Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:02:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy5_11550/12_2022/6zy5_11550_updated_updated.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.097 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 870": "NH1" <-> "NH2" Residue "B ARG 1148": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.87, per 1000 atoms: 0.58 Number of scatterers: 13504 At special positions: 0 Unit cell: (103.983, 116.039, 119.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 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: 5.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 8 sheets defined 45.4% alpha, 5.5% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.578A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 544 through 560 removed outlier: 4.014A pdb=" N ASN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.595A pdb=" N PHE B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.547A pdb=" N VAL B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.775A pdb=" N MET B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 847 through 851 removed outlier: 4.216A pdb=" N ASN B 851 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 4.589A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 974 through 983 Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 1015 through 1060 removed outlier: 3.884A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1040 " --> pdb=" O TRP B1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1080 removed outlier: 3.686A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU B1143 " --> pdb=" O GLU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1192 removed outlier: 3.696A pdb=" N ALA B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1189 " --> pdb=" O GLU B1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.578A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 544 through 560 removed outlier: 4.013A pdb=" N ASN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.596A pdb=" N PHE A 668 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.547A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.773A pdb=" N MET A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 847 through 851 removed outlier: 4.216A pdb=" N ASN A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.587A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 1015 through 1060 removed outlier: 3.885A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 3.686A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1133 through 1136 Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1192 removed outlier: 3.696A pdb=" N ALA A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 483 through 485 removed outlier: 8.576A pdb=" N PHE B 484 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 458 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS B 535 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 459 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 537 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 853 through 856 Processing sheet with id= C, first strand: chain 'B' and resid 898 through 901 Processing sheet with id= D, first strand: chain 'B' and resid 956 through 959 removed outlier: 6.340A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 483 through 485 removed outlier: 8.574A pdb=" N PHE A 484 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 458 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 535 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 459 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 537 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 853 through 856 Processing sheet with id= G, first strand: chain 'A' and resid 898 through 901 Processing sheet with id= H, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.342A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 6.14 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: 2331 1.32 - 1.44: 3733 1.44 - 1.57: 7640 1.57 - 1.69: 112 1.69 - 1.82: 92 Bond restraints: 13908 Sorted by residual: bond pdb=" C LYS B1071 " pdb=" O LYS B1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.89e+01 bond pdb=" C LYS A1071 " pdb=" O LYS A1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.88e+01 bond pdb=" C ILE B1074 " pdb=" O ILE B1074 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.87e+01 bond pdb=" C ILE A1074 " pdb=" O ILE A1074 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" CA SER B 861 " pdb=" CB SER B 861 " ideal model delta sigma weight residual 1.534 1.469 0.066 1.77e-02 3.19e+03 1.38e+01 ... (remaining 13903 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.12: 652 106.12 - 113.20: 7527 113.20 - 120.29: 6633 120.29 - 127.37: 4032 127.37 - 134.45: 186 Bond angle restraints: 19030 Sorted by residual: angle pdb=" CA SER A 861 " pdb=" C SER A 861 " pdb=" O SER A 861 " ideal model delta sigma weight residual 121.51 116.15 5.36 1.12e+00 7.97e-01 2.29e+01 angle pdb=" CA SER B 861 " pdb=" C SER B 861 " pdb=" O SER B 861 " ideal model delta sigma weight residual 121.51 116.29 5.22 1.12e+00 7.97e-01 2.17e+01 angle pdb=" N LEU B1166 " pdb=" CA LEU B1166 " pdb=" C LEU B1166 " ideal model delta sigma weight residual 112.23 106.62 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N LEU A1166 " pdb=" CA LEU A1166 " pdb=" C LEU A1166 " ideal model delta sigma weight residual 112.23 106.63 5.60 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N ILE B1065 " pdb=" CA ILE B1065 " pdb=" C ILE B1065 " ideal model delta sigma weight residual 112.43 108.58 3.85 9.20e-01 1.18e+00 1.75e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 7870 28.12 - 56.24: 281 56.24 - 84.36: 43 84.36 - 112.48: 2 112.48 - 140.60: 2 Dihedral angle restraints: 8198 sinusoidal: 3778 harmonic: 4420 Sorted by residual: dihedral pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " pdb=" O3' DC E 9 " pdb=" P DG E 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.40 140.60 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " pdb=" O3' DC C 9 " pdb=" P DG C 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.49 140.51 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C TYR A 830 " pdb=" N TYR A 830 " pdb=" CA TYR A 830 " pdb=" CB TYR A 830 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 8195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1060 0.058 - 0.115: 634 0.115 - 0.173: 308 0.173 - 0.230: 82 0.230 - 0.288: 10 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ILE B 915 " pdb=" N ILE B 915 " pdb=" C ILE B 915 " pdb=" CB ILE B 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2091 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 824 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C HIS B 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 824 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C HIS A 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 936 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LYS A 936 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS A 936 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 937 " -0.014 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1629 2.76 - 3.29: 13232 3.29 - 3.83: 20997 3.83 - 4.36: 25401 4.36 - 4.90: 41092 Nonbonded interactions: 102351 Sorted by model distance: nonbonded pdb=" O6 DG E 13 " pdb=" O13 EVP F 101 " model vdw 2.219 2.440 nonbonded pdb=" OE1 GLN B1094 " pdb=" NE2 GLN B1095 " model vdw 2.348 2.520 nonbonded pdb=" OE1 GLN A1094 " pdb=" NE2 GLN A1095 " model vdw 2.348 2.520 nonbonded pdb=" NH2 ARG A 870 " pdb=" OE1 GLU A1182 " model vdw 2.348 2.520 nonbonded pdb=" NH2 ARG B 870 " pdb=" OE1 GLU B1182 " model vdw 2.349 2.520 ... (remaining 102346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.750 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: 3.110 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.100 Process input model: 39.420 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 0.066 13908 Z= 0.697 Angle : 1.165 7.628 19030 Z= 0.866 Chirality : 0.086 0.288 2094 Planarity : 0.007 0.039 2220 Dihedral : 13.745 140.604 5350 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.15 % 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: -0.64 (0.21), residues: 1512 helix: 1.50 (0.19), residues: 678 sheet: -1.37 (0.37), residues: 198 loop : -2.35 (0.23), residues: 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 471 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.3029 time to fit residues: 193.7874 Evaluate side-chains 219 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1224 time to fit residues: 2.6078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 HIS B 559 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN B 875 ASN A 559 HIS A 634 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN A 875 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13908 Z= 0.215 Angle : 0.550 5.545 19030 Z= 0.290 Chirality : 0.040 0.190 2094 Planarity : 0.004 0.037 2220 Dihedral : 18.004 136.678 2234 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.86 % 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: -0.14 (0.22), residues: 1512 helix: 1.98 (0.20), residues: 672 sheet: -1.43 (0.36), residues: 216 loop : -2.02 (0.24), residues: 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 231 average time/residue: 0.2448 time to fit residues: 82.9498 Evaluate side-chains 163 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1330 time to fit residues: 7.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN B1153 GLN A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN A1153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13908 Z= 0.205 Angle : 0.514 7.569 19030 Z= 0.271 Chirality : 0.039 0.151 2094 Planarity : 0.004 0.032 2220 Dihedral : 17.975 135.532 2234 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.88 % 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: 0.12 (0.22), residues: 1512 helix: 2.14 (0.20), residues: 674 sheet: -0.23 (0.51), residues: 134 loop : -2.05 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 185 average time/residue: 0.2176 time to fit residues: 61.6882 Evaluate side-chains 141 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1190 time to fit residues: 3.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 74 optimal weight: 0.0770 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 13908 Z= 0.154 Angle : 0.476 6.089 19030 Z= 0.252 Chirality : 0.038 0.175 2094 Planarity : 0.003 0.030 2220 Dihedral : 17.923 135.063 2234 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.98 % 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: 0.35 (0.23), residues: 1512 helix: 2.29 (0.20), residues: 676 sheet: -0.47 (0.46), residues: 164 loop : -1.87 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.363 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 149 average time/residue: 0.2305 time to fit residues: 52.4377 Evaluate side-chains 132 residues out of total 1358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1304 time to fit residues: 3.2312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 54.2163 > 50: distance: 59 - 63: 6.990 distance: 63 - 64: 9.735 distance: 64 - 65: 19.082 distance: 65 - 66: 19.905 distance: 65 - 67: 22.713 distance: 67 - 68: 20.553 distance: 68 - 69: 28.142 distance: 68 - 71: 20.417 distance: 69 - 70: 17.558 distance: 69 - 76: 32.877 distance: 71 - 72: 7.983 distance: 72 - 73: 11.487 distance: 73 - 74: 4.849 distance: 73 - 75: 4.890 distance: 76 - 77: 21.875 distance: 77 - 78: 15.600 distance: 77 - 80: 12.768 distance: 78 - 79: 22.151 distance: 78 - 85: 21.294 distance: 80 - 81: 20.132 distance: 81 - 82: 12.279 distance: 82 - 83: 8.534 distance: 82 - 84: 4.947 distance: 85 - 86: 26.269 distance: 85 - 91: 12.892 distance: 86 - 87: 23.514 distance: 86 - 89: 8.021 distance: 87 - 88: 23.228 distance: 87 - 92: 31.271 distance: 89 - 90: 13.808 distance: 90 - 91: 18.220 distance: 92 - 93: 16.204 distance: 93 - 94: 19.974 distance: 93 - 96: 27.709 distance: 94 - 95: 22.921 distance: 94 - 100: 27.026 distance: 96 - 97: 30.177 distance: 97 - 98: 26.561 distance: 97 - 99: 25.044 distance: 100 - 101: 27.662 distance: 100 - 106: 19.166 distance: 101 - 102: 21.606 distance: 101 - 104: 21.980 distance: 102 - 107: 42.729 distance: 104 - 105: 33.162 distance: 105 - 106: 37.840 distance: 107 - 108: 18.014 distance: 108 - 109: 45.675 distance: 108 - 111: 12.421 distance: 109 - 110: 39.800 distance: 109 - 115: 47.128 distance: 111 - 112: 25.435 distance: 112 - 113: 29.930 distance: 113 - 114: 12.195 distance: 115 - 116: 17.143 distance: 116 - 117: 8.586 distance: 116 - 119: 13.172 distance: 117 - 123: 15.187 distance: 119 - 120: 7.086 distance: 120 - 121: 4.618 distance: 120 - 122: 3.743 distance: 123 - 124: 7.030 distance: 123 - 129: 9.419 distance: 124 - 125: 25.676 distance: 124 - 127: 22.611 distance: 125 - 126: 24.427 distance: 125 - 130: 27.826 distance: 127 - 128: 24.742 distance: 128 - 129: 5.946 distance: 130 - 131: 17.700 distance: 131 - 132: 19.687 distance: 131 - 134: 26.842 distance: 132 - 133: 29.947 distance: 132 - 136: 28.796 distance: 134 - 135: 36.705