Starting phenix.real_space_refine on Sat Aug 23 17:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.map" model { file = "/net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zes_14692/08_2025/7zes_14692.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.106 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 86 5.16 5 C 8604 2.51 5 N 2356 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 71.891 74.522 73.975 1.00 67.29 S ATOM 2310 SG CYS A 321 71.507 75.478 77.639 1.00 45.08 S ATOM 2316 SG CYS A 322 71.129 71.926 76.538 1.00 41.17 S ATOM 8698 SG CYS B 287 38.684 34.161 74.110 1.00 65.53 S ATOM 8975 SG CYS B 321 39.255 33.258 77.786 1.00 45.53 S ATOM 8981 SG CYS B 322 39.705 36.860 76.573 1.00 42.58 S Time building chain proxies: 2.80, per 1000 atoms: 0.21 Number of scatterers: 13538 At special positions: 0 Unit cell: (111.922, 109.83, 126.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 86 16.00 P 10 15.00 Mg 2 11.99 O 2478 8.00 N 2356 7.00 C 8604 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: 1.08 Conformation dependent library (CDL) restraints added in 558.9 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 322 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " Number of angles added : 6 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 45.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.591A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.558A pdb=" N PHE A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix removed outlier: 3.689A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.500A pdb=" N ARG A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 481 through 501 removed outlier: 4.355A pdb=" N ASP A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER A 540 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 563 through 586 removed outlier: 3.543A pdb=" N GLU A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 removed outlier: 3.883A pdb=" N ARG A 590 " --> pdb=" O ARG A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.612A pdb=" N ARG A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.577A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.602A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 761 removed outlier: 4.154A pdb=" N LEU A 761 " --> pdb=" O THR A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.633A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 825 " --> pdb=" O HIS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.589A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.346A pdb=" N PHE B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.557A pdb=" N PHE B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix removed outlier: 3.691A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 481 through 501 removed outlier: 4.321A pdb=" N ASP B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 499 " --> pdb=" O LYS B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 540 removed outlier: 3.573A pdb=" N SER B 540 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.542A pdb=" N GLU B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 590 removed outlier: 3.881A pdb=" N ARG B 590 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 587 through 590' Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.616A pdb=" N ARG B 637 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.605A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 4.155A pdb=" N LEU B 761 " --> pdb=" O THR B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 818 through 831 removed outlier: 3.624A pdb=" N TYR B 824 " --> pdb=" O GLU B 820 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 825 " --> pdb=" O HIS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 855 through 858 Processing helix chain 'B' and resid 877 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.196A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.567A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A 304 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.528A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU A 472 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU A 515 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 474 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.329A pdb=" N ILE A 627 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU A 649 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 629 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.151A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER A 839 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER A 853 " --> pdb=" O SER A 839 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.184A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.557A pdb=" N LEU B 199 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS B 304 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB4, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB5, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.543A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 472 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 515 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR B 474 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.317A pdb=" N ILE B 627 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU B 649 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B 629 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.168A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2276 1.32 - 1.44: 3601 1.44 - 1.57: 7827 1.57 - 1.69: 18 1.69 - 1.81: 122 Bond restraints: 13844 Sorted by residual: bond pdb=" C HIS A 598 " pdb=" O HIS A 598 " ideal model delta sigma weight residual 1.232 1.199 0.033 1.20e-02 6.94e+03 7.48e+00 bond pdb=" N ARG B 124 " pdb=" CA ARG B 124 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.79e+00 bond pdb=" N ARG A 124 " pdb=" CA ARG A 124 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.65e+00 bond pdb=" C VAL A 597 " pdb=" N HIS A 598 " ideal model delta sigma weight residual 1.329 1.305 0.024 1.51e-02 4.39e+03 2.51e+00 bond pdb=" CD2 HIS A 598 " pdb=" NE2 HIS A 598 " ideal model delta sigma weight residual 1.374 1.357 0.017 1.10e-02 8.26e+03 2.31e+00 ... (remaining 13839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 17955 1.33 - 2.65: 612 2.65 - 3.98: 133 3.98 - 5.30: 21 5.30 - 6.63: 7 Bond angle restraints: 18728 Sorted by residual: angle pdb=" C VAL A 731 " pdb=" CA VAL A 731 " pdb=" CB VAL A 731 " ideal model delta sigma weight residual 112.46 108.09 4.37 1.33e+00 5.65e-01 1.08e+01 angle pdb=" C VAL B 731 " pdb=" CA VAL B 731 " pdb=" CB VAL B 731 " ideal model delta sigma weight residual 112.46 108.11 4.35 1.33e+00 5.65e-01 1.07e+01 angle pdb=" N ILE A 193 " pdb=" CA ILE A 193 " pdb=" C ILE A 193 " ideal model delta sigma weight residual 112.35 108.28 4.07 1.41e+00 5.03e-01 8.32e+00 angle pdb=" CA HIS A 598 " pdb=" CB HIS A 598 " pdb=" CG HIS A 598 " ideal model delta sigma weight residual 113.80 116.68 -2.88 1.00e+00 1.00e+00 8.28e+00 angle pdb=" CA MET A 830 " pdb=" CB MET A 830 " pdb=" CG MET A 830 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.14e+00 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7623 17.48 - 34.95: 606 34.95 - 52.42: 149 52.42 - 69.90: 25 69.90 - 87.37: 13 Dihedral angle restraints: 8416 sinusoidal: 3584 harmonic: 4832 Sorted by residual: dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N CYS B 126 " pdb=" CA CYS B 126 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLU B 11 " pdb=" C GLU B 11 " pdb=" N PRO B 12 " pdb=" CA PRO B 12 " ideal model delta harmonic sigma weight residual 180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1205 0.031 - 0.062: 570 0.062 - 0.092: 169 0.092 - 0.123: 101 0.123 - 0.154: 13 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CG LEU A 569 " pdb=" CB LEU A 569 " pdb=" CD1 LEU A 569 " pdb=" CD2 LEU A 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CG LEU B 569 " pdb=" CB LEU B 569 " pdb=" CD1 LEU B 569 " pdb=" CD2 LEU B 569 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE B 248 " pdb=" N ILE B 248 " pdb=" C ILE B 248 " pdb=" CB ILE B 248 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2055 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 878 " 0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 879 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 879 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 879 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 878 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO B 879 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 879 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 879 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 598 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C HIS A 598 " -0.030 2.00e-02 2.50e+03 pdb=" O HIS A 598 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 599 " 0.010 2.00e-02 2.50e+03 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 79 2.55 - 3.14: 10265 3.14 - 3.73: 20108 3.73 - 4.31: 29834 4.31 - 4.90: 50395 Nonbonded interactions: 110681 Sorted by model distance: nonbonded pdb=" OE2 GLU A 214 " pdb="MG MG A1002 " model vdw 1.966 2.170 nonbonded pdb=" OE2 GLU B 214 " pdb="MG MG B1002 " model vdw 1.969 2.170 nonbonded pdb=" OE2 GLU A 209 " pdb="MG MG A1002 " model vdw 2.184 2.170 nonbonded pdb=" NH2 ARG B 797 " pdb=" O LYS B 833 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG A 797 " pdb=" O LYS A 833 " model vdw 2.235 3.120 ... (remaining 110676 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.007 0.500 13852 Z= 0.263 Angle : 0.641 19.254 18734 Z= 0.340 Chirality : 0.043 0.154 2058 Planarity : 0.005 0.093 2372 Dihedral : 13.688 87.374 5292 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.21), residues: 1638 helix: 0.35 (0.20), residues: 622 sheet: 1.00 (0.32), residues: 268 loop : -0.01 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 271 TYR 0.013 0.001 TYR A 782 PHE 0.022 0.002 PHE A 218 TRP 0.006 0.001 TRP B 347 HIS 0.010 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00483 (13844) covalent geometry : angle 0.60937 (18728) hydrogen bonds : bond 0.24773 ( 584) hydrogen bonds : angle 7.46007 ( 1656) metal coordination : bond 0.19382 ( 8) metal coordination : angle 11.05661 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.330 Fit side-chains REVERT: A 280 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8132 (ttpt) REVERT: A 479 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 729 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7434 (mtt90) REVERT: B 729 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7464 (mtt90) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1150 time to fit residues: 36.4203 Evaluate side-chains 190 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 264 ASN A 580 GLN A 618 ASN B 222 HIS B 264 ASN B 580 GLN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123250 restraints weight = 14786.937| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.88 r_work: 0.3275 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13852 Z= 0.135 Angle : 0.535 6.050 18734 Z= 0.282 Chirality : 0.042 0.153 2058 Planarity : 0.005 0.060 2372 Dihedral : 7.805 57.406 1918 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.41 % Allowed : 5.82 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.21), residues: 1638 helix: 1.46 (0.20), residues: 640 sheet: 0.88 (0.33), residues: 244 loop : 0.10 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.025 0.001 TYR A 681 PHE 0.023 0.002 PHE B 295 TRP 0.008 0.001 TRP B 413 HIS 0.008 0.001 HIS B 821 Details of bonding type rmsd covalent geometry : bond 0.00308 (13844) covalent geometry : angle 0.53186 (18728) hydrogen bonds : bond 0.04898 ( 584) hydrogen bonds : angle 4.83931 ( 1656) metal coordination : bond 0.00929 ( 8) metal coordination : angle 3.47563 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.579 Fit side-chains REVERT: A 195 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 256 GLU cc_start: 0.8047 (pt0) cc_final: 0.7835 (pt0) REVERT: A 258 LEU cc_start: 0.8302 (mt) cc_final: 0.8086 (mp) REVERT: A 280 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8045 (ttpt) REVERT: A 288 GLN cc_start: 0.7917 (pm20) cc_final: 0.7701 (pm20) REVERT: B 195 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8086 (mm-40) REVERT: B 256 GLU cc_start: 0.8069 (pt0) cc_final: 0.7864 (pt0) REVERT: B 258 LEU cc_start: 0.8292 (mt) cc_final: 0.8076 (mp) REVERT: B 280 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7669 (ptpt) REVERT: B 288 GLN cc_start: 0.7897 (pm20) cc_final: 0.7665 (pm20) REVERT: B 729 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7886 (mtt90) REVERT: B 787 GLN cc_start: 0.8049 (tt0) cc_final: 0.7824 (mt0) outliers start: 6 outliers final: 2 residues processed: 213 average time/residue: 0.1216 time to fit residues: 35.9513 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 280 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.767 > 50: distance: 32 - 36: 7.528 distance: 36 - 37: 20.762 distance: 37 - 38: 31.573 distance: 37 - 40: 18.840 distance: 38 - 39: 14.008 distance: 38 - 43: 34.202 distance: 40 - 41: 6.271 distance: 40 - 42: 16.649 distance: 43 - 44: 6.560 distance: 44 - 45: 26.757 distance: 44 - 47: 12.566 distance: 45 - 46: 17.807 distance: 45 - 51: 13.892 distance: 46 - 72: 24.976 distance: 47 - 48: 13.737 distance: 48 - 49: 9.626 distance: 48 - 50: 10.127 distance: 51 - 52: 5.864 distance: 51 - 57: 32.384 distance: 52 - 53: 9.172 distance: 52 - 55: 10.734 distance: 53 - 54: 18.738 distance: 53 - 58: 14.347 distance: 54 - 80: 21.669 distance: 55 - 56: 17.515 distance: 56 - 57: 18.199 distance: 58 - 59: 12.936 distance: 59 - 60: 7.502 distance: 59 - 62: 15.412 distance: 60 - 61: 13.818 distance: 60 - 66: 12.068 distance: 62 - 63: 14.242 distance: 63 - 64: 5.685 distance: 63 - 65: 8.888 distance: 67 - 68: 5.515 distance: 67 - 70: 13.117 distance: 68 - 72: 8.239 distance: 69 - 102: 10.760 distance: 70 - 71: 8.322 distance: 72 - 73: 7.874 distance: 73 - 74: 4.575 distance: 73 - 76: 9.578 distance: 74 - 75: 9.936 distance: 74 - 80: 7.531 distance: 75 - 111: 12.311 distance: 76 - 77: 18.628 distance: 77 - 78: 5.912 distance: 77 - 79: 28.492 distance: 80 - 81: 8.483 distance: 81 - 82: 6.552 distance: 81 - 84: 5.544 distance: 82 - 83: 9.971 distance: 82 - 91: 10.586 distance: 83 - 119: 16.458 distance: 84 - 85: 9.503 distance: 85 - 86: 14.961 distance: 86 - 87: 7.457 distance: 87 - 88: 13.045 distance: 88 - 89: 9.951 distance: 88 - 90: 11.126 distance: 91 - 92: 7.253 distance: 92 - 93: 3.770 distance: 92 - 95: 6.402 distance: 93 - 94: 5.148 distance: 93 - 102: 5.018 distance: 94 - 128: 9.032 distance: 95 - 96: 7.090 distance: 96 - 97: 10.695 distance: 97 - 98: 3.986 distance: 98 - 99: 16.285 distance: 99 - 100: 9.782 distance: 99 - 101: 13.350 distance: 102 - 103: 8.004 distance: 103 - 104: 5.553 distance: 103 - 106: 5.811 distance: 104 - 105: 3.761 distance: 104 - 111: 3.484 distance: 105 - 136: 11.090 distance: 106 - 107: 11.193 distance: 107 - 108: 13.462 distance: 108 - 109: 5.736 distance: 109 - 110: 10.423 distance: 112 - 113: 5.010 distance: 112 - 115: 5.233 distance: 113 - 114: 4.459 distance: 114 - 141: 6.803 distance: 115 - 116: 12.409 distance: 115 - 117: 8.394 distance: 116 - 118: 29.266