Starting phenix.real_space_refine on Fri Jul 3 12:27:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.map" model { file = "/net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7t_70208/07_2026/9o7t_70208.cif" } resolution = 3.26 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= 1.000 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 P 28 5.49 5 Mg 12 5.21 5 S 58 5.16 5 C 8758 2.51 5 N 2410 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 13958 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "E" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1687 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "F" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2515 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "G" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "H" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 5} Link IDs: {'rna2p': 5, 'rna3p': 5} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' MG': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13958 At special positions: 0 Unit cell: (117.975, 108.9, 106.425, 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) S 58 16.00 P 28 15.00 Mg 12 11.99 O 2692 8.00 N 2410 7.00 C 8758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 593.2 milliseconds 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 4 sheets defined 54.2% alpha, 11.0% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.636A pdb=" N MET A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.666A pdb=" N GLU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.888A pdb=" N TYR A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 3.622A pdb=" N SER A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.513A pdb=" N SER A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.506A pdb=" N ILE A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 289 removed outlier: 3.530A pdb=" N GLU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.569A pdb=" N GLU A 302 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.669A pdb=" N HIS B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 157 through 177 removed outlier: 3.741A pdb=" N SER B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.307A pdb=" N ALA B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 removed outlier: 4.456A pdb=" N ARG B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 216 through 233 removed outlier: 3.506A pdb=" N VAL B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 263 through 287 removed outlier: 3.539A pdb=" N CYS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.604A pdb=" N GLU B 302 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.645A pdb=" N GLN C 99 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 4.000A pdb=" N GLU C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.573A pdb=" N GLN C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.689A pdb=" N TYR C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 209 through 232 removed outlier: 7.913A pdb=" N HIS C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ILE C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.546A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 286 removed outlier: 3.866A pdb=" N GLU C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.594A pdb=" N ILE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 124 through 138 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.852A pdb=" N TYR D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 3.533A pdb=" N TYR D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 166 " --> pdb=" O HIS D 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 209 through 233 removed outlier: 8.087A pdb=" N HIS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 248 removed outlier: 4.272A pdb=" N MET D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 289 removed outlier: 3.874A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.559A pdb=" N HIS E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 138 through 143 removed outlier: 3.871A pdb=" N TYR E 143 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.706A pdb=" N SER E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.669A pdb=" N VAL E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 233 removed outlier: 7.789A pdb=" N HIS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ILE E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 263 through 287 removed outlier: 3.523A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.628A pdb=" N TYR F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 138 Processing helix chain 'F' and resid 138 through 143 removed outlier: 3.893A pdb=" N TYR F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 177 removed outlier: 3.656A pdb=" N SER F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 215 through 232 removed outlier: 4.197A pdb=" N SER F 219 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 289 removed outlier: 3.927A pdb=" N ILE F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 283 " --> pdb=" O MET F 279 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.533A pdb=" N GLY A 70 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 65 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 88 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS A 67 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 86 " --> pdb=" O HIS A 67 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 69 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 83 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR A 33 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLN A 24 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 35 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 22 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS A 37 " --> pdb=" O HIS A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 25 removed outlier: 5.610A pdb=" N VAL C 19 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN C 39 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 21 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS C 37 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 34 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 49 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N MET C 81 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU C 46 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL C 83 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LYS C 48 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLN C 85 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 69 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE C 86 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU C 88 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE C 65 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 16 through 24 removed outlier: 5.064A pdb=" N VAL D 19 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN D 39 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS D 21 " --> pdb=" O HIS D 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D 37 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N MET D 81 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU D 46 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL D 83 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS D 48 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLN D 85 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS D 69 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE D 86 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS D 67 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU D 88 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE D 65 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 12 through 13 removed outlier: 7.840A pdb=" N ILE F 65 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE F 86 " --> pdb=" O HIS F 67 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS F 69 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N MET F 81 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU F 46 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 83 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 48 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN F 85 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR F 27 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS F 21 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN F 39 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL F 19 " --> pdb=" O GLN F 39 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2283 1.31 - 1.43: 3839 1.43 - 1.56: 8009 1.56 - 1.68: 43 1.68 - 1.81: 104 Bond restraints: 14278 Sorted by residual: bond pdb=" CA SER D 160 " pdb=" CB SER D 160 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.56e-02 4.11e+03 2.17e+01 bond pdb=" CA TYR F 208 " pdb=" C TYR F 208 " ideal model delta sigma weight residual 1.527 1.468 0.059 1.35e-02 5.49e+03 1.91e+01 bond pdb=" C ARG F 243 " pdb=" O ARG F 243 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA ARG F 243 " pdb=" C ARG F 243 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.35e-02 5.49e+03 1.64e+01 bond pdb=" CA ALA A 148 " pdb=" CB ALA A 148 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.72e-02 3.38e+03 1.63e+01 ... (remaining 14273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 19186 3.02 - 6.04: 173 6.04 - 9.06: 22 9.06 - 12.08: 2 12.08 - 15.10: 1 Bond angle restraints: 19384 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 113.47 98.37 15.10 1.01e+00 9.80e-01 2.23e+02 angle pdb=" N VAL C 197 " pdb=" CA VAL C 197 " pdb=" C VAL C 197 " ideal model delta sigma weight residual 112.96 103.07 9.89 1.00e+00 1.00e+00 9.78e+01 angle pdb=" N VAL D 197 " pdb=" CA VAL D 197 " pdb=" C VAL D 197 " ideal model delta sigma weight residual 111.90 104.94 6.96 8.10e-01 1.52e+00 7.38e+01 angle pdb=" N HIS E 250 " pdb=" CA HIS E 250 " pdb=" C HIS E 250 " ideal model delta sigma weight residual 113.97 106.35 7.62 1.28e+00 6.10e-01 3.54e+01 angle pdb=" N HIS C 192 " pdb=" CA HIS C 192 " pdb=" C HIS C 192 " ideal model delta sigma weight residual 113.28 106.55 6.73 1.22e+00 6.72e-01 3.04e+01 ... (remaining 19379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.76: 8097 27.76 - 55.51: 459 55.51 - 83.27: 64 83.27 - 111.02: 6 111.02 - 138.78: 4 Dihedral angle restraints: 8630 sinusoidal: 3728 harmonic: 4902 Sorted by residual: dihedral pdb=" C5' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" O3' A H 6 " ideal model delta sinusoidal sigma weight residual 147.00 95.12 51.88 1 8.00e+00 1.56e-02 5.74e+01 dihedral pdb=" O4' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" C2' A H 6 " ideal model delta sinusoidal sigma weight residual 24.00 -21.38 45.38 1 8.00e+00 1.56e-02 4.46e+01 dihedral pdb=" C5' U H 7 " pdb=" C4' U H 7 " pdb=" C3' U H 7 " pdb=" O3' U H 7 " ideal model delta sinusoidal sigma weight residual 147.00 107.42 39.58 1 8.00e+00 1.56e-02 3.44e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2071 0.110 - 0.221: 63 0.221 - 0.331: 7 0.331 - 0.442: 5 0.442 - 0.552: 10 Chirality restraints: 2156 Sorted by residual: chirality pdb=" P U H 5 " pdb=" OP1 U H 5 " pdb=" OP2 U H 5 " pdb=" O5' U H 5 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" P U H 7 " pdb=" OP1 U H 7 " pdb=" OP2 U H 7 " pdb=" O5' U H 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" P U G 5 " pdb=" OP1 U G 5 " pdb=" OP2 U G 5 " pdb=" O5' U G 5 " both_signs ideal model delta sigma weight residual True 2.41 2.94 -0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 2153 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 146 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C PRO F 146 " -0.051 2.00e-02 2.50e+03 pdb=" O PRO F 146 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA F 147 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 260 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO D 261 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 152 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C HIS C 152 " -0.048 2.00e-02 2.50e+03 pdb=" O HIS C 152 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS C 153 " 0.016 2.00e-02 2.50e+03 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 63 2.39 - 3.02: 7246 3.02 - 3.65: 20267 3.65 - 4.27: 31307 4.27 - 4.90: 53326 Nonbonded interactions: 112209 Sorted by model distance: nonbonded pdb=" NE2 HIS F 162 " pdb="MG MG F 401 " model vdw 1.767 2.250 nonbonded pdb=" NE2 HIS E 249 " pdb="MG MG E 401 " model vdw 1.816 2.250 nonbonded pdb=" NE2 HIS B 249 " pdb="MG MG B 401 " model vdw 1.877 2.250 nonbonded pdb=" CE1 HIS C 162 " pdb="MG MG C 403 " model vdw 1.882 2.390 nonbonded pdb="MG MG F 401 " pdb=" O1 PO4 F 402 " model vdw 1.898 2.170 ... (remaining 112204 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.140 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 0.073 14278 Z= 0.329 Angle : 0.718 15.097 19384 Z= 0.453 Chirality : 0.061 0.552 2156 Planarity : 0.004 0.072 2398 Dihedral : 16.838 138.780 5478 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.74 % Favored : 96.14 % Rotamer: Outliers : 1.16 % Allowed : 1.02 % Favored : 97.81 % 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: -1.86 (0.19), residues: 1658 helix: -1.36 (0.16), residues: 780 sheet: -1.07 (0.33), residues: 238 loop : -0.82 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 243 TYR 0.011 0.001 TYR D 75 PHE 0.023 0.001 PHE E 299 TRP 0.010 0.001 TRP D 50 HIS 0.012 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.33 (14278) covalent geometry : angle 0.71844 / 0.45 (19384) hydrogen bonds : bond 0.29267 / 19.97 ( 607) hydrogen bonds : angle 8.28291 / 5.73 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.479 Fit side-chains REVERT: B 299 PHE cc_start: 0.8359 (t80) cc_final: 0.8155 (t80) REVERT: C 196 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8514 (mtpp) outliers start: 17 outliers final: 7 residues processed: 184 average time/residue: 0.1178 time to fit residues: 32.5190 Evaluate side-chains 153 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain F residue 149 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 68.7476 > 50: distance: 27 - 35: 22.603 distance: 35 - 36: 7.494 distance: 36 - 37: 11.434 distance: 36 - 39: 31.036 distance: 37 - 38: 18.638 distance: 37 - 45: 20.956 distance: 39 - 40: 16.742 distance: 40 - 41: 25.373 distance: 40 - 42: 17.132 distance: 41 - 43: 34.575 distance: 42 - 44: 29.575 distance: 43 - 44: 14.545 distance: 45 - 46: 17.860 distance: 46 - 47: 23.261 distance: 47 - 48: 32.473 distance: 47 - 49: 41.876 distance: 49 - 50: 51.088 distance: 50 - 51: 48.488 distance: 50 - 53: 12.520 distance: 51 - 52: 4.152 distance: 51 - 58: 13.897 distance: 53 - 54: 32.109 distance: 54 - 55: 43.192 distance: 55 - 56: 28.944 distance: 56 - 57: 33.508 distance: 58 - 59: 46.300 distance: 59 - 60: 23.763 distance: 59 - 62: 21.336 distance: 60 - 61: 5.255 distance: 60 - 66: 13.768 distance: 62 - 63: 25.811 distance: 63 - 64: 13.560 distance: 63 - 65: 46.736 distance: 66 - 67: 12.600 distance: 67 - 68: 18.185 distance: 67 - 70: 43.839 distance: 68 - 69: 25.476 distance: 68 - 75: 24.660 distance: 70 - 71: 18.338 distance: 71 - 72: 34.170 distance: 72 - 73: 8.766 distance: 72 - 74: 11.539 distance: 75 - 76: 21.997 distance: 76 - 77: 24.620 distance: 76 - 79: 23.261 distance: 77 - 78: 46.166 distance: 77 - 87: 17.242 distance: 79 - 80: 26.433 distance: 80 - 81: 18.227 distance: 80 - 82: 30.424 distance: 81 - 83: 21.734 distance: 82 - 84: 41.725 distance: 83 - 85: 34.247 distance: 84 - 85: 20.752 distance: 85 - 86: 26.623 distance: 87 - 88: 34.109 distance: 88 - 89: 23.839 distance: 89 - 90: 49.059 distance: 89 - 91: 35.592 distance: 91 - 92: 3.361 distance: 92 - 95: 42.390 distance: 93 - 94: 38.273 distance: 93 - 97: 18.363 distance: 95 - 96: 41.171 distance: 97 - 98: 23.685 distance: 97 - 103: 34.440 distance: 98 - 99: 30.775 distance: 98 - 101: 24.699 distance: 99 - 100: 41.006 distance: 101 - 102: 29.264 distance: 102 - 103: 24.733 distance: 104 - 105: 56.708 distance: 105 - 106: 41.830 distance: 105 - 108: 19.359 distance: 106 - 107: 39.627 distance: 106 - 113: 34.744 distance: 108 - 109: 21.018 distance: 109 - 110: 55.550 distance: 110 - 111: 43.945 distance: 111 - 112: 44.797 distance: 149 - 159: 3.096