Starting phenix.real_space_refine on Fri Aug 2 15:43:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7l_18219/08_2024/8q7l_18219.cif" } resolution = 2.82 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= 0.003 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 6 5.16 5 C 2124 2.51 5 N 618 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3375 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.50, per 1000 atoms: 1.04 Number of scatterers: 3375 At special positions: 0 Unit cell: (127.72, 140.08, 48.616, 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 6 16.00 O 627 8.00 N 618 7.00 C 2124 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 - 3.50 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: 0.98 Conformation dependent library (CDL) restraints added in 746.4 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 54.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.817A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.787A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.396A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.451A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346 removed outlier: 6.822A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP A 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE C 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.470A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.400A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.381A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.381A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.957A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.748A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.582A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS E 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER D 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY E 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS D 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU E 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER F 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY D 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.495A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.553A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.530A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.439A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.237A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 372 Processing sheet with id=AC1, first strand: chain 'E' and resid 376 through 377 removed outlier: 6.812A pdb=" N LEU D 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 219 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: 0.84 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 935 1.33 - 1.45: 431 1.45 - 1.57: 2057 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3429 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.79e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.74e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.67e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.47e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.40e+00 ... (remaining 3424 not shown) Histogram of bond angle deviations from ideal: 101.91 - 107.45: 212 107.45 - 112.99: 1685 112.99 - 118.53: 864 118.53 - 124.07: 1558 124.07 - 129.61: 271 Bond angle restraints: 4590 Sorted by residual: angle pdb=" C GLY C 334 " pdb=" N GLY C 335 " pdb=" CA GLY C 335 " ideal model delta sigma weight residual 122.83 129.61 -6.78 1.21e+00 6.83e-01 3.14e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.91 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 121.83 -3.67 7.00e-01 2.04e+00 2.74e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.57 5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.63 4.97 1.00e+00 1.00e+00 2.47e+01 ... (remaining 4585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.30: 1855 12.30 - 24.60: 174 24.60 - 36.89: 35 36.89 - 49.19: 11 49.19 - 61.49: 13 Dihedral angle restraints: 2088 sinusoidal: 873 harmonic: 1215 Sorted by residual: dihedral pdb=" C LYS E 311 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " pdb=" CB LYS E 311 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" CA VAL E 306 " pdb=" C VAL E 306 " pdb=" N GLN E 307 " pdb=" CA GLN E 307 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA VAL D 306 " pdb=" C VAL D 306 " pdb=" N GLN D 307 " pdb=" CA GLN D 307 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 362 0.099 - 0.198: 124 0.198 - 0.297: 21 0.297 - 0.395: 9 0.395 - 0.494: 3 Chirality restraints: 519 Sorted by residual: chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 516 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.038 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.037 2.00e-02 2.50e+03 2.76e-02 1.14e+01 pdb=" CG HIS A 374 " -0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 334 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLY C 334 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY C 334 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 335 " 0.019 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 31 2.71 - 3.26: 2815 3.26 - 3.80: 4737 3.80 - 4.35: 6362 4.35 - 4.90: 11409 Nonbonded interactions: 25354 Sorted by model distance: nonbonded pdb=" NZ LYS B 343 " pdb=" OE1 GLU F 338 " model vdw 2.159 3.120 nonbonded pdb=" NZ LYS C 347 " pdb=" O GLY E 333 " model vdw 2.250 3.120 nonbonded pdb=" O LYS B 347 " pdb=" NZ LYS F 331 " model vdw 2.276 3.120 nonbonded pdb=" O LYS A 347 " pdb=" NZ LYS D 331 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS A 343 " pdb=" OE1 GLU D 338 " model vdw 2.385 3.120 ... (remaining 25349 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 306 through 378) selection = (chain 'B' and resid 306 through 378) selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.760 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:16.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.011 0.040 3429 Z= 0.739 Angle : 1.904 9.709 4590 Z= 1.254 Chirality : 0.110 0.494 519 Planarity : 0.009 0.046 582 Dihedral : 11.675 61.489 1314 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 1.03 % 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: -2.15 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 330 PHE 0.033 0.010 PHE D 346 TYR 0.056 0.012 TYR E 310 ARG 0.008 0.002 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 324 SER cc_start: 0.8807 (m) cc_final: 0.8539 (t) REVERT: A 338 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6983 (tt0) REVERT: A 340 LYS cc_start: 0.7573 (mttt) cc_final: 0.7261 (mttm) REVERT: A 369 LYS cc_start: 0.7499 (ttmt) cc_final: 0.6875 (tttp) REVERT: A 370 LYS cc_start: 0.8031 (tttt) cc_final: 0.7823 (tttt) REVERT: B 311 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8273 (pttp) REVERT: B 338 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 340 LYS cc_start: 0.8404 (mttt) cc_final: 0.8115 (mttm) REVERT: B 369 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7533 (tttt) REVERT: C 311 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7617 (mmtm) REVERT: C 356 SER cc_start: 0.7815 (t) cc_final: 0.7497 (t) REVERT: C 369 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7132 (tttt) REVERT: C 370 LYS cc_start: 0.8610 (tttt) cc_final: 0.8153 (tttm) REVERT: D 353 LYS cc_start: 0.7858 (mttt) cc_final: 0.7534 (mttt) REVERT: D 358 ASP cc_start: 0.8451 (m-30) cc_final: 0.8128 (m-30) REVERT: E 311 LYS cc_start: 0.8348 (pttt) cc_final: 0.8024 (ptmt) REVERT: E 345 ASP cc_start: 0.8077 (t0) cc_final: 0.7665 (t0) REVERT: E 375 LYS cc_start: 0.7949 (tttt) cc_final: 0.7695 (ttpp) REVERT: E 378 PHE cc_start: 0.5921 (t80) cc_final: 0.5550 (t80) REVERT: F 307 GLN cc_start: 0.8121 (pt0) cc_final: 0.7274 (pm20) REVERT: F 311 LYS cc_start: 0.8162 (pttt) cc_final: 0.7782 (ttpt) REVERT: F 342 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7614 (mp0) REVERT: F 358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8217 (m-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 1.2857 time to fit residues: 201.2950 Evaluate side-chains 111 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS C 368 ASN D 330 HIS D 359 ASN E 330 HIS E 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3429 Z= 0.204 Angle : 0.663 5.854 4590 Z= 0.330 Chirality : 0.052 0.137 519 Planarity : 0.003 0.030 582 Dihedral : 5.697 16.016 450 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.81 % Allowed : 13.18 % Favored : 85.01 % 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: -1.88 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE A 346 TYR 0.025 0.003 TYR D 310 ARG 0.006 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8820 (m) cc_final: 0.8435 (t) REVERT: A 338 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6937 (tt0) REVERT: A 340 LYS cc_start: 0.7681 (mttt) cc_final: 0.7204 (mttm) REVERT: A 349 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7615 (mtt-85) REVERT: B 311 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8273 (pttm) REVERT: B 338 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7609 (tt0) REVERT: B 340 LYS cc_start: 0.8370 (mttt) cc_final: 0.7818 (mttm) REVERT: B 369 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7414 (tttt) REVERT: B 373 THR cc_start: 0.8281 (m) cc_final: 0.8003 (p) REVERT: C 311 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7605 (mmtm) REVERT: C 338 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6993 (tt0) REVERT: C 369 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7303 (tttt) REVERT: C 370 LYS cc_start: 0.8581 (tttt) cc_final: 0.8149 (tttm) REVERT: C 375 LYS cc_start: 0.7586 (ptmt) cc_final: 0.6847 (ptpp) REVERT: E 311 LYS cc_start: 0.8381 (pttt) cc_final: 0.7821 (ptmt) REVERT: E 322 CYS cc_start: 0.8290 (p) cc_final: 0.7790 (m) REVERT: E 345 ASP cc_start: 0.7824 (t0) cc_final: 0.7392 (t70) REVERT: E 375 LYS cc_start: 0.8105 (tttt) cc_final: 0.7870 (ttpp) REVERT: F 311 LYS cc_start: 0.8093 (pttt) cc_final: 0.7644 (ptmt) REVERT: F 342 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7596 (mp0) REVERT: F 349 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7209 (mtm180) outliers start: 7 outliers final: 2 residues processed: 123 average time/residue: 1.2809 time to fit residues: 161.4498 Evaluate side-chains 107 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 362 HIS C 362 HIS F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3429 Z= 0.252 Angle : 0.667 6.564 4590 Z= 0.326 Chirality : 0.051 0.133 519 Planarity : 0.003 0.020 582 Dihedral : 5.150 12.892 450 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.33 % Allowed : 17.05 % Favored : 80.62 % 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: -2.04 (0.33), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.009 0.002 PHE B 378 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6884 (tt0) REVERT: A 340 LYS cc_start: 0.7651 (mttt) cc_final: 0.7215 (mttm) REVERT: A 349 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7744 (mtt-85) REVERT: A 369 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6751 (tttp) REVERT: B 311 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8121 (pttm) REVERT: B 338 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7635 (tt0) REVERT: B 340 LYS cc_start: 0.8400 (mttt) cc_final: 0.7844 (mttm) REVERT: B 369 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7499 (tttt) REVERT: B 373 THR cc_start: 0.8354 (m) cc_final: 0.8011 (p) REVERT: C 311 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7654 (mmtm) REVERT: C 369 LYS cc_start: 0.7699 (ttmt) cc_final: 0.7392 (ttmm) REVERT: C 370 LYS cc_start: 0.8570 (tttt) cc_final: 0.8093 (tttm) REVERT: C 375 LYS cc_start: 0.7681 (ptmt) cc_final: 0.7278 (ptpp) REVERT: E 311 LYS cc_start: 0.8415 (pttt) cc_final: 0.7896 (ptmt) REVERT: E 343 LYS cc_start: 0.7756 (ttmt) cc_final: 0.6917 (mmtt) REVERT: E 345 ASP cc_start: 0.7791 (t0) cc_final: 0.7251 (t70) REVERT: E 370 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7528 (tmtt) REVERT: F 311 LYS cc_start: 0.8209 (pttt) cc_final: 0.7662 (ptmt) REVERT: F 342 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7562 (mp0) REVERT: F 343 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7741 (tttm) REVERT: F 349 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7336 (mtm180) outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 1.2558 time to fit residues: 157.0869 Evaluate side-chains 112 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 370 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 58.4115 > 50: distance: 32 - 36: 17.763 distance: 36 - 37: 10.038 distance: 37 - 38: 9.897 distance: 37 - 40: 16.564 distance: 38 - 39: 20.381 distance: 38 - 44: 28.345 distance: 40 - 41: 6.160 distance: 41 - 42: 16.600 distance: 41 - 43: 22.729 distance: 44 - 45: 26.264 distance: 45 - 46: 38.356 distance: 46 - 47: 20.633 distance: 46 - 48: 18.524 distance: 48 - 49: 25.055 distance: 49 - 50: 16.706 distance: 49 - 52: 5.347 distance: 50 - 51: 19.986 distance: 50 - 56: 27.355 distance: 52 - 53: 9.540 distance: 53 - 54: 11.779 distance: 53 - 55: 30.263 distance: 56 - 57: 7.676 distance: 57 - 58: 7.986 distance: 57 - 60: 35.544 distance: 58 - 59: 19.196 distance: 58 - 64: 13.614 distance: 60 - 61: 34.176 distance: 60 - 62: 27.211 distance: 61 - 63: 19.187 distance: 64 - 65: 22.663 distance: 64 - 146: 19.143 distance: 65 - 66: 10.906 distance: 65 - 68: 12.740 distance: 66 - 67: 16.589 distance: 66 - 74: 14.745 distance: 67 - 161: 19.953 distance: 68 - 69: 7.963 distance: 69 - 70: 16.341 distance: 69 - 71: 30.749 distance: 70 - 72: 19.277 distance: 71 - 73: 13.074 distance: 72 - 73: 19.235 distance: 74 - 75: 12.870 distance: 75 - 76: 10.531 distance: 75 - 78: 14.114 distance: 76 - 77: 18.977 distance: 76 - 84: 5.950 distance: 78 - 79: 4.906 distance: 79 - 80: 8.847 distance: 79 - 81: 4.549 distance: 80 - 82: 5.075 distance: 81 - 83: 4.899 distance: 82 - 83: 6.692 distance: 84 - 85: 5.092 distance: 85 - 86: 19.057 distance: 85 - 88: 20.441 distance: 86 - 87: 23.815 distance: 86 - 93: 11.083 distance: 88 - 89: 9.376 distance: 89 - 90: 10.980 distance: 90 - 91: 4.872 distance: 93 - 94: 31.104 distance: 93 - 99: 22.897 distance: 94 - 95: 23.924 distance: 94 - 97: 14.340 distance: 95 - 96: 25.823 distance: 95 - 100: 34.616 distance: 97 - 98: 19.139 distance: 100 - 101: 25.275 distance: 101 - 102: 15.589 distance: 102 - 103: 36.591 distance: 102 - 104: 31.655 distance: 104 - 105: 38.058 distance: 105 - 106: 5.362 distance: 106 - 107: 5.845 distance: 106 - 108: 22.672