-02 1.11e+02 7.45e-02 2.63e+01 pdb=" NE ARG C 335 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 335 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 335 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 335 " 0.133 9.50e-02 1.11e+02 7.40e-02 2.63e+01 pdb=" NE ARG D 335 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 335 " 0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG D 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG D 335 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " 0.133 9.50e-02 1.11e+02 7.39e-02 2.60e+01 pdb=" NE ARG B 335 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " 0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.023 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 69 2.60 - 3.17: 7471 3.17 - 3.75: 13405 3.75 - 4.32: 19423 4.32 - 4.90: 32273 Nonbonded interactions: 72641 Sorted by model distance: nonbonded pdb=" O3B ADP D 402 " pdb="MG MG D 404 " model vdw 2.019 2.170 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR B 169 " pdb=" OH TYR D 53 " model vdw 2.258 3.040 nonbonded pdb=" NZ LYS B 18 " pdb=" O2B ADP B 401 " model vdw 2.292 3.120 nonbonded pdb=" OG SER B 234 " pdb=" OE1 GLU B 237 " model vdw 2.321 3.040 ... (remaining 72636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) } 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: 2.220 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.110 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.005 0.063 9138 Z= 0.252 Angle : 0.984 12.251 12414 Z= 0.518 Chirality : 0.062 0.416 1371 Planarity : 0.010 0.074 1578 Dihedral : 24.621 179.605 3477 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1098 helix: -1.68 (0.19), residues: 435 sheet: 0.13 (0.31), residues: 207 loop : 0.36 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.019 ARG D 335 TYR 0.029 0.006 TYR C 53 PHE 0.021 0.002 PHE D 262 TRP 0.020 0.003 TRP C 79 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 9138) covalent geometry : angle 0.98382 (12414) hydrogen bonds : bond 0.18269 ( 426) hydrogen bonds : angle 6.80154 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: C 47 MET cc_start: 0.6837 (tmm) cc_final: 0.6118 (tmm) REVERT: C 190 MET cc_start: 0.7621 (mtp) cc_final: 0.7396 (mtp) REVERT: C 269 MET cc_start: 0.7419 (mtt) cc_final: 0.7215 (mtm) REVERT: D 190 MET cc_start: 0.7986 (mtp) cc_final: 0.7655 (mtt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0949 time to fit residues: 20.2020 Evaluate side-chains 73 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081543 restraints weight = 14972.074| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.97 r_work: 0.3128 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9138 Z= 0.151 Angle : 0.716 9.046 12414 Z= 0.344 Chirality : 0.051 0.374 1371 Planarity : 0.005 0.046 1578 Dihedral : 29.146 175.036 1389 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.21 % Allowed : 3.83 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1098 helix: 0.42 (0.24), residues: 447 sheet: 0.28 (0.33), residues: 210 loop : 1.44 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 312 TYR 0.013 0.001 TYR B 143 PHE 0.024 0.002 PHE C 352 TRP 0.014 0.002 TRP D 356 HIS 0.007 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9138) covalent geometry : angle 0.71574 (12414) hydrogen bonds : bond 0.03693 ( 426) hydrogen bonds : angle 4.80026 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.294 Fit side-chains REVERT: C 47 MET cc_start: 0.7298 (tmm) cc_final: 0.6586 (tmm) REVERT: C 190 MET cc_start: 0.8584 (mtp) cc_final: 0.8359 (mtp) REVERT: D 47 MET cc_start: 0.7532 (tmm) cc_final: 0.6585 (tmm) REVERT: D 190 MET cc_start: 0.8626 (mtp) cc_final: 0.8305 (mtt) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.0663 time to fit residues: 8.6736 Evaluate side-chains 70 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078375 restraints weight = 15157.005| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.02 r_work: 0.3068 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9138 Z= 0.164 Angle : 0.667 8.833 12414 Z= 0.317 Chirality : 0.050 0.331 1371 Planarity : 0.005 0.044 1578 Dihedral : 27.110 178.555 1389 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.32 % Allowed : 5.96 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1098 helix: 0.95 (0.25), residues: 447 sheet: 0.39 (0.34), residues: 210 loop : 1.53 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 256 TYR 0.011 0.001 TYR B 143 PHE 0.013 0.002 PHE B 375 TRP 0.012 0.002 TRP D 356 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9138) covalent geometry : angle 0.66700 (12414) hydrogen bonds : bond 0.03816 ( 426) hydrogen bonds : angle 4.52291 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.353 Fit side-chains REVERT: B 206 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7551 (ttt180) REVERT: B 354 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 47 MET cc_start: 0.7271 (tmm) cc_final: 0.6842 (tmm) REVERT: C 269 MET cc_start: 0.7757 (mtm) cc_final: 0.7360 (mtm) REVERT: D 47 MET cc_start: 0.7444 (tmm) cc_final: 0.6498 (tmm) REVERT: D 190 MET cc_start: 0.8618 (mtp) cc_final: 0.8279 (mtt) REVERT: D 269 MET cc_start: 0.8479 (mtp) cc_final: 0.8155 (mtp) REVERT: D 305 MET cc_start: 0.8609 (mtp) cc_final: 0.8284 (mtm) outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 0.0783 time to fit residues: 9.5571 Evaluate side-chains 69 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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-2.0-5913/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: 53.6859 > 50: distance: 32 - 122: 32.194 distance: 35 - 119: 8.416 distance: 42 - 107: 13.928 distance: 45 - 104: 15.437 distance: 86 - 88: 6.820 distance: 89 - 90: 3.679 distance: 89 - 92: 15.603 distance: 90 - 91: 16.059 distance: 90 - 96: 5.690 distance: 92 - 93: 6.442 distance: 92 - 94: 12.583 distance: 93 - 95: 10.511 distance: 96 - 97: 4.680 distance: 97 - 98: 8.263 distance: 97 - 100: 4.283 distance: 98 - 99: 14.188 distance: 98 - 104: 16.306 distance: 100 - 101: 3.435 distance: 101 - 102: 9.630 distance: 101 - 103: 4.728 distance: 104 - 105: 8.195 distance: 105 - 106: 5.451 distance: 105 - 108: 7.694 distance: 106 - 107: 4.463 distance: 106 - 111: 12.844 distance: 108 - 109: 9.098 distance: 108 - 110: 7.424 distance: 111 - 112: 13.073 distance: 112 - 113: 6.949 distance: 112 - 115: 6.022 distance: 113 - 114: 24.728 distance: 113 - 119: 7.306 distance: 115 - 116: 4.987 distance: 116 - 117: 20.246 distance: 116 - 118: 13.835 distance: 119 - 120: 20.054 distance: 120 - 121: 10.076 distance: 120 - 123: 8.290 distance: 121 - 122: 33.662 distance: 121 - 128: 30.101 distance: 123 - 124: 26.487 distance: 124 - 125: 25.867 distance: 125 - 126: 10.370 distance: 126 - 127: 24.317 distance: 128 - 129: 21.616 distance: 129 - 130: 8.285 distance: 129 - 132: 10.354 distance: 130 - 131: 14.351 distance: 130 - 140: 15.382 distance: 132 - 133: 4.106 distance: 133 - 134: 10.790 distance: 133 - 135: 6.649 distance: 134 - 136: 6.276 distance: 135 - 137: 10.696 distance: 136 - 138: 7.661 distance: 137 - 138: 11.040 distance: 138 - 139: 7.159 distance: 140 - 141: 13.281 distance: 140 - 146: 16.445 distance: 141 - 142: 11.495 distance: 141 - 144: 19.389 distance: 142 - 143: 25.956 distance: 142 - 147: 14.331 distance: 144 - 145: 4.144 distance: 145 - 146: 41.412 distance: 147 - 148: 9.532 distance: 148 - 149: 11.425 distance: 148 - 151: 17.366 distance: 149 - 150: 22.211 distance: 149 - 155: 13.252 distance: 151 - 152: 5.125 distance: 151 - 153: 23.394 distance: 152 - 154: 18.449 distance: 155 - 156: 22.778 distance: 155 - 182: 18.225 distance: 156 - 157: 3.154 distance: 156 - 159: 9.262 distance: 157 - 164: 4.028 distance: 158 - 179: 9.401 distance: 159 - 160: 4.069 distance: 160 - 161: 4.452 distance: 164 - 165: 4.710 distance: 165 - 168: 4.194 distance: 168 - 169: 3.553 distance: 200 - 207: 3.257