Starting phenix.real_space_refine on Thu Jul 2 08:11:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.map" model { file = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c99_30309/07_2026/7c99_30309.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 27 5.49 5 S 33 5.16 5 C 4755 2.51 5 N 1341 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.25 Number of scatterers: 7656 At special positions: 0 Unit cell: (107.52, 78.12, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 27 15.00 O 1497 8.00 N 1341 7.00 C 4755 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: 0.61 Conformation dependent library (CDL) restraints added in 427.1 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 40.2% alpha, 11.9% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.697A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.560A pdb=" N ARG A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.269A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.502A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.697A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.500A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.024A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.562A pdb=" N ARG B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.934A pdb=" N LEU B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 removed outlier: 4.270A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.503A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.660A pdb=" N LYS C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.698A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.814A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.501A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 4.023A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.564A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.561A pdb=" N ARG C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.933A pdb=" N LEU C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR A 122 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN A 268 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 124 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 218 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE A 265 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 220 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR A 267 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 155 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 219 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.835A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR B 122 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN B 268 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 124 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 218 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE B 265 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 220 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 155 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 219 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.372A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS C 155 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 219 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 218 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N PHE C 265 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 220 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR C 267 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE C 222 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR C 122 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN C 268 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA C 124 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AA9, first strand: chain 'C' and resid 330 through 331 203 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.81 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: 2021 1.33 - 1.45: 1371 1.45 - 1.57: 4313 1.57 - 1.69: 51 1.69 - 1.81: 57 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 10525 4.51 - 9.02: 67 9.02 - 13.53: 5 13.53 - 18.04: 0 18.04 - 22.55: 3 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 104.40 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 104.41 22.54 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 105.31 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" N VAL A 184 " pdb=" CA VAL A 184 " pdb=" C VAL A 184 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 angle pdb=" N VAL B 184 " pdb=" CA VAL B 184 " pdb=" C VAL B 184 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.06e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4346 25.94 - 51.89: 273 51.89 - 77.83: 31 77.83 - 103.78: 12 103.78 - 129.72: 3 Dihedral angle restraints: 4665 sinusoidal: 2031 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN A 163 " pdb=" C ASN A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN B 163 " pdb=" C ASN B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 4662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 915 0.060 - 0.120: 243 0.120 - 0.180: 32 0.180 - 0.241: 1 0.241 - 0.301: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 317 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASP B 317 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 317 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 317 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP C 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP C 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 317 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C ASP A 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 318 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 29 2.40 - 3.03: 3868 3.03 - 3.65: 10308 3.65 - 4.28: 16421 4.28 - 4.90: 27920 Nonbonded interactions: 58546 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb=" NH2 ARG A 171 " model vdw 1.776 3.120 nonbonded pdb=" OD1 ASP B 168 " pdb=" NH2 ARG B 171 " model vdw 1.777 3.120 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.084 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.084 2.510 nonbonded pdb=" O2G ANP C 401 " pdb="CA CA C 402 " model vdw 2.099 2.510 ... (remaining 58541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } 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: 4.020 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.070 Find NCS groups from input model: 0.160 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 0.149 7813 Z= 0.423 Angle : 1.065 22.547 10600 Z= 0.592 Chirality : 0.054 0.301 1194 Planarity : 0.004 0.028 1290 Dihedral : 16.529 129.722 2973 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -5.91 (0.18), residues: 915 helix: -4.79 (0.09), residues: 384 sheet: -1.97 (0.34), residues: 162 loop : -3.63 (0.23), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 192 TYR 0.008 0.002 TYR B 260 PHE 0.028 0.003 PHE C 128 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.42 ( 7813) covalent geometry : angle 1.06481 / 0.59 (10600) hydrogen bonds : bond 0.32240 / 20.75 ( 219) hydrogen bonds : angle 9.96492 / 6.75 ( 590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8728 (m) cc_final: 0.8486 (t) REVERT: A 244 GLN cc_start: 0.8191 (mt0) cc_final: 0.7938 (mt0) REVERT: A 273 ASP cc_start: 0.7986 (t0) cc_final: 0.7747 (t70) REVERT: A 331 THR cc_start: 0.9030 (p) cc_final: 0.8795 (t) REVERT: B 94 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7987 (mmtp) REVERT: B 119 MET cc_start: 0.8618 (mtt) cc_final: 0.8339 (mtm) REVERT: B 202 LEU cc_start: 0.9130 (tp) cc_final: 0.8626 (tt) REVERT: B 314 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8577 (tttt) REVERT: C 123 GLU cc_start: 0.7574 (tt0) cc_final: 0.7350 (tt0) REVERT: C 155 LYS cc_start: 0.8574 (mttt) cc_final: 0.8241 (mtpt) REVERT: C 335 ILE cc_start: 0.8922 (mm) cc_final: 0.8561 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1179 time to fit residues: 37.3495 Evaluate side-chains 153 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 30 HIS A 261 ASN B 22 GLN B 30 HIS B 199 GLN B 243 GLN C 22 GLN C 30 HIS C 199 GLN C 243 GLN C 244 GLN C 291 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121188 restraints weight = 10465.468| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.08 r_work: 0.3139 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7813 Z= 0.144 Angle : 0.616 7.118 10600 Z= 0.343 Chirality : 0.046 0.171 1194 Planarity : 0.004 0.028 1290 Dihedral : 16.562 155.477 1215 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.98 % Allowed : 11.07 % Favored : 86.96 % 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: -4.54 (0.21), residues: 915 helix: -3.39 (0.18), residues: 387 sheet: -1.59 (0.35), residues: 159 loop : -3.05 (0.25), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 192 TYR 0.013 0.001 TYR B 194 PHE 0.017 0.002 PHE B 128 HIS 0.003 0.001 HIS C 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 7813) covalent geometry : angle 0.61594 / 0.34 (10600) hydrogen bonds : bond 0.06056 / 3.67 ( 219) hydrogen bonds : angle 5.24979 / 3.43 ( 590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8768 (m) cc_final: 0.8533 (m) REVERT: A 93 GLU cc_start: 0.8296 (mp0) cc_final: 0.7675 (mm-30) REVERT: A 151 TYR cc_start: 0.8694 (t80) cc_final: 0.8484 (t80) REVERT: A 194 TYR cc_start: 0.9087 (m-80) cc_final: 0.8620 (m-80) REVERT: A 268 ASN cc_start: 0.9166 (p0) cc_final: 0.8904 (p0) REVERT: A 324 ASN cc_start: 0.8742 (m-40) cc_final: 0.8467 (m110) REVERT: A 331 THR cc_start: 0.8986 (p) cc_final: 0.8772 (t) REVERT: B 119 MET cc_start: 0.9039 (mtt) cc_final: 0.8835 (mtm) REVERT: B 180 ASP cc_start: 0.8134 (m-30) cc_final: 0.7595 (t0) REVERT: C 119 MET cc_start: 0.8841 (mtt) cc_final: 0.8636 (mtt) REVERT: C 155 LYS cc_start: 0.8738 (mttt) cc_final: 0.8315 (mtpt) REVERT: C 335 ILE cc_start: 0.8961 (mm) cc_final: 0.8658 (mm) outliers start: 15 outliers final: 9 residues processed: 179 average time/residue: 0.0978 time to fit residues: 23.2949 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1941 > 50: distance: 13 - 33: 5.192 distance: 17 - 40: 11.492 distance: 26 - 27: 4.007 distance: 27 - 28: 4.840 distance: 27 - 30: 3.326 distance: 28 - 29: 14.846 distance: 28 - 33: 5.326 distance: 30 - 31: 12.383 distance: 30 - 32: 10.827 distance: 34 - 35: 7.742 distance: 34 - 37: 3.893 distance: 35 - 36: 16.859 distance: 35 - 40: 6.620 distance: 37 - 39: 6.910 distance: 41 - 42: 14.904 distance: 41 - 44: 7.343 distance: 42 - 43: 15.067 distance: 42 - 45: 19.237 distance: 45 - 46: 5.404 distance: 46 - 47: 6.959 distance: 46 - 49: 8.473 distance: 47 - 48: 3.634 distance: 49 - 50: 6.534 distance: 51 - 52: 3.005 distance: 51 - 53: 3.189 distance: 54 - 55: 9.758 distance: 55 - 56: 7.269 distance: 55 - 58: 17.692 distance: 56 - 57: 5.790 distance: 56 - 62: 3.229 distance: 58 - 59: 13.566 distance: 59 - 60: 5.230 distance: 59 - 61: 14.005 distance: 62 - 63: 8.504 distance: 62 - 68: 6.486 distance: 63 - 64: 17.707 distance: 63 - 66: 10.895 distance: 64 - 65: 5.267 distance: 64 - 69: 14.966 distance: 66 - 67: 4.401 distance: 67 - 68: 15.836 distance: 69 - 70: 7.647 distance: 70 - 71: 11.317 distance: 71 - 72: 3.277 distance: 71 - 73: 9.204 distance: 73 - 74: 6.546 distance: 74 - 75: 18.968 distance: 74 - 77: 15.606 distance: 75 - 76: 22.701 distance: 75 - 78: 24.147 distance: 78 - 79: 28.122 distance: 79 - 80: 14.934 distance: 80 - 81: 13.877 distance: 80 - 82: 20.023 distance: 82 - 83: 21.634 distance: 83 - 84: 11.242 distance: 84 - 85: 11.097 distance: 84 - 86: 16.902