Starting phenix.real_space_refine on Fri Jun 28 11:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uze_26886/06_2024/7uze_26886_trim_updated.pdb" } resolution = 2.4 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= 0.006 sd= 0.357 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 S 20 5.16 5 C 4884 2.51 5 N 1264 2.21 5 O 1409 1.98 5 H 7392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 163": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14969 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3670 Chain: "B" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3670 Chain: "C" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3670 Chain: "A" Number of atoms: 3686 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 3661 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3670 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 234 " occ=0.48 ... (46 atoms not shown) pdb="HH22BARG D 234 " occ=0.52 residue: pdb=" N AARG B 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 234 " occ=0.50 residue: pdb=" N AARG C 234 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG C 234 " occ=0.50 residue: pdb=" N AARG A 234 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG A 234 " occ=0.49 Time building chain proxies: 12.64, per 1000 atoms: 0.84 Number of scatterers: 14969 At special positions: 0 Unit cell: (70.55, 90.885, 90.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1409 8.00 N 1264 7.00 C 4884 6.00 H 7392 1.00 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 - 3.50 Amino acid : False - 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: 12.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 49 through 71 removed outlier: 5.737A pdb=" N HIS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 135 through 156 Processing helix chain 'D' and resid 168 through 187 removed outlier: 5.628A pdb=" N ASP D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.699A pdb=" N SER D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 229 removed outlier: 5.576A pdb=" N GLY D 215 " --> pdb=" O PHE D 212 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.675A pdb=" N ASP D 228 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 229 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.611A pdb=" N LYS D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 71 removed outlier: 5.686A pdb=" N HIS B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 91 through 115 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 168 through 187 removed outlier: 5.611A pdb=" N ASP B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 203 removed outlier: 3.694A pdb=" N SER B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 229 removed outlier: 5.554A pdb=" N GLY B 215 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 3.674A pdb=" N ASP B 228 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 229 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.610A pdb=" N LYS B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 6 No H-bonds generated for 'chain 'C' and resid 4 through 6' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 49 through 71 removed outlier: 5.736A pdb=" N HIS C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 91 through 115 Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 168 through 187 removed outlier: 5.633A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 202 removed outlier: 3.707A pdb=" N SER C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 229 removed outlier: 5.561A pdb=" N GLY C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.675A pdb=" N ASP C 228 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE C 229 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.626A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 49 through 71 removed outlier: 5.726A pdb=" N HIS A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 91 through 115 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 168 through 187 removed outlier: 5.618A pdb=" N ASP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.690A pdb=" N SER A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 229 removed outlier: 5.559A pdb=" N GLY A 215 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.669A pdb=" N ASP A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.612A pdb=" N LYS A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1257 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: 5.06 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7380 1.03 - 1.23: 26 1.23 - 1.42: 3074 1.42 - 1.62: 4504 1.62 - 1.81: 28 Bond restraints: 15012 Sorted by residual: bond pdb=" CA CYS C 189 " pdb=" C CYS C 189 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.68e+00 bond pdb=" CA CYS A 189 " pdb=" C CYS A 189 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.52e+00 bond pdb=" CA CYS B 189 " pdb=" C CYS B 189 " ideal model delta sigma weight residual 1.532 1.521 0.011 9.60e-03 1.09e+04 1.37e+00 bond pdb=" CG PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.60e-01 bond pdb=" CA ILE D 191 " pdb=" CB ILE D 191 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 5.21e-01 ... (remaining 15007 not shown) Histogram of bond angle deviations from ideal: 101.51 - 108.00: 2536 108.00 - 114.49: 15911 114.49 - 120.99: 5474 120.99 - 127.48: 3031 127.48 - 133.97: 76 Bond angle restraints: 27028 Sorted by residual: angle pdb=" CA CYS D 189 " pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " ideal model delta sigma weight residual 114.40 107.07 7.33 2.30e+00 1.89e-01 1.02e+01 angle pdb=" N GLY D 190 " pdb=" CA GLY D 190 " pdb=" C GLY D 190 " ideal model delta sigma weight residual 113.18 107.15 6.03 2.37e+00 1.78e-01 6.47e+00 angle pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 114.17 117.70 -3.53 1.45e+00 4.76e-01 5.92e+00 angle pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N GLY B 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.70e+00 angle pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N GLY C 190 " ideal model delta sigma weight residual 114.17 117.63 -3.46 1.45e+00 4.76e-01 5.68e+00 ... (remaining 27023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6493 17.97 - 35.94: 462 35.94 - 53.91: 226 53.91 - 71.88: 63 71.88 - 89.85: 12 Dihedral angle restraints: 7256 sinusoidal: 4000 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU B 182 " pdb=" C LEU B 182 " pdb=" N ALA B 183 " pdb=" CA ALA B 183 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU A 182 " pdb=" C LEU A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N ALA C 183 " pdb=" CA ALA C 183 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 828 0.031 - 0.061: 313 0.061 - 0.092: 101 0.092 - 0.123: 21 0.123 - 0.153: 5 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA CYS D 189 " pdb=" N CYS D 189 " pdb=" C CYS D 189 " pdb=" CB CYS D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL D 133 " pdb=" N VAL D 133 " pdb=" C VAL D 133 " pdb=" CB VAL D 133 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1265 not shown) Planarity restraints: 2236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 191 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C ILE A 191 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 191 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN A 192 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 76 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 77 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 225 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C LEU C 225 " -0.020 2.00e-02 2.50e+03 pdb=" O LEU C 225 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 226 " 0.007 2.00e-02 2.50e+03 ... (remaining 2233 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1910 2.25 - 2.84: 34396 2.84 - 3.42: 43628 3.42 - 4.01: 60426 4.01 - 4.60: 91675 Nonbonded interactions: 232035 Sorted by model distance: nonbonded pdb=" HH TYR D 186 " pdb=" O GLY C 30 " model vdw 1.661 1.850 nonbonded pdb=" HH TYR C 186 " pdb=" O GLY A 30 " model vdw 1.664 1.850 nonbonded pdb=" O VAL D 244 " pdb=" H GLY D 248 " model vdw 1.667 1.850 nonbonded pdb=" O GLY D 30 " pdb=" HH TYR B 186 " model vdw 1.671 1.850 nonbonded pdb=" O GLY B 30 " pdb=" HH TYR A 186 " model vdw 1.674 1.850 ... (remaining 232030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'B' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'C' and (resid 3 through 233 or resid 236 through 249 or resid 301)) selection = (chain 'D' and (resid 3 through 233 or resid 236 through 249 or resid 301)) } 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=0.48 max=1.00 mean=0.99 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: 0.720 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: 0.260 Extract box with map and model: 3.360 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 57.020 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.003 0.022 7620 Z= 0.210 Angle : 0.584 7.334 10392 Z= 0.313 Chirality : 0.037 0.153 1268 Planarity : 0.003 0.029 1272 Dihedral : 14.965 89.846 2816 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.00 % Favored : 96.59 % Rotamer: Outliers : 0.68 % Allowed : 14.86 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.69 (0.26), residues: 980 helix: 1.85 (0.19), residues: 644 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 11 HIS 0.004 0.001 HIS B 180 PHE 0.018 0.002 PHE D 212 TYR 0.010 0.002 TYR D 227 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.047 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 2.1821 time to fit residues: 177.7408 Evaluate side-chains 73 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7620 Z= 0.284 Angle : 0.591 7.380 10392 Z= 0.320 Chirality : 0.039 0.159 1268 Planarity : 0.005 0.033 1272 Dihedral : 8.959 55.907 1376 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.31 % Favored : 96.28 % Rotamer: Outliers : 2.30 % Allowed : 13.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.08 (0.26), residues: 980 helix: 1.34 (0.18), residues: 640 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 213 HIS 0.005 0.001 HIS A 69 PHE 0.020 0.002 PHE A 212 TYR 0.010 0.002 TYR D 227 ARG 0.002 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue SER 236 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue SER 247 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.091 Fit side-chains REVERT: D 191 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8107 (mp) REVERT: D 225 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8210 (tm) REVERT: B 36 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8681 (mttm) REVERT: B 225 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8216 (tm) REVERT: C 225 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8165 (tm) REVERT: A 225 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8106 (tm) outliers start: 17 outliers final: 6 residues processed: 88 average time/residue: 2.0129 time to fit residues: 190.8389 Evaluate side-chains 79 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1259 > 50: distance: 3 - 36: 15.472 distance: 27 - 36: 15.723 distance: 36 - 37: 9.511 distance: 36 - 41: 24.227 distance: 37 - 38: 38.724 distance: 37 - 40: 24.592 distance: 37 - 42: 12.985 distance: 38 - 39: 12.845 distance: 38 - 46: 52.378 distance: 40 - 43: 26.761 distance: 40 - 44: 16.362 distance: 40 - 45: 32.469 distance: 46 - 47: 30.750 distance: 46 - 54: 20.059 distance: 47 - 48: 25.886 distance: 47 - 50: 24.817 distance: 47 - 55: 32.135 distance: 48 - 49: 23.014 distance: 48 - 65: 11.060 distance: 50 - 51: 29.084 distance: 50 - 56: 17.829 distance: 50 - 57: 17.931 distance: 51 - 52: 5.117 distance: 51 - 53: 9.563 distance: 51 - 58: 8.716 distance: 52 - 59: 3.734 distance: 52 - 61: 3.266 distance: 53 - 63: 4.383 distance: 53 - 64: 3.014 distance: 65 - 66: 6.285 distance: 65 - 69: 3.682 distance: 66 - 67: 11.353 distance: 67 - 68: 30.795 distance: 67 - 72: 59.141 distance: 72 - 73: 39.694 distance: 72 - 83: 33.973 distance: 73 - 74: 23.690 distance: 73 - 76: 44.639 distance: 73 - 84: 32.984 distance: 74 - 75: 30.924 distance: 74 - 92: 43.604 distance: 76 - 77: 16.218 distance: 76 - 85: 23.468 distance: 76 - 86: 14.701 distance: 77 - 78: 4.232 distance: 77 - 79: 4.443 distance: 78 - 80: 3.276 distance: 78 - 87: 7.540 distance: 79 - 81: 5.461 distance: 79 - 88: 15.488 distance: 80 - 82: 3.473 distance: 80 - 89: 7.068 distance: 81 - 82: 5.958 distance: 81 - 90: 8.244 distance: 82 - 91: 5.987 distance: 92 - 93: 20.133 distance: 92 - 101: 14.516 distance: 93 - 94: 27.604 distance: 93 - 96: 59.975 distance: 93 - 102: 44.626 distance: 94 - 95: 25.960 distance: 94 - 114: 34.403 distance: 96 - 97: 20.186 distance: 96 - 103: 27.040 distance: 96 - 104: 33.860 distance: 97 - 98: 19.641 distance: 97 - 105: 12.801 distance: 97 - 106: 22.157 distance: 98 - 99: 21.415 distance: 98 - 107: 25.346 distance: 98 - 108: 11.524 distance: 99 - 100: 7.376 distance: 99 - 109: 6.179 distance: 99 - 110: 5.734 distance: 114 - 115: 33.078 distance: 114 - 126: 7.813 distance: 115 - 116: 25.246 distance: 115 - 118: 53.906 distance: 115 - 127: 56.963 distance: 116 - 117: 39.550 distance: 116 - 135: 20.604 distance: 118 - 119: 34.935 distance: 118 - 128: 18.414 distance: 119 - 120: 15.464 distance: 120 - 122: 20.805 distance: 120 - 130: 6.258 distance: 121 - 123: 26.842 distance: 121 - 131: 4.661 distance: 122 - 124: 16.576 distance: 122 - 132: 13.437 distance: 123 - 124: 17.794 distance: 123 - 133: 13.598 distance: 124 - 125: 19.125 distance: 125 - 134: 28.177 distance: 135 - 136: 42.076 distance: 135 - 141: 12.587 distance: 136 - 137: 39.179 distance: 136 - 139: 16.608 distance: 136 - 142: 17.269 distance: 137 - 138: 41.099 distance: 137 - 149: 33.317 distance: 139 - 140: 22.215 distance: 139 - 143: 13.652 distance: 139 - 144: 13.422 distance: 140 - 141: 20.021 distance: 140 - 145: 32.337 distance: 140 - 146: 6.764 distance: 141 - 147: 49.701 distance: 141 - 148: 21.975 distance: 149 - 150: 22.903 distance: 149 - 156: 37.469 distance: 150 - 151: 34.676 distance: 150 - 153: 11.701 distance: 150 - 157: 32.595 distance: 151 - 152: 30.877 distance: 151 - 165: 34.595 distance: 153 - 154: 25.685 distance: 153 - 155: 27.212 distance: 153 - 158: 42.841 distance: 154 - 159: 14.801 distance: 154 - 160: 12.905 distance: 154 - 161: 4.946 distance: 155 - 162: 13.694 distance: 155 - 163: 4.333 distance: 155 - 164: 12.056 distance: 165 - 166: 44.523 distance: 165 - 169: 30.776 distance: 166 - 170: 19.286 distance: 167 - 168: 41.211 distance: 167 - 172: 50.681 distance: 172 - 173: 15.195 distance: 172 - 180: 22.464 distance: 173 - 174: 39.346 distance: 173 - 176: 45.533 distance: 173 - 181: 26.126 distance: 174 - 175: 33.869 distance: 174 - 186: 20.224 distance: 176 - 177: 16.487 distance: 176 - 182: 21.933 distance: 176 - 183: 20.571 distance: 177 - 178: 19.709 distance: 177 - 179: 5.050 distance: 179 - 184: 22.022 distance: 179 - 185: 12.653