Starting phenix.real_space_refine on Fri Dec 8 09:11:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx2_30489/12_2023/7cx2_30489_updated.pdb" } resolution = 2.8 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= -0.000 sd= 0.009 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 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.75, per 1000 atoms: 0.60 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 36.7% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'R' and resid 27 through 47 removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 139 Processing helix chain 'R' and resid 141 through 147 Processing helix chain 'R' and resid 150 through 173 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 155 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 157 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.556A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Proline residue: R 171 - end of helix Processing helix chain 'R' and resid 196 through 227 Processing helix chain 'R' and resid 259 through 276 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 291 through 294 No H-bonds generated for 'chain 'R' and resid 291 through 294' Processing helix chain 'R' and resid 297 through 316 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 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 6 through 23 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.615A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.931A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 999 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: 2.21 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 182 106.64 - 113.50: 4432 113.50 - 120.36: 3089 120.36 - 127.21: 3179 127.21 - 134.07: 81 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4337 16.25 - 32.49: 395 32.49 - 48.74: 83 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4841 sinusoidal: 1870 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 45 2.58 - 3.16: 6354 3.16 - 3.74: 11864 3.74 - 4.32: 17380 4.32 - 4.90: 28736 Nonbonded interactions: 64379 Sorted by model distance: nonbonded pdb=" O ILE A 56 " pdb=" N MET A 60 " model vdw 1.994 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 2.440 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 2.440 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 2.520 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 2.520 ... (remaining 64374 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: 0.400 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: 1.960 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.004 0.079 8086 Z= 0.281 Angle : 0.712 14.865 10963 Z= 0.396 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.642 81.229 2908 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % 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: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.024 0.002 TYR B 59 ARG 0.007 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 1.4091 time to fit residues: 254.8287 Evaluate side-chains 124 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 213 GLN A 390 GLN B 17 GLN B 32 GLN B 175 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 77 ASN N 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8086 Z= 0.159 Angle : 0.523 10.107 10963 Z= 0.264 Chirality : 0.041 0.145 1252 Planarity : 0.004 0.053 1402 Dihedral : 5.558 59.735 1140 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.79 % Allowed : 13.83 % Favored : 84.39 % 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: -0.72 (0.25), residues: 1002 helix: 0.96 (0.27), residues: 385 sheet: -0.30 (0.33), residues: 210 loop : -2.02 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 119 TYR 0.010 0.001 TYR B 124 ARG 0.003 0.000 ARG R 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 153 average time/residue: 1.3633 time to fit residues: 219.5236 Evaluate side-chains 132 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1633 time to fit residues: 1.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN B 32 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8086 Z= 0.244 Angle : 0.543 9.826 10963 Z= 0.277 Chirality : 0.042 0.149 1252 Planarity : 0.004 0.053 1402 Dihedral : 5.256 53.668 1140 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.86 % Allowed : 16.57 % Favored : 80.57 % 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: -0.25 (0.26), residues: 1002 helix: 1.33 (0.27), residues: 386 sheet: -0.14 (0.33), residues: 210 loop : -1.67 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 142 average time/residue: 1.5226 time to fit residues: 227.0946 Evaluate side-chains 128 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1853 time to fit residues: 2.0052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 72.1963 > 50: distance: 31 - 34: 34.699 distance: 34 - 35: 40.552 distance: 35 - 36: 39.177 distance: 35 - 38: 41.060 distance: 36 - 41: 69.315 distance: 38 - 39: 39.738 distance: 38 - 40: 12.501 distance: 41 - 42: 57.642 distance: 42 - 43: 51.104 distance: 42 - 45: 38.508 distance: 43 - 44: 41.013 distance: 43 - 48: 40.872 distance: 45 - 46: 40.202 distance: 46 - 47: 57.754 distance: 49 - 50: 41.235 distance: 49 - 52: 39.851 distance: 50 - 51: 39.645 distance: 50 - 57: 40.942 distance: 52 - 53: 41.172 distance: 54 - 55: 54.613 distance: 54 - 56: 56.625 distance: 57 - 63: 39.502 distance: 58 - 59: 38.905 distance: 58 - 61: 40.771 distance: 59 - 64: 56.688 distance: 61 - 62: 57.035 distance: 62 - 63: 56.635 distance: 64 - 65: 40.492 distance: 65 - 66: 34.882 distance: 66 - 67: 40.947 distance: 66 - 68: 52.451 distance: 68 - 69: 39.077 distance: 69 - 70: 56.952 distance: 69 - 72: 57.774 distance: 70 - 71: 40.121 distance: 70 - 77: 40.938 distance: 72 - 73: 56.625 distance: 73 - 74: 41.290 distance: 74 - 75: 39.086 distance: 74 - 76: 40.549 distance: 77 - 78: 39.088 distance: 78 - 81: 40.421 distance: 79 - 80: 40.102 distance: 79 - 85: 56.846 distance: 81 - 82: 39.827 distance: 82 - 83: 34.776 distance: 85 - 86: 40.594 distance: 85 - 91: 40.079 distance: 86 - 87: 39.864 distance: 86 - 89: 56.475 distance: 87 - 88: 39.181 distance: 87 - 92: 40.934 distance: 88 - 117: 35.830 distance: 89 - 90: 39.829 distance: 90 - 91: 40.381 distance: 93 - 96: 40.201 distance: 94 - 103: 56.650 distance: 95 - 124: 31.919 distance: 96 - 97: 41.169 distance: 97 - 98: 69.027 distance: 98 - 99: 40.574 distance: 99 - 100: 39.534 distance: 104 - 105: 39.557 distance: 105 - 106: 51.037 distance: 105 - 110: 34.628 distance: 106 - 129: 29.720 distance: 107 - 108: 40.835 distance: 107 - 109: 57.117