Starting phenix.real_space_refine on Fri Jan 17 09:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.map" model { file = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzq_34401/01_2025/8gzq_34401.cif" } resolution = 3.9 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 68 5.49 5 S 39 5.16 5 C 6285 2.51 5 N 1918 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10372 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6423 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 40, 'TRANS': 811} Chain breaks: 3 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 408 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 12, 'GLU:plan': 37, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 296 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2513 Classifications: {'peptide': 408} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 25, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 27, 'TYR:plan': 1, 'ASN:plan1': 11, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 393 Chain: "S" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1406 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 7, 'rna3p': 58} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5166 SG CYS A 728 58.412 41.457 34.079 1.00 92.91 S ATOM 6106 SG CYS A 847 61.688 43.262 34.948 1.00111.96 S ATOM 3115 SG CYS A 446 18.025 60.139 39.318 1.00135.00 S ATOM 3131 SG CYS A 449 18.877 57.138 38.017 1.00131.52 S Time building chain proxies: 7.13, per 1000 atoms: 0.69 Number of scatterers: 10372 At special positions: 0 Unit cell: (122.618, 96.9345, 108.533, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 39 16.00 P 68 15.00 O 2060 8.00 N 1918 7.00 C 6285 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 714 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 712 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 847 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 728 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 446 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 441 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 449 " Number of angles added : 2 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 49.0% alpha, 9.0% beta 22 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.769A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.790A pdb=" N GLY A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 241 Processing helix chain 'A' and resid 272 through 287 removed outlier: 5.210A pdb=" N GLU A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 332' Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.715A pdb=" N ALA A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 428 through 444 Processing helix chain 'A' and resid 472 through 489 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 510 through 524 removed outlier: 3.595A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.675A pdb=" N ILE A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.560A pdb=" N MET A 556 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.614A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 625 Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 639 through 656 removed outlier: 4.584A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 677 through 685 removed outlier: 4.102A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 removed outlier: 3.971A pdb=" N LEU A 734 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 766 removed outlier: 3.542A pdb=" N CYS A 753 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.536A pdb=" N VAL A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 853 through 875 removed outlier: 5.833A pdb=" N LEU A 864 " --> pdb=" O ALA A 860 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.920A pdb=" N ALA B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.816A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 390 through 400 removed outlier: 4.846A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.080A pdb=" N ASP B 485 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 Processing helix chain 'B' and resid 527 through 540 Processing helix chain 'B' and resid 544 through 554 removed outlier: 3.762A pdb=" N GLU B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.698A pdb=" N SER B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 127 removed outlier: 8.754A pdb=" N LYS A 125 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 100 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET A 127 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY A 102 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLY A 75 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 99 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 309 removed outlier: 5.594A pdb=" N TYR A 304 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER A 593 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 306 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 451 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 578 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 661 Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 717 Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 192 removed outlier: 6.337A pdb=" N LEU B 220 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP B 285 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 222 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 219 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET B 261 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE B 221 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG B 242 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS B 262 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 334 through 337 removed outlier: 6.721A pdb=" N GLN B 334 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE B 475 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU B 336 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 423 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 432 through 435 442 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 3.14 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: 2984 1.33 - 1.45: 2607 1.45 - 1.57: 4978 1.57 - 1.70: 133 1.70 - 1.82: 64 Bond restraints: 10766 Sorted by residual: bond pdb=" CB TRP A 817 " pdb=" CG TRP A 817 " ideal model delta sigma weight residual 1.498 1.414 0.084 3.10e-02 1.04e+03 7.28e+00 bond pdb=" CB TRP A 762 " pdb=" CG TRP A 762 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.17e+00 bond pdb=" C VAL A 836 " pdb=" N PRO A 837 " ideal model delta sigma weight residual 1.334 1.278 0.056 2.34e-02 1.83e+03 5.72e+00 bond pdb=" CB ASN A 609 " pdb=" CG ASN A 609 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.74e+00 bond pdb=" CB TRP A 703 " pdb=" CG TRP A 703 " ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.25e+00 ... (remaining 10761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 14073 1.56 - 3.11: 821 3.11 - 4.67: 112 4.67 - 6.22: 22 6.22 - 7.78: 10 Bond angle restraints: 15038 Sorted by residual: angle pdb=" C ARG A 737 " pdb=" N ALA A 738 " pdb=" CA ALA A 738 " ideal model delta sigma weight residual 122.65 117.57 5.08 1.60e+00 3.91e-01 1.01e+01 angle pdb=" C3' A S 19 " pdb=" O3' A S 19 " pdb=" P C S 20 " ideal model delta sigma weight residual 120.20 124.86 -4.66 1.50e+00 4.44e-01 9.67e+00 angle pdb=" C3' U S 61 " pdb=" O3' U S 61 " pdb=" P U S 62 " ideal model delta sigma weight residual 120.20 124.55 -4.35 1.50e+00 4.44e-01 8.41e+00 angle pdb=" C HIS A 52 " pdb=" N HIS A 53 " pdb=" CA HIS A 53 " ideal model delta sigma weight residual 122.33 117.47 4.86 1.68e+00 3.54e-01 8.38e+00 angle pdb=" C4' A S 19 " pdb=" C3' A S 19 " pdb=" O3' A S 19 " ideal model delta sigma weight residual 113.00 109.00 4.00 1.50e+00 4.44e-01 7.12e+00 ... (remaining 15033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 6068 33.99 - 67.97: 266 67.97 - 101.96: 27 101.96 - 135.94: 2 135.94 - 169.93: 1 Dihedral angle restraints: 6364 sinusoidal: 2732 harmonic: 3632 Sorted by residual: dihedral pdb=" O2B GDP S 201 " pdb=" O3A GDP S 201 " pdb=" PB GDP S 201 " pdb=" PA GDP S 201 " ideal model delta sinusoidal sigma weight residual 180.00 47.70 132.30 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA PRO B 544 " pdb=" C PRO B 544 " pdb=" N VAL B 545 " pdb=" CA VAL B 545 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" O5' GDP S 201 " pdb=" O3A GDP S 201 " pdb=" PA GDP S 201 " pdb=" PB GDP S 201 " ideal model delta sinusoidal sigma weight residual -179.98 -101.15 -78.83 1 2.00e+01 2.50e-03 1.93e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1144 0.043 - 0.087: 439 0.087 - 0.130: 131 0.130 - 0.173: 18 0.173 - 0.216: 3 Chirality restraints: 1735 Sorted by residual: chirality pdb=" P A S 1 " pdb=" OP1 A S 1 " pdb=" OP2 A S 1 " pdb=" O5' A S 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.63 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' U S 61 " pdb=" C4' U S 61 " pdb=" O3' U S 61 " pdb=" C2' U S 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" P C S 67 " pdb=" OP1 C S 67 " pdb=" OP2 C S 67 " pdb=" O5' C S 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1732 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 726 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 727 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 727 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 727 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 502 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C SER A 502 " -0.032 2.00e-02 2.50e+03 pdb=" O SER A 502 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 503 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 364 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.023 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 24 2.46 - 3.07: 7792 3.07 - 3.68: 16848 3.68 - 4.29: 22885 4.29 - 4.90: 35965 Nonbonded interactions: 83514 Sorted by model distance: nonbonded pdb=" OE2 GLU A 437 " pdb="ZN ZN A1002 " model vdw 1.852 2.230 nonbonded pdb=" O GLN A 602 " pdb=" OG1 THR A 605 " model vdw 2.242 3.040 nonbonded pdb=" N3 G S 18 " pdb=" O2' A S 45 " model vdw 2.270 3.120 nonbonded pdb=" N2 G S 18 " pdb=" N3 A S 45 " model vdw 2.328 3.200 nonbonded pdb=" NH1 ARG A 386 " pdb=" O ASN A 501 " model vdw 2.352 3.120 ... (remaining 83509 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 ========== 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 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: 0.790 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 0.084 10766 Z= 0.737 Angle : 0.836 7.779 15038 Z= 0.459 Chirality : 0.049 0.216 1735 Planarity : 0.005 0.051 1707 Dihedral : 17.512 169.926 4016 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.27 % Allowed : 4.63 % Favored : 95.10 % 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: -1.11 (0.23), residues: 1242 helix: 0.59 (0.22), residues: 557 sheet: -1.39 (0.42), residues: 148 loop : -1.98 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 703 HIS 0.007 0.002 HIS A 512 PHE 0.016 0.003 PHE A 25 TYR 0.012 0.002 TYR A 308 ARG 0.005 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8854 (t0) cc_final: 0.8580 (t0) REVERT: A 246 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 824 MET cc_start: 0.8735 (tpt) cc_final: 0.8507 (tpt) REVERT: B 217 LEU cc_start: 0.9056 (mt) cc_final: 0.8566 (tt) REVERT: B 279 TYR cc_start: 0.8647 (m-80) cc_final: 0.7896 (m-80) REVERT: B 284 MET cc_start: 0.8338 (ttt) cc_final: 0.7941 (tmm) REVERT: B 379 ASN cc_start: 0.8761 (m-40) cc_final: 0.8429 (m110) REVERT: B 418 PHE cc_start: 0.8834 (m-10) cc_final: 0.8559 (m-10) REVERT: B 510 PHE cc_start: 0.9177 (t80) cc_final: 0.8967 (t80) REVERT: B 563 TRP cc_start: 0.8498 (p-90) cc_final: 0.7600 (p-90) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.2058 time to fit residues: 39.4336 Evaluate side-chains 98 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 771 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 66 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050032 restraints weight = 48013.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.051519 restraints weight = 25112.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052524 restraints weight = 16275.195| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10766 Z= 0.154 Angle : 0.528 6.686 15038 Z= 0.271 Chirality : 0.039 0.187 1735 Planarity : 0.004 0.046 1707 Dihedral : 17.925 166.905 2372 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.09 % Allowed : 9.54 % Favored : 89.37 % 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: 0.48 (0.25), residues: 1242 helix: 2.12 (0.23), residues: 551 sheet: -0.82 (0.43), residues: 145 loop : -1.30 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 859 HIS 0.004 0.001 HIS A 712 PHE 0.016 0.001 PHE B 614 TYR 0.010 0.001 TYR B 395 ARG 0.006 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8834 (t0) cc_final: 0.8600 (t0) REVERT: A 246 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 252 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7834 (mp0) REVERT: A 356 GLU cc_start: 0.8380 (pp20) cc_final: 0.8132 (pp20) REVERT: A 533 ASP cc_start: 0.8052 (p0) cc_final: 0.7816 (p0) REVERT: A 589 MET cc_start: 0.9242 (tpp) cc_final: 0.8685 (tpt) REVERT: B 279 TYR cc_start: 0.8646 (m-80) cc_final: 0.7867 (m-80) REVERT: B 379 ASN cc_start: 0.8665 (m-40) cc_final: 0.8223 (m110) REVERT: B 418 PHE cc_start: 0.8787 (m-10) cc_final: 0.8535 (m-10) REVERT: B 510 PHE cc_start: 0.9161 (t80) cc_final: 0.8949 (t80) REVERT: B 563 TRP cc_start: 0.8594 (p-90) cc_final: 0.7778 (p-90) outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.1804 time to fit residues: 31.7883 Evaluate side-chains 107 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 496 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 11 optimal weight: 0.0980 chunk 104 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 GLN ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050026 restraints weight = 47530.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051576 restraints weight = 24335.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052628 restraints weight = 15577.106| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10766 Z= 0.141 Angle : 0.504 6.749 15038 Z= 0.251 Chirality : 0.038 0.183 1735 Planarity : 0.004 0.057 1707 Dihedral : 17.586 168.159 2372 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.95 % Allowed : 11.72 % Favored : 87.33 % 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: 0.81 (0.25), residues: 1242 helix: 2.38 (0.23), residues: 551 sheet: -0.74 (0.44), residues: 146 loop : -1.07 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 351 HIS 0.004 0.001 HIS A 712 PHE 0.020 0.001 PHE A 25 TYR 0.008 0.001 TYR A 308 ARG 0.005 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.163 Fit side-chains REVERT: A 79 ASP cc_start: 0.8802 (t0) cc_final: 0.8582 (t0) REVERT: A 252 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7888 (mp0) REVERT: A 356 GLU cc_start: 0.8421 (pp20) cc_final: 0.8105 (pp20) REVERT: A 589 MET cc_start: 0.9268 (tpp) cc_final: 0.8661 (tpt) REVERT: A 765 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8661 (mmm) REVERT: B 279 TYR cc_start: 0.8656 (m-80) cc_final: 0.7656 (m-80) REVERT: B 284 MET cc_start: 0.7862 (tmm) cc_final: 0.7659 (tmm) REVERT: B 379 ASN cc_start: 0.8574 (m-40) cc_final: 0.8143 (m110) REVERT: B 418 PHE cc_start: 0.8846 (m-10) cc_final: 0.8568 (m-10) REVERT: B 563 TRP cc_start: 0.8604 (p-90) cc_final: 0.7808 (p-90) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.1737 time to fit residues: 29.0131 Evaluate side-chains 102 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 69.4211 > 50: distance: 45 - 48: 12.900 distance: 48 - 49: 29.936 distance: 49 - 50: 5.803 distance: 49 - 52: 12.518 distance: 50 - 51: 11.564 distance: 50 - 53: 16.362 distance: 54 - 55: 25.684 distance: 54 - 57: 11.100 distance: 55 - 56: 7.148 distance: 55 - 64: 58.153 distance: 57 - 58: 17.055 distance: 58 - 59: 27.580 distance: 58 - 60: 17.635 distance: 59 - 61: 13.362 distance: 60 - 62: 25.693 distance: 61 - 63: 24.161 distance: 62 - 63: 41.622 distance: 64 - 65: 46.822 distance: 65 - 66: 39.302 distance: 65 - 68: 32.552 distance: 66 - 67: 42.608 distance: 66 - 69: 18.737 distance: 69 - 70: 14.830 distance: 69 - 75: 28.663 distance: 70 - 71: 38.247 distance: 70 - 73: 22.467 distance: 71 - 72: 55.812 distance: 71 - 76: 13.632 distance: 74 - 75: 50.962 distance: 77 - 78: 33.011 distance: 78 - 79: 30.016 distance: 78 - 81: 13.955 distance: 81 - 82: 23.112 distance: 82 - 83: 27.568 distance: 82 - 85: 28.611 distance: 83 - 84: 21.877 distance: 83 - 92: 17.310 distance: 85 - 86: 10.621 distance: 86 - 87: 8.189 distance: 87 - 88: 10.125 distance: 88 - 89: 19.486 distance: 89 - 90: 32.195 distance: 89 - 91: 24.958 distance: 92 - 93: 14.935 distance: 93 - 94: 35.600 distance: 93 - 96: 24.305 distance: 94 - 95: 34.686 distance: 94 - 97: 23.085 distance: 97 - 98: 6.312 distance: 98 - 99: 14.940 distance: 98 - 101: 8.014 distance: 99 - 100: 13.484 distance: 101 - 102: 17.570 distance: 102 - 103: 8.374 distance: 103 - 104: 20.053 distance: 104 - 105: 10.909 distance: 107 - 108: 40.699 distance: 108 - 109: 29.594 distance: 108 - 110: 16.229 distance: 110 - 111: 6.238 distance: 111 - 112: 24.289 distance: 111 - 114: 12.642 distance: 112 - 113: 32.341 distance: 112 - 119: 21.872 distance: 114 - 115: 33.455 distance: 115 - 116: 16.871 distance: 116 - 117: 5.835 distance: 116 - 118: 22.597