Starting phenix.real_space_refine on Fri Jun 13 22:15:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.map" model { file = "/net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cno_7539/06_2025/6cno_7539.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 108 5.16 5 C 9884 2.51 5 N 2744 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15428 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: G, F, H, C, B, D Time building chain proxies: 7.25, per 1000 atoms: 0.47 Number of scatterers: 15428 At special positions: 0 Unit cell: (116.39, 116.39, 106.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 108 16.00 O 2680 8.00 N 2744 7.00 C 9884 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: 3.96 Conformation dependent library (CDL) restraints added in 2.0 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 75.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 162 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.630A pdb=" N GLY A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 3.935A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 367 removed outlier: 4.221A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'B' and resid 9 through 49 removed outlier: 3.599A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 162 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.345A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 Processing helix chain 'C' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 162 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'D' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 162 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 367 removed outlier: 4.220A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 386 Processing helix chain 'E' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 92 Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.671A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id=A, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=B, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=D, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=E, first strand: chain 'G' and resid 26 through 27 Processing sheet with id=F, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=G, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=H, first strand: chain 'H' and resid 99 through 101 1076 hydrogen bonds defined for protein. 3204 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: 4.18 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4963 1.34 - 1.46: 2695 1.46 - 1.57: 7850 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15696 Sorted by residual: bond pdb=" CG1 ILE C 244 " pdb=" CD1 ILE C 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE D 244 " pdb=" CD1 ILE D 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE B 244 " pdb=" CD1 ILE B 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE A 244 " pdb=" CD1 ILE A 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CA ALA D 220 " pdb=" CB ALA D 220 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.59e-02 3.96e+03 1.97e+00 ... (remaining 15691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 20070 1.94 - 3.89: 946 3.89 - 5.83: 152 5.83 - 7.77: 48 7.77 - 9.71: 16 Bond angle restraints: 21232 Sorted by residual: angle pdb=" C ASP F 64 " pdb=" N PHE F 65 " pdb=" CA PHE F 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP E 64 " pdb=" N PHE E 65 " pdb=" CA PHE E 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP G 64 " pdb=" N PHE G 65 " pdb=" CA PHE G 65 " ideal model delta sigma weight residual 120.58 127.16 -6.58 1.32e+00 5.74e-01 2.49e+01 angle pdb=" C ASP H 64 " pdb=" N PHE H 65 " pdb=" CA PHE H 65 " ideal model delta sigma weight residual 120.58 127.13 -6.55 1.32e+00 5.74e-01 2.46e+01 angle pdb=" C THR E 5 " pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 120.28 124.98 -4.70 1.34e+00 5.57e-01 1.23e+01 ... (remaining 21227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.69: 8093 9.69 - 19.37: 991 19.37 - 29.06: 124 29.06 - 38.74: 96 38.74 - 48.43: 16 Dihedral angle restraints: 9320 sinusoidal: 3512 harmonic: 5808 Sorted by residual: dihedral pdb=" CA GLU F 114 " pdb=" C GLU F 114 " pdb=" N LYS F 115 " pdb=" CA LYS F 115 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N LYS E 115 " pdb=" CA LYS E 115 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU G 114 " pdb=" C GLU G 114 " pdb=" N LYS G 115 " pdb=" CA LYS G 115 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1592 0.044 - 0.088: 694 0.088 - 0.131: 159 0.131 - 0.175: 27 0.175 - 0.219: 8 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 377 " pdb=" CA ILE B 377 " pdb=" CG1 ILE B 377 " pdb=" CG2 ILE B 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE C 377 " pdb=" CA ILE C 377 " pdb=" CG1 ILE C 377 " pdb=" CG2 ILE C 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2477 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 189 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.43e+00 pdb=" C ARG C 189 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG C 189 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 190 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 189 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ARG A 189 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 189 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 190 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 369 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C VAL C 369 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL C 369 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP C 370 " 0.014 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 251 2.53 - 3.12: 11797 3.12 - 3.71: 24852 3.71 - 4.31: 32150 4.31 - 4.90: 51120 Nonbonded interactions: 120170 Sorted by model distance: nonbonded pdb=" OD1 ASP E 93 " pdb=" OD1 ASN E 97 " model vdw 1.936 3.040 nonbonded pdb=" OD1 ASP H 93 " pdb=" OD1 ASN H 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP G 93 " pdb=" OD1 ASN G 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP F 93 " pdb=" OD1 ASN F 97 " model vdw 1.937 3.040 nonbonded pdb=" OD2 ASP F 24 " pdb="CA CA F 201 " model vdw 1.939 2.510 ... (remaining 120165 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: 0.12 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 34.130 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.006 0.066 15696 Z= 0.324 Angle : 1.029 9.714 21232 Z= 0.595 Chirality : 0.049 0.219 2480 Planarity : 0.006 0.054 2660 Dihedral : 9.243 48.428 5560 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.26 % Allowed : 0.53 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.15), residues: 2000 helix: -1.61 (0.10), residues: 1528 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 221 HIS 0.011 0.003 HIS A 80 PHE 0.017 0.003 PHE G 92 TYR 0.022 0.003 TYR D 307 ARG 0.007 0.001 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.13878 ( 1076) hydrogen bonds : angle 6.37617 ( 3204) covalent geometry : bond 0.00619 (15696) covalent geometry : angle 1.02937 (21232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9065 (tp) cc_final: 0.8852 (tp) REVERT: E 9 ILE cc_start: 0.9586 (mt) cc_final: 0.9346 (mt) REVERT: E 16 PHE cc_start: 0.9531 (t80) cc_final: 0.9146 (t80) REVERT: E 48 LEU cc_start: 0.9689 (mt) cc_final: 0.9402 (tt) REVERT: E 54 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8136 (mt-10) REVERT: E 68 PHE cc_start: 0.9296 (t80) cc_final: 0.9017 (t80) REVERT: E 74 ARG cc_start: 0.8871 (mtm110) cc_final: 0.8536 (mtm-85) REVERT: E 75 LYS cc_start: 0.9330 (mmtt) cc_final: 0.8782 (mmmt) REVERT: E 90 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9100 (ttm110) REVERT: E 92 PHE cc_start: 0.8926 (m-10) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1871 time to fit residues: 13.1392 Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.116 Evaluate side-chains 149 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9531 (mt) cc_final: 0.9146 (pp) REVERT: A 22 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 82 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9067 (mmmm) REVERT: A 87 PHE cc_start: 0.9171 (t80) cc_final: 0.8950 (t80) REVERT: A 176 ASN cc_start: 0.9284 (t0) cc_final: 0.8677 (t0) REVERT: A 179 TYR cc_start: 0.9090 (m-80) cc_final: 0.8337 (m-10) REVERT: A 186 ASN cc_start: 0.9406 (t0) cc_final: 0.9183 (t0) REVERT: A 194 PHE cc_start: 0.8762 (t80) cc_final: 0.8096 (t80) REVERT: A 200 MET cc_start: 0.9434 (ttm) cc_final: 0.8812 (tpp) REVERT: A 201 ASN cc_start: 0.9348 (m-40) cc_final: 0.9076 (p0) REVERT: A 261 MET cc_start: 0.8292 (tmm) cc_final: 0.7964 (mmt) REVERT: A 273 MET cc_start: 0.9087 (mtm) cc_final: 0.8842 (ptt) REVERT: A 278 THR cc_start: 0.9168 (m) cc_final: 0.8927 (p) REVERT: A 288 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8381 (tmtt) REVERT: A 292 ASN cc_start: 0.9399 (t0) cc_final: 0.9183 (t0) REVERT: A 303 MET cc_start: 0.8791 (mmm) cc_final: 0.8500 (mmm) REVERT: A 309 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9184 (ttmm) REVERT: A 312 LYS cc_start: 0.9498 (mttm) cc_final: 0.9137 (tmtt) REVERT: A 321 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8504 (tp30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1903 time to fit residues: 32.2190 Evaluate side-chains 90 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.0000 chunk 116 optimal weight: 0.0670 chunk 181 optimal weight: 0.1980 overall best weight: 0.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.050940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041073 restraints weight = 5736.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.042732 restraints weight = 3562.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.043948 restraints weight = 2482.393| |-----------------------------------------------------------------------------| r_work (final): 0.2748 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071934 restraints weight = 11606.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073952 restraints weight = 6866.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075268 restraints weight = 4805.597| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.880 15696 Z= 1.151 Angle : 0.796 21.855 21232 Z= 0.404 Chirality : 0.037 0.121 2480 Planarity : 0.004 0.044 2660 Dihedral : 5.425 25.404 2168 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2000 helix: 0.34 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.30 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 242 HIS 0.004 0.001 HIS C 328 PHE 0.026 0.002 PHE G 89 TYR 0.014 0.001 TYR H 138 ARG 0.007 0.001 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 1076) hydrogen bonds : angle 4.51939 ( 3204) covalent geometry : bond 0.03285 (15696) covalent geometry : angle 0.79640 (21232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.9611 (tppt) cc_final: 0.9296 (mmmm) REVERT: H 16 PHE cc_start: 0.9618 (t80) cc_final: 0.9073 (t80) REVERT: H 36 MET cc_start: 0.9414 (tpt) cc_final: 0.9158 (mmm) REVERT: H 48 LEU cc_start: 0.9786 (mt) cc_final: 0.9503 (tt) REVERT: H 51 MET cc_start: 0.9074 (tpp) cc_final: 0.8829 (tpp) REVERT: H 54 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8531 (mt-10) REVERT: H 74 ARG cc_start: 0.9231 (mtm110) cc_final: 0.8787 (mtm-85) REVERT: H 75 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8572 (mttt) REVERT: H 84 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8251 (mm-30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1798 time to fit residues: 12.8268 Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.110 Evaluate side-chains 125 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9670 (mt) cc_final: 0.9282 (pp) REVERT: A 19 LEU cc_start: 0.9617 (mt) cc_final: 0.9314 (mt) REVERT: A 82 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9083 (mmmt) REVERT: A 111 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 115 CYS cc_start: 0.9330 (t) cc_final: 0.8723 (p) REVERT: A 186 ASN cc_start: 0.9407 (t0) cc_final: 0.9187 (t0) REVERT: A 194 PHE cc_start: 0.8956 (t80) cc_final: 0.8711 (t80) REVERT: A 198 LEU cc_start: 0.9263 (mt) cc_final: 0.8799 (mt) REVERT: A 200 MET cc_start: 0.9497 (ttm) cc_final: 0.9066 (tpp) REVERT: A 201 ASN cc_start: 0.9475 (m-40) cc_final: 0.9160 (p0) REVERT: A 207 LEU cc_start: 0.8967 (mt) cc_final: 0.8498 (pp) REVERT: A 261 MET cc_start: 0.8550 (tmm) cc_final: 0.8172 (mmt) REVERT: A 264 LYS cc_start: 0.7933 (mttt) cc_final: 0.7636 (tttp) REVERT: A 270 THR cc_start: 0.8815 (p) cc_final: 0.8511 (p) REVERT: A 273 MET cc_start: 0.9219 (mtm) cc_final: 0.8798 (ptp) REVERT: A 288 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8740 (tmtt) REVERT: A 292 ASN cc_start: 0.9674 (t0) cc_final: 0.9250 (t0) REVERT: A 303 MET cc_start: 0.9301 (mmm) cc_final: 0.8852 (mmp) REVERT: A 309 LYS cc_start: 0.9657 (ttpt) cc_final: 0.9327 (ttmm) REVERT: A 310 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9070 (mt-10) REVERT: A 320 GLN cc_start: 0.9172 (tt0) cc_final: 0.8963 (pp30) REVERT: A 321 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8346 (tp30) REVERT: A 324 MET cc_start: 0.9593 (tpt) cc_final: 0.9229 (tpp) REVERT: A 343 LYS cc_start: 0.9608 (mttt) cc_final: 0.9118 (mptt) REVERT: A 359 ARG cc_start: 0.8708 (ttt180) cc_final: 0.8076 (ttp80) REVERT: A 364 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9327 (tp-100) REVERT: A 373 LYS cc_start: 0.7654 (pttp) cc_final: 0.7304 (pttm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1748 time to fit residues: 25.0462 Evaluate side-chains 91 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 165 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 141 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.042105 restraints weight = 6085.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043815 restraints weight = 3663.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.044988 restraints weight = 2483.868| |-----------------------------------------------------------------------------| r_work (final): 0.2765 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071831 restraints weight = 11527.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073913 restraints weight = 6668.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075248 restraints weight = 4633.459| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.916 15696 Z= 1.165 Angle : 0.860 19.037 21232 Z= 0.434 Chirality : 0.043 0.398 2480 Planarity : 0.006 0.070 2660 Dihedral : 5.460 23.610 2168 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.53 % Allowed : 3.69 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2000 helix: 0.96 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.30 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP D 242 HIS 0.005 0.001 HIS D 340 PHE 0.027 0.003 PHE D 144 TYR 0.025 0.003 TYR C 253 ARG 0.019 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 1076) hydrogen bonds : angle 4.42679 ( 3204) covalent geometry : bond 0.03330 (15696) covalent geometry : angle 0.85967 (21232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4 LEU cc_start: 0.8971 (tp) cc_final: 0.8122 (tp) REVERT: G 8 GLN cc_start: 0.9448 (mp10) cc_final: 0.9247 (mp10) REVERT: G 12 PHE cc_start: 0.9657 (m-80) cc_final: 0.9137 (m-80) REVERT: G 16 PHE cc_start: 0.9648 (t80) cc_final: 0.9024 (t80) REVERT: G 36 MET cc_start: 0.9516 (tpt) cc_final: 0.9181 (tpt) REVERT: G 39 LEU cc_start: 0.9012 (mm) cc_final: 0.8810 (mm) REVERT: G 48 LEU cc_start: 0.9779 (mt) cc_final: 0.9505 (tt) REVERT: G 51 MET cc_start: 0.9149 (tpp) cc_final: 0.8795 (tpp) REVERT: G 54 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8475 (mt-10) REVERT: G 75 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8243 (mttt) REVERT: G 86 ARG cc_start: 0.9404 (ttm170) cc_final: 0.9172 (ttm170) REVERT: G 92 PHE cc_start: 0.8726 (m-10) cc_final: 0.8253 (m-80) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1960 time to fit residues: 13.5855 Evaluate side-chains 50 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.135 Evaluate side-chains 112 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LEU cc_start: 0.9573 (mt) cc_final: 0.9169 (mm) REVERT: B 22 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8929 (mt-10) REVERT: B 82 LYS cc_start: 0.9472 (mmtt) cc_final: 0.9051 (mmmm) REVERT: B 176 ASN cc_start: 0.9476 (t0) cc_final: 0.9208 (t0) REVERT: B 179 TYR cc_start: 0.8589 (m-80) cc_final: 0.8310 (m-80) REVERT: B 186 ASN cc_start: 0.9256 (t0) cc_final: 0.9045 (t0) REVERT: B 198 LEU cc_start: 0.9259 (mt) cc_final: 0.8755 (mt) REVERT: B 201 ASN cc_start: 0.9465 (m-40) cc_final: 0.9087 (p0) REVERT: B 261 MET cc_start: 0.8499 (tmm) cc_final: 0.8135 (mmt) REVERT: B 270 THR cc_start: 0.8954 (p) cc_final: 0.8597 (p) REVERT: B 273 MET cc_start: 0.9282 (mtm) cc_final: 0.8931 (ptp) REVERT: B 295 GLU cc_start: 0.9419 (mp0) cc_final: 0.9196 (mp0) REVERT: B 303 MET cc_start: 0.9334 (mmm) cc_final: 0.8793 (mmm) REVERT: B 309 LYS cc_start: 0.9619 (ttpt) cc_final: 0.9318 (ttmm) REVERT: B 310 GLU cc_start: 0.9235 (mt-10) cc_final: 0.9021 (mt-10) REVERT: B 321 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8325 (tp30) REVERT: B 359 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8027 (ttp80) REVERT: B 364 GLN cc_start: 0.9519 (tp-100) cc_final: 0.9291 (tp-100) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1437 time to fit residues: 19.2824 Evaluate side-chains 90 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 101 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.0010 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.038923 restraints weight = 6537.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.040555 restraints weight = 4123.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.041727 restraints weight = 2889.275| |-----------------------------------------------------------------------------| r_work (final): 0.2736 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072401 restraints weight = 12027.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074522 restraints weight = 6897.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.075814 restraints weight = 4760.021| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.920 15696 Z= 1.160 Angle : 0.804 19.151 21232 Z= 0.417 Chirality : 0.043 0.313 2480 Planarity : 0.007 0.096 2660 Dihedral : 5.342 21.537 2168 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.53 % Allowed : 3.17 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2000 helix: 0.78 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 242 HIS 0.005 0.001 HIS B 328 PHE 0.027 0.003 PHE D 144 TYR 0.039 0.003 TYR B 253 ARG 0.028 0.001 ARG A 159 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1076) hydrogen bonds : angle 4.28620 ( 3204) covalent geometry : bond 0.03324 (15696) covalent geometry : angle 0.80405 (21232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9049 (tp) cc_final: 0.8144 (tp) REVERT: E 8 GLN cc_start: 0.9533 (mp10) cc_final: 0.9096 (mp10) REVERT: E 12 PHE cc_start: 0.9665 (m-80) cc_final: 0.9033 (m-80) REVERT: E 16 PHE cc_start: 0.9631 (t80) cc_final: 0.8988 (t80) REVERT: E 36 MET cc_start: 0.9590 (tpt) cc_final: 0.9165 (tpt) REVERT: E 39 LEU cc_start: 0.8979 (mm) cc_final: 0.8723 (mm) REVERT: E 48 LEU cc_start: 0.9781 (mt) cc_final: 0.9514 (tt) REVERT: E 51 MET cc_start: 0.9196 (tpp) cc_final: 0.8823 (tpp) REVERT: E 53 ASN cc_start: 0.9601 (m110) cc_final: 0.9382 (m110) REVERT: E 54 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8439 (mt-10) REVERT: E 75 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8185 (mttt) REVERT: E 83 GLU cc_start: 0.9021 (pp20) cc_final: 0.8701 (pp20) REVERT: E 92 PHE cc_start: 0.8767 (m-10) cc_final: 0.8258 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1682 time to fit residues: 11.0189 Evaluate side-chains 50 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.117 Evaluate side-chains 115 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9647 (mt) cc_final: 0.9409 (mt) REVERT: A 19 LEU cc_start: 0.9581 (mt) cc_final: 0.9229 (mm) REVERT: A 22 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 82 LYS cc_start: 0.9486 (mmtt) cc_final: 0.9049 (mmmt) REVERT: A 111 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: A 112 LEU cc_start: 0.8899 (mt) cc_final: 0.8571 (mt) REVERT: A 115 CYS cc_start: 0.9552 (p) cc_final: 0.8674 (p) REVERT: A 161 TYR cc_start: 0.8667 (p90) cc_final: 0.8231 (p90) REVERT: A 198 LEU cc_start: 0.9334 (mt) cc_final: 0.8852 (mt) REVERT: A 207 LEU cc_start: 0.8724 (mt) cc_final: 0.8203 (pp) REVERT: A 261 MET cc_start: 0.8499 (tmm) cc_final: 0.8129 (mmt) REVERT: A 270 THR cc_start: 0.8955 (p) cc_final: 0.8624 (p) REVERT: A 273 MET cc_start: 0.9318 (mtm) cc_final: 0.8955 (ptp) REVERT: A 292 ASN cc_start: 0.9465 (t0) cc_final: 0.9234 (t0) REVERT: A 295 GLU cc_start: 0.9310 (mp0) cc_final: 0.9108 (mp0) REVERT: A 303 MET cc_start: 0.9261 (mmm) cc_final: 0.8822 (mmm) REVERT: A 309 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9296 (ttmm) REVERT: A 321 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8513 (tp30) REVERT: A 326 TYR cc_start: 0.8782 (t80) cc_final: 0.8494 (t80) REVERT: A 349 ASN cc_start: 0.9439 (m110) cc_final: 0.8925 (m110) REVERT: A 364 GLN cc_start: 0.9486 (tp-100) cc_final: 0.9262 (tp-100) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1461 time to fit residues: 19.4779 Evaluate side-chains 89 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 0.0570 chunk 3 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 80 HIS A 186 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.048860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.040419 restraints weight = 6452.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.041922 restraints weight = 3951.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.043111 restraints weight = 2695.932| |-----------------------------------------------------------------------------| r_work (final): 0.2748 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071973 restraints weight = 12405.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073811 restraints weight = 7014.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075197 restraints weight = 5046.179| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.922 15696 Z= 1.166 Angle : 0.912 19.363 21232 Z= 0.459 Chirality : 0.044 0.345 2480 Planarity : 0.005 0.055 2660 Dihedral : 5.308 26.154 2168 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.79 % Allowed : 2.37 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2000 helix: 0.50 (0.12), residues: 1508 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 242 HIS 0.017 0.002 HIS B 340 PHE 0.027 0.003 PHE A 144 TYR 0.024 0.003 TYR E 138 ARG 0.014 0.001 ARG C 14 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 1076) hydrogen bonds : angle 4.48844 ( 3204) covalent geometry : bond 0.03338 (15696) covalent geometry : angle 0.91247 (21232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9066 (tp) cc_final: 0.8219 (tp) REVERT: E 8 GLN cc_start: 0.9515 (mp10) cc_final: 0.9125 (mp10) REVERT: E 12 PHE cc_start: 0.9634 (m-80) cc_final: 0.9044 (m-80) REVERT: E 16 PHE cc_start: 0.9630 (t80) cc_final: 0.8992 (t80) REVERT: E 18 LEU cc_start: 0.9541 (mm) cc_final: 0.9340 (mm) REVERT: E 36 MET cc_start: 0.9557 (tpt) cc_final: 0.9116 (tpt) REVERT: E 39 LEU cc_start: 0.8912 (mm) cc_final: 0.8657 (mm) REVERT: E 48 LEU cc_start: 0.9785 (mt) cc_final: 0.9511 (tt) REVERT: E 75 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8323 (mttt) REVERT: E 87 GLU cc_start: 0.9178 (tt0) cc_final: 0.8964 (pp20) REVERT: E 92 PHE cc_start: 0.8731 (m-10) cc_final: 0.8193 (m-80) outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.1651 time to fit residues: 9.9594 Evaluate side-chains 49 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.116 Evaluate side-chains 111 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9649 (mt) cc_final: 0.9232 (pp) REVERT: A 22 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8827 (mt-10) REVERT: A 82 LYS cc_start: 0.9520 (mmtt) cc_final: 0.9083 (mmmt) REVERT: A 176 ASN cc_start: 0.9428 (t0) cc_final: 0.7934 (t0) REVERT: A 179 TYR cc_start: 0.8082 (m-80) cc_final: 0.7636 (m-80) REVERT: A 198 LEU cc_start: 0.9240 (mt) cc_final: 0.8745 (mt) REVERT: A 207 LEU cc_start: 0.8675 (mt) cc_final: 0.8192 (pp) REVERT: A 261 MET cc_start: 0.8596 (tmm) cc_final: 0.8101 (mmt) REVERT: A 270 THR cc_start: 0.8973 (p) cc_final: 0.8670 (p) REVERT: A 273 MET cc_start: 0.9330 (mtm) cc_final: 0.8949 (ptp) REVERT: A 295 GLU cc_start: 0.9334 (mp0) cc_final: 0.9070 (mp0) REVERT: A 303 MET cc_start: 0.9265 (mmm) cc_final: 0.8810 (mmm) REVERT: A 309 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9299 (ttmm) REVERT: A 310 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8902 (mt-10) REVERT: A 321 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8490 (tp30) REVERT: A 326 TYR cc_start: 0.8794 (t80) cc_final: 0.8442 (t80) REVERT: A 349 ASN cc_start: 0.9376 (m110) cc_final: 0.9118 (m110) REVERT: A 364 GLN cc_start: 0.9493 (tp-100) cc_final: 0.9276 (tp-100) outliers start: 2 outliers final: 0 residues processed: 109 average time/residue: 0.1611 time to fit residues: 20.7301 Evaluate side-chains 86 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 0.3980 chunk 178 optimal weight: 0.3980 chunk 163 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 190 optimal weight: 0.0570 chunk 112 optimal weight: 0.0570 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 50.0000 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041187 restraints weight = 6270.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.042876 restraints weight = 3707.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.044125 restraints weight = 2487.428| |-----------------------------------------------------------------------------| r_work (final): 0.2784 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.072618 restraints weight = 11899.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074744 restraints weight = 6822.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075954 restraints weight = 4709.559| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.915 15696 Z= 1.158 Angle : 0.825 19.415 21232 Z= 0.425 Chirality : 0.044 0.358 2480 Planarity : 0.005 0.068 2660 Dihedral : 5.091 27.867 2168 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2000 helix: 0.73 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 242 HIS 0.012 0.002 HIS A 80 PHE 0.027 0.003 PHE C 144 TYR 0.022 0.002 TYR H 138 ARG 0.015 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1076) hydrogen bonds : angle 4.32675 ( 3204) covalent geometry : bond 0.03318 (15696) covalent geometry : angle 0.82542 (21232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9048 (tp) cc_final: 0.7944 (tp) REVERT: H 8 GLN cc_start: 0.9555 (mp10) cc_final: 0.9162 (mp10) REVERT: H 12 PHE cc_start: 0.9559 (m-80) cc_final: 0.8964 (m-80) REVERT: H 16 PHE cc_start: 0.9576 (t80) cc_final: 0.9183 (t80) REVERT: H 36 MET cc_start: 0.9567 (tpt) cc_final: 0.9246 (tpt) REVERT: H 48 LEU cc_start: 0.9751 (mt) cc_final: 0.9472 (tt) REVERT: H 68 PHE cc_start: 0.9611 (t80) cc_final: 0.9349 (t80) REVERT: H 92 PHE cc_start: 0.8706 (m-10) cc_final: 0.8320 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1810 time to fit residues: 10.4801 Evaluate side-chains 47 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.128 Evaluate side-chains 107 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 LEU cc_start: 0.9660 (mt) cc_final: 0.9377 (mt) REVERT: D 19 LEU cc_start: 0.9636 (mt) cc_final: 0.9402 (mm) REVERT: D 22 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8787 (mt-10) REVERT: D 82 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9080 (mmmt) REVERT: D 176 ASN cc_start: 0.9326 (t0) cc_final: 0.8545 (t0) REVERT: D 179 TYR cc_start: 0.8271 (m-80) cc_final: 0.7884 (m-80) REVERT: D 198 LEU cc_start: 0.9359 (mt) cc_final: 0.8862 (mt) REVERT: D 261 MET cc_start: 0.8562 (tmm) cc_final: 0.8083 (mmt) REVERT: D 270 THR cc_start: 0.8922 (p) cc_final: 0.8597 (p) REVERT: D 273 MET cc_start: 0.9407 (mtm) cc_final: 0.9100 (ptp) REVERT: D 303 MET cc_start: 0.9266 (mmm) cc_final: 0.8792 (mmm) REVERT: D 309 LYS cc_start: 0.9594 (ttpt) cc_final: 0.9296 (ttmm) REVERT: D 321 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8374 (tp30) REVERT: D 344 LEU cc_start: 0.9664 (tt) cc_final: 0.9423 (tt) REVERT: D 364 GLN cc_start: 0.9488 (tp-100) cc_final: 0.9258 (tp-100) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1624 time to fit residues: 20.4113 Evaluate side-chains 92 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.743 > 50: distance: 0 - 1: 23.179 distance: 1 - 2: 12.615 distance: 4 - 5: 37.068 distance: 5 - 6: 49.054 distance: 5 - 8: 62.962 distance: 6 - 7: 39.903 distance: 6 - 15: 56.547 distance: 8 - 9: 43.562 distance: 9 - 10: 26.506 distance: 9 - 11: 20.330 distance: 10 - 12: 8.894 distance: 11 - 13: 36.285 distance: 12 - 14: 36.290 distance: 13 - 14: 8.422 distance: 15 - 16: 38.657 distance: 16 - 17: 69.544 distance: 16 - 19: 38.937 distance: 17 - 18: 12.568 distance: 17 - 23: 52.944 distance: 19 - 20: 57.874 distance: 20 - 21: 38.920 distance: 21 - 22: 58.965 distance: 23 - 24: 56.928 distance: 24 - 25: 55.114 distance: 24 - 27: 40.235 distance: 25 - 26: 41.230 distance: 25 - 30: 69.378 distance: 27 - 28: 68.977 distance: 27 - 29: 38.670 distance: 31 - 32: 39.254 distance: 31 - 34: 56.299 distance: 32 - 33: 32.872 distance: 32 - 38: 66.757 distance: 34 - 35: 40.925 distance: 35 - 36: 39.934 distance: 35 - 37: 46.305 distance: 38 - 39: 39.811 distance: 39 - 40: 40.778 distance: 39 - 42: 58.642 distance: 40 - 41: 39.565 distance: 40 - 46: 38.804 distance: 42 - 43: 54.973 distance: 43 - 44: 5.675 distance: 43 - 45: 32.657 distance: 46 - 47: 53.238 distance: 48 - 49: 62.637 distance: 48 - 50: 48.279 distance: 50 - 51: 18.704 distance: 51 - 52: 49.594 distance: 51 - 54: 60.489 distance: 52 - 53: 28.478 distance: 52 - 58: 57.121 distance: 54 - 55: 7.843 distance: 55 - 56: 32.569 distance: 55 - 57: 6.547 distance: 59 - 60: 55.116 distance: 59 - 62: 39.110 distance: 60 - 61: 39.759 distance: 60 - 69: 35.909 distance: 62 - 63: 38.019 distance: 63 - 64: 46.915 distance: 64 - 65: 18.154 distance: 65 - 66: 38.528 distance: 66 - 67: 11.055 distance: 66 - 68: 16.267 distance: 69 - 70: 39.786 distance: 70 - 71: 40.333 distance: 70 - 73: 55.987 distance: 71 - 72: 41.088 distance: 75 - 76: 19.289 distance: 75 - 78: 19.666 distance: 76 - 77: 20.996 distance: 78 - 79: 16.701 distance: 79 - 80: 30.649 distance: 79 - 81: 29.546 distance: 80 - 82: 16.242 distance: 81 - 83: 44.323 distance: 81 - 84: 29.487 distance: 82 - 83: 36.617 distance: 83 - 85: 35.980 distance: 84 - 86: 9.277 distance: 85 - 87: 11.543 distance: 86 - 87: 11.457