Starting phenix.real_space_refine on Tue Jun 10 06:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxg_40851/06_2025/8sxg_40851.cif" } resolution = 4.14 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= 0.047 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 17 5.16 5 C 7109 2.51 5 N 2021 2.21 5 O 2225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11372 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2748 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2723 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 20, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4248 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 512} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1623 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain breaks: 2 Time building chain proxies: 7.83, per 1000 atoms: 0.69 Number of scatterers: 11372 At special positions: 0 Unit cell: (91.908, 141.588, 142.83, 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 17 16.00 O 2225 8.00 N 2021 7.00 C 7109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.902A pdb=" N LEU A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 82 removed outlier: 4.183A pdb=" N ASP A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.808A pdb=" N PHE A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.885A pdb=" N SER A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.581A pdb=" N SER A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.873A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.851A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.631A pdb=" N GLU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.572A pdb=" N ALA B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.013A pdb=" N GLU B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.637A pdb=" N GLN B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.791A pdb=" N SER B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 4.022A pdb=" N VAL B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.617A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.741A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 163 removed outlier: 4.171A pdb=" N GLU C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.951A pdb=" N LEU C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 4.295A pdb=" N ALA C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 removed outlier: 4.075A pdb=" N ARG C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 233 removed outlier: 3.577A pdb=" N LEU C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 250 Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 253 through 267 removed outlier: 4.161A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.617A pdb=" N ARG C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 320 through 335 Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.958A pdb=" N VAL C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 369 removed outlier: 3.577A pdb=" N ALA C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.856A pdb=" N GLN C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 423 through 438 removed outlier: 3.619A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 454 Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.678A pdb=" N LEU C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 492 through 507 Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.630A pdb=" N ALA C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.682A pdb=" N PHE E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.866A pdb=" N SER E 416 " --> pdb=" O ARG E 412 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP E 417 " --> pdb=" O PRO E 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 412 through 417' Processing helix chain 'E' and resid 417 through 433 removed outlier: 3.558A pdb=" N SER E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.637A pdb=" N TYR A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 5.686A pdb=" N LYS A 343 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 334 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 345 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 332 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.650A pdb=" N ALA A 187 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.996A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 138 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.996A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 138 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 171 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE A 143 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 169 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 200 removed outlier: 7.073A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 204 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP A 240 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 206 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 296 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 114 removed outlier: 7.021A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 119 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 114 removed outlier: 7.021A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 119 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B 171 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 143 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR B 169 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 172 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 180 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.688A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 278 removed outlier: 3.646A pdb=" N LEU B 277 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 269 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 347 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 335 Processing sheet with id=AB4, first strand: chain 'E' and resid 197 through 200 removed outlier: 5.556A pdb=" N VAL E 198 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR E 205 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA E 204 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASP E 240 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 206 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU E 237 " --> pdb=" O VAL E 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 264 through 266 647 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3954 1.34 - 1.46: 1228 1.46 - 1.57: 6320 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 11535 Sorted by residual: bond pdb=" CG GLU C 344 " pdb=" CD GLU C 344 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N SER B 193 " pdb=" CA SER B 193 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 6.02e-01 bond pdb=" C GLU A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.332 1.340 -0.008 1.12e-02 7.97e+03 5.73e-01 bond pdb=" N VAL B 290 " pdb=" CA VAL B 290 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.69e-01 bond pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.92e-01 ... (remaining 11530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 14991 1.07 - 2.14: 466 2.14 - 3.21: 94 3.21 - 4.28: 48 4.28 - 5.35: 5 Bond angle restraints: 15604 Sorted by residual: angle pdb=" N ARG E 434 " pdb=" CA ARG E 434 " pdb=" CB ARG E 434 " ideal model delta sigma weight residual 114.17 110.82 3.35 1.14e+00 7.69e-01 8.65e+00 angle pdb=" N GLU C 344 " pdb=" CA GLU C 344 " pdb=" CB GLU C 344 " ideal model delta sigma weight residual 110.22 114.27 -4.05 1.54e+00 4.22e-01 6.92e+00 angle pdb=" C ALA B 302 " pdb=" CA ALA B 302 " pdb=" CB ALA B 302 " ideal model delta sigma weight residual 110.42 115.65 -5.23 1.99e+00 2.53e-01 6.91e+00 angle pdb=" C SER B 193 " pdb=" CA SER B 193 " pdb=" CB SER B 193 " ideal model delta sigma weight residual 110.42 115.60 -5.18 1.99e+00 2.53e-01 6.78e+00 angle pdb=" C LEU B 311 " pdb=" N GLN B 312 " pdb=" CA GLN B 312 " ideal model delta sigma weight residual 121.64 116.29 5.35 2.13e+00 2.20e-01 6.30e+00 ... (remaining 15599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6422 17.94 - 35.88: 568 35.88 - 53.82: 90 53.82 - 71.76: 13 71.76 - 89.70: 13 Dihedral angle restraints: 7106 sinusoidal: 2862 harmonic: 4244 Sorted by residual: dihedral pdb=" CA ASP A 313 " pdb=" C ASP A 313 " pdb=" N GLN A 314 " pdb=" CA GLN A 314 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN E 230 " pdb=" C ASN E 230 " pdb=" N LYS E 231 " pdb=" CA LYS E 231 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ALA A 58 " pdb=" C ALA A 58 " pdb=" N ALA A 59 " pdb=" CA ALA A 59 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 7103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1175 0.028 - 0.056: 380 0.056 - 0.084: 104 0.084 - 0.112: 78 0.112 - 0.140: 34 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 168 " pdb=" N ILE B 168 " pdb=" C ILE B 168 " pdb=" CB ILE B 168 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 143 " pdb=" N ILE A 143 " pdb=" C ILE A 143 " pdb=" CB ILE A 143 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1768 not shown) Planarity restraints: 2081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 89 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 90 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 415 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.00e+00 pdb=" C GLU C 415 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU C 415 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY C 416 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 57 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LEU C 57 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU C 57 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 58 " -0.008 2.00e-02 2.50e+03 ... (remaining 2078 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 110 2.49 - 3.09: 9088 3.09 - 3.70: 18427 3.70 - 4.30: 25336 4.30 - 4.90: 41450 Nonbonded interactions: 94411 Sorted by model distance: nonbonded pdb=" OG SER B 193 " pdb=" OE1 GLU B 218 " model vdw 1.889 3.040 nonbonded pdb=" O ASN E 297 " pdb=" OG1 THR E 322 " model vdw 2.038 3.040 nonbonded pdb=" O SER B 193 " pdb=" OG1 THR B 209 " model vdw 2.063 3.040 nonbonded pdb=" NH1 ARG B 207 " pdb=" O ILE B 208 " model vdw 2.073 3.120 nonbonded pdb=" O VAL E 248 " pdb=" OG SER E 251 " model vdw 2.091 3.040 ... (remaining 94406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 373 or resid 410 through 436)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 45.410 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.110 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.002 0.026 11535 Z= 0.106 Angle : 0.499 5.347 15604 Z= 0.263 Chirality : 0.038 0.140 1771 Planarity : 0.004 0.050 2081 Dihedral : 14.007 89.698 4378 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 0.78 (0.23), residues: 1461 helix: 1.78 (0.20), residues: 745 sheet: -0.96 (0.42), residues: 178 loop : -0.72 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 537 HIS 0.006 0.001 HIS C 325 PHE 0.010 0.001 PHE C 326 TYR 0.012 0.001 TYR C 54 ARG 0.003 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.16273 ( 632) hydrogen bonds : angle 6.50276 ( 1872) covalent geometry : bond 0.00220 (11535) covalent geometry : angle 0.49949 (15604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 MET cc_start: 0.1539 (tpp) cc_final: 0.1306 (tpp) REVERT: E 265 ILE cc_start: 0.8830 (mm) cc_final: 0.8468 (mm) REVERT: E 320 MET cc_start: 0.8992 (ttp) cc_final: 0.8589 (ttt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2967 time to fit residues: 28.1185 Evaluate side-chains 44 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN E 396 ASN E 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.095276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076534 restraints weight = 54601.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.073813 restraints weight = 64358.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074516 restraints weight = 62610.365| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11535 Z= 0.131 Angle : 0.559 6.196 15604 Z= 0.289 Chirality : 0.041 0.144 1771 Planarity : 0.004 0.036 2081 Dihedral : 4.248 19.740 1613 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: 0.94 (0.22), residues: 1461 helix: 1.84 (0.19), residues: 763 sheet: -0.83 (0.43), residues: 166 loop : -0.65 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 537 HIS 0.003 0.001 HIS C 218 PHE 0.009 0.001 PHE B 104 TYR 0.017 0.002 TYR C 54 ARG 0.006 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 632) hydrogen bonds : angle 4.71784 ( 1872) covalent geometry : bond 0.00292 (11535) covalent geometry : angle 0.55946 (15604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 MET cc_start: 0.1311 (tpp) cc_final: 0.1059 (tpp) REVERT: E 265 ILE cc_start: 0.8560 (mm) cc_final: 0.8160 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2543 time to fit residues: 21.8780 Evaluate side-chains 40 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 127 optimal weight: 0.9990 chunk 138 optimal weight: 0.0040 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 0.0040 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.078181 restraints weight = 55259.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.075966 restraints weight = 63938.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076540 restraints weight = 60082.000| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11535 Z= 0.106 Angle : 0.532 6.249 15604 Z= 0.269 Chirality : 0.040 0.137 1771 Planarity : 0.004 0.037 2081 Dihedral : 4.074 17.867 1613 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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: 1.00 (0.23), residues: 1461 helix: 1.84 (0.19), residues: 767 sheet: -0.85 (0.42), residues: 174 loop : -0.50 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 410 HIS 0.001 0.000 HIS A 84 PHE 0.009 0.001 PHE B 104 TYR 0.014 0.001 TYR A 349 ARG 0.004 0.000 ARG C 437 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 632) hydrogen bonds : angle 4.31186 ( 1872) covalent geometry : bond 0.00222 (11535) covalent geometry : angle 0.53198 (15604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 432 MET cc_start: 0.1569 (tpp) cc_final: 0.1315 (tpp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3234 time to fit residues: 26.7641 Evaluate side-chains 41 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6617 > 50: distance: 2 - 22: 7.450 distance: 9 - 31: 6.088 distance: 14 - 36: 9.779 distance: 17 - 22: 4.674 distance: 18 - 41: 18.008 distance: 23 - 24: 6.974 distance: 23 - 26: 9.457 distance: 24 - 25: 6.670 distance: 24 - 31: 6.015 distance: 26 - 27: 17.954 distance: 27 - 28: 16.228 distance: 28 - 29: 5.549 distance: 29 - 30: 12.835 distance: 31 - 32: 5.848 distance: 32 - 33: 9.409 distance: 32 - 35: 23.558 distance: 33 - 34: 24.709 distance: 33 - 36: 10.791 distance: 36 - 37: 10.881 distance: 37 - 38: 15.938 distance: 37 - 40: 19.209 distance: 38 - 39: 14.983 distance: 38 - 41: 7.751 distance: 41 - 42: 26.721 distance: 42 - 43: 14.386 distance: 42 - 45: 23.567 distance: 43 - 44: 19.231 distance: 43 - 53: 35.353 distance: 45 - 46: 13.829 distance: 46 - 47: 17.447 distance: 46 - 48: 12.971 distance: 47 - 49: 17.967 distance: 48 - 50: 12.358 distance: 49 - 51: 23.669 distance: 50 - 51: 6.906 distance: 51 - 52: 18.983 distance: 53 - 54: 12.402 distance: 54 - 55: 39.497 distance: 54 - 57: 28.838 distance: 55 - 56: 11.815 distance: 55 - 60: 11.704 distance: 57 - 58: 4.379 distance: 57 - 59: 14.698 distance: 60 - 61: 7.643 distance: 61 - 62: 33.170 distance: 61 - 64: 21.499 distance: 62 - 63: 37.275 distance: 62 - 69: 27.696 distance: 64 - 65: 24.275 distance: 65 - 66: 8.439 distance: 66 - 67: 30.637 distance: 66 - 68: 9.427 distance: 69 - 70: 16.164 distance: 69 - 75: 16.005 distance: 70 - 71: 23.143 distance: 70 - 73: 11.235 distance: 71 - 72: 5.197 distance: 73 - 74: 28.211 distance: 74 - 75: 14.330 distance: 76 - 77: 4.404 distance: 77 - 78: 3.684 distance: 77 - 80: 7.839 distance: 78 - 79: 8.611 distance: 78 - 83: 6.987 distance: 80 - 81: 42.493 distance: 80 - 82: 10.715 distance: 83 - 84: 10.095 distance: 84 - 85: 17.401 distance: 84 - 87: 13.533 distance: 85 - 86: 16.015 distance: 85 - 91: 3.812 distance: 86 - 112: 29.570 distance: 87 - 88: 18.313 distance: 88 - 89: 11.568 distance: 88 - 90: 6.364 distance: 91 - 92: 10.928 distance: 92 - 93: 10.881 distance: 92 - 95: 17.815 distance: 93 - 94: 16.975 distance: 93 - 99: 8.437 distance: 94 - 120: 19.164 distance: 95 - 96: 21.398 distance: 96 - 97: 17.581 distance: 96 - 98: 19.457