Starting phenix.real_space_refine on Thu Mar 14 15:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p00_13140/03_2024/7p00_13140_updated.pdb" } resolution = 2.71 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= 0.054 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5837 2.51 5 N 1547 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9110 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 405 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1879 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2359 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "P" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 95 Unusual residues: {'NH2': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 8} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.56 Number of scatterers: 9110 At special positions: 0 Unit cell: (87.234, 121.737, 122.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1663 8.00 N 1547 7.00 C 5837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.05 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.04 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 15 sheets defined 34.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 105 through 107 No H-bonds generated for 'chain 'H' and resid 105 through 107' Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 13 through 24 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.512A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.580A pdb=" N GLN A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 231 " --> pdb=" O TRP A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 231' Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 315 through 334 removed outlier: 3.546A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'R' and resid 29 through 59 Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.190A pdb=" N PHE R 70 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA R 77 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.570A pdb=" N THR R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 135 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 144 through 167 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 191 through 204 Processing helix chain 'R' and resid 206 through 224 Processing helix chain 'R' and resid 237 through 273 removed outlier: 4.007A pdb=" N VAL R 247 " --> pdb=" O LYS R 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 282 through 308 removed outlier: 4.252A pdb=" N MET R 291 " --> pdb=" O LEU R 288 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 301 " --> pdb=" O THR R 298 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 4.050A pdb=" N LEU R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 318 removed outlier: 3.551A pdb=" N GLY R 315 " --> pdb=" O ARG R 311 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 20 through 24 Processing sheet with id= B, first strand: chain 'H' and resid 132 through 134 removed outlier: 6.175A pdb=" N ARG H 55 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP H 64 " --> pdb=" O ARG H 55 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.422A pdb=" N LYS H 261 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU H 195 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU H 204 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 172 through 177 Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.744A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.939A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.916A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.910A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.492A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.560A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.516A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.564A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= N, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.493A pdb=" N PHE A 273 " --> pdb=" O VAL A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'R' and resid 169 through 173 388 hydrogen bonds defined for protein. 1023 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: 2.55 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1480 1.32 - 1.44: 2630 1.44 - 1.57: 5125 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9329 Sorted by residual: bond pdb=" C THR R 91 " pdb=" O THR R 91 " ideal model delta sigma weight residual 1.237 1.301 -0.065 1.17e-02 7.31e+03 3.06e+01 bond pdb=" ND1 HIS A 340 " pdb=" CE1 HIS A 340 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.62e+01 bond pdb=" CD2 HIS A 340 " pdb=" NE2 HIS A 340 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.32e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.25e+01 ... (remaining 9324 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.58: 337 106.58 - 113.53: 4818 113.53 - 120.48: 4468 120.48 - 127.43: 2956 127.43 - 134.38: 86 Bond angle restraints: 12665 Sorted by residual: angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" C GLN A 229 " ideal model delta sigma weight residual 111.28 103.41 7.87 1.09e+00 8.42e-01 5.22e+01 angle pdb=" N MET G 38 " pdb=" CA MET G 38 " pdb=" C MET G 38 " ideal model delta sigma weight residual 111.28 104.11 7.17 1.09e+00 8.42e-01 4.33e+01 angle pdb=" CB HIS A 340 " pdb=" CG HIS A 340 " pdb=" CD2 HIS A 340 " ideal model delta sigma weight residual 131.20 122.75 8.45 1.30e+00 5.92e-01 4.22e+01 angle pdb=" N ARG A 224 " pdb=" CA ARG A 224 " pdb=" C ARG A 224 " ideal model delta sigma weight residual 113.16 105.30 7.86 1.24e+00 6.50e-01 4.02e+01 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " ideal model delta sigma weight residual 110.23 119.59 -9.36 1.62e+00 3.81e-01 3.34e+01 ... (remaining 12660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5129 17.34 - 34.68: 350 34.68 - 52.03: 61 52.03 - 69.37: 12 69.37 - 86.71: 7 Dihedral angle restraints: 5559 sinusoidal: 2216 harmonic: 3343 Sorted by residual: dihedral pdb=" C ASP G 36 " pdb=" N ASP G 36 " pdb=" CA ASP G 36 " pdb=" CB ASP G 36 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C ARG H 208 " pdb=" N ARG H 208 " pdb=" CA ARG H 208 " pdb=" CB ARG H 208 " ideal model delta harmonic sigma weight residual -122.60 -133.96 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C ASN H 186 " pdb=" N ASN H 186 " pdb=" CA ASN H 186 " pdb=" CB ASN H 186 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 632 0.078 - 0.155: 544 0.155 - 0.233: 195 0.233 - 0.311: 35 0.311 - 0.388: 8 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ASP G 36 " pdb=" N ASP G 36 " pdb=" C ASP G 36 " pdb=" CB ASP G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PHE A 212 " pdb=" N PHE A 212 " pdb=" C PHE A 212 " pdb=" CB PHE A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1411 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 205 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PHE A 205 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE A 205 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN A 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 45 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C MET B 45 " 0.050 2.00e-02 2.50e+03 pdb=" O MET B 45 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 114 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C CYS B 114 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS B 114 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 115 " -0.015 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1144 2.77 - 3.30: 9248 3.30 - 3.83: 15018 3.83 - 4.37: 20750 4.37 - 4.90: 32293 Nonbonded interactions: 78453 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.236 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 2.440 nonbonded pdb=" O ILE R 273 " pdb=" OD1 ASN R 274 " model vdw 2.334 3.040 nonbonded pdb=" O ARG A 266 " pdb=" ND1 HIS A 340 " model vdw 2.393 2.520 nonbonded pdb=" N PHE B 253 " pdb=" O PHE B 253 " model vdw 2.468 2.496 ... (remaining 78448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.160 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 25.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.012 0.100 9329 Z= 0.790 Angle : 1.680 9.357 12665 Z= 1.284 Chirality : 0.115 0.388 1414 Planarity : 0.006 0.037 1597 Dihedral : 12.349 86.708 3394 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.81 % Allowed : 7.92 % Favored : 91.27 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 2.50 % 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: -0.50 (0.24), residues: 1126 helix: 0.29 (0.26), residues: 373 sheet: -0.44 (0.32), residues: 248 loop : -0.62 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 PHE 0.030 0.003 PHE A 205 TYR 0.022 0.002 TYR H 207 ARG 0.005 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 239 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.8172 (mmm) cc_final: 0.7715 (mmp) REVERT: B 325 MET cc_start: 0.7847 (tpp) cc_final: 0.7629 (mmm) REVERT: R 279 LEU cc_start: 0.8203 (mt) cc_final: 0.7982 (mt) REVERT: P 8 PHE cc_start: 0.7850 (m-80) cc_final: 0.7649 (m-80) outliers start: 8 outliers final: 1 residues processed: 246 average time/residue: 1.1968 time to fit residues: 313.3640 Evaluate side-chains 148 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 GLN B 156 GLN B 266 HIS B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 229 GLN A 354 ASN ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9329 Z= 0.215 Angle : 0.545 5.897 12665 Z= 0.301 Chirality : 0.043 0.150 1414 Planarity : 0.005 0.040 1597 Dihedral : 5.008 71.904 1319 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.86 % Allowed : 14.31 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.23), residues: 1126 helix: 0.90 (0.25), residues: 374 sheet: -0.00 (0.31), residues: 247 loop : -0.25 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 227 HIS 0.008 0.002 HIS B 54 PHE 0.014 0.001 PHE B 151 TYR 0.021 0.002 TYR B 105 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 0.952 Fit side-chains REVERT: H 63 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: H 110 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8050 (ttm) REVERT: H 203 GLN cc_start: 0.8088 (pt0) cc_final: 0.7879 (pp30) REVERT: B 42 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6803 (mmp-170) REVERT: B 129 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7467 (tpt90) REVERT: B 188 MET cc_start: 0.8250 (mmm) cc_final: 0.7843 (mmp) REVERT: R 171 THR cc_start: 0.7670 (p) cc_final: 0.7399 (p) REVERT: R 174 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6389 (mtt) REVERT: P 8 PHE cc_start: 0.8063 (m-80) cc_final: 0.7853 (m-80) outliers start: 38 outliers final: 17 residues processed: 197 average time/residue: 1.2556 time to fit residues: 262.7232 Evaluate side-chains 176 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 176 GLN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN A 206 GLN A 229 GLN A 275 ASN A 368 GLN R 50 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9329 Z= 0.287 Angle : 0.561 6.438 12665 Z= 0.304 Chirality : 0.044 0.156 1414 Planarity : 0.005 0.047 1597 Dihedral : 5.055 70.314 1317 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.38 % Allowed : 15.23 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.31 (0.24), residues: 1126 helix: 0.82 (0.25), residues: 372 sheet: 0.06 (0.31), residues: 258 loop : -0.03 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.008 0.002 HIS A 340 PHE 0.017 0.002 PHE R 264 TYR 0.015 0.002 TYR R 99 ARG 0.007 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 1.024 Fit side-chains REVERT: H 173 SER cc_start: 0.8060 (m) cc_final: 0.7838 (p) REVERT: B 42 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6792 (mmp-170) REVERT: B 46 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7132 (mmt180) REVERT: B 78 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: A 24 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: R 57 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7613 (mp) REVERT: R 174 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6429 (mtt) REVERT: P 6 GLN cc_start: 0.7424 (tt0) cc_final: 0.7142 (tt0) REVERT: P 8 PHE cc_start: 0.8029 (m-80) cc_final: 0.7508 (m-80) outliers start: 53 outliers final: 20 residues processed: 186 average time/residue: 1.2325 time to fit residues: 244.2990 Evaluate side-chains 171 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1163 > 50: distance: 50 - 158: 28.261 distance: 53 - 155: 25.864 distance: 67 - 143: 23.146 distance: 97 - 101: 29.873 distance: 101 - 102: 45.315 distance: 102 - 103: 33.797 distance: 102 - 105: 26.722 distance: 103 - 104: 24.312 distance: 103 - 106: 47.798 distance: 106 - 107: 20.164 distance: 107 - 108: 25.131 distance: 107 - 110: 44.643 distance: 108 - 109: 37.154 distance: 108 - 114: 30.574 distance: 110 - 111: 15.205 distance: 111 - 112: 37.330 distance: 111 - 113: 21.742 distance: 114 - 115: 9.137 distance: 115 - 116: 11.313 distance: 115 - 118: 20.361 distance: 116 - 117: 38.672 distance: 116 - 123: 15.470 distance: 118 - 119: 31.343 distance: 119 - 120: 13.351 distance: 120 - 121: 5.857 distance: 120 - 122: 14.450 distance: 123 - 124: 5.884 distance: 124 - 125: 7.103 distance: 124 - 127: 9.902 distance: 125 - 126: 26.914 distance: 125 - 132: 7.617 distance: 127 - 128: 19.949 distance: 128 - 129: 16.027 distance: 129 - 130: 7.797 distance: 129 - 131: 5.198 distance: 132 - 133: 8.693 distance: 133 - 134: 19.799 distance: 133 - 136: 8.724 distance: 134 - 135: 41.460 distance: 134 - 140: 11.283 distance: 136 - 137: 27.311 distance: 137 - 138: 14.106 distance: 137 - 139: 17.432 distance: 140 - 141: 3.525 distance: 141 - 142: 9.311 distance: 141 - 144: 19.032 distance: 142 - 143: 32.343 distance: 142 - 148: 19.999 distance: 144 - 145: 20.502 distance: 145 - 146: 14.485 distance: 146 - 147: 22.360 distance: 148 - 149: 37.791 distance: 149 - 150: 24.272 distance: 149 - 152: 11.853 distance: 150 - 151: 15.041 distance: 150 - 155: 22.264 distance: 152 - 153: 43.953 distance: 152 - 154: 42.572 distance: 155 - 156: 33.243 distance: 156 - 157: 21.969 distance: 156 - 159: 28.670 distance: 157 - 158: 26.015 distance: 157 - 167: 20.035 distance: 159 - 160: 28.016 distance: 160 - 161: 20.683 distance: 160 - 162: 18.732 distance: 161 - 163: 7.314 distance: 162 - 164: 7.216 distance: 163 - 165: 8.973 distance: 164 - 165: 16.116 distance: 165 - 166: 15.256 distance: 167 - 168: 15.906 distance: 168 - 169: 19.459 distance: 168 - 171: 20.943 distance: 169 - 170: 35.666 distance: 169 - 173: 17.951 distance: 171 - 172: 23.573 distance: 173 - 174: 7.059 distance: 174 - 175: 7.055 distance: 174 - 177: 15.777 distance: 175 - 176: 14.530 distance: 175 - 183: 8.019 distance: 177 - 178: 14.698 distance: 178 - 179: 17.655 distance: 178 - 180: 10.844 distance: 179 - 181: 11.455 distance: 180 - 182: 15.975 distance: 181 - 182: 6.048