Starting phenix.real_space_refine on Tue Sep 24 08:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg4_33807/09_2024/7yg4_33807.cif" } resolution = 3.1 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= 0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4779 2.51 5 N 1270 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6432 Classifications: {'peptide': 819} Link IDs: {'PTRANS': 27, 'TRANS': 791} Chain breaks: 7 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 539 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "E" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 539 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Time building chain proxies: 4.54, per 1000 atoms: 0.60 Number of scatterers: 7510 At special positions: 0 Unit cell: (91.8, 113.05, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1421 8.00 N 1270 7.00 C 4779 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: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 397 through 413 Proline residue: A 408 - end of helix removed outlier: 3.882A pdb=" N ILE A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 452 through 458 removed outlier: 3.799A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 4.240A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.688A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.893A pdb=" N LEU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 509 removed outlier: 3.636A pdb=" N ASN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.864A pdb=" N ALA A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.606A pdb=" N LEU A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 575 removed outlier: 3.516A pdb=" N THR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 640 removed outlier: 4.740A pdb=" N ARG A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 681 through 689 removed outlier: 4.095A pdb=" N LEU A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.833A pdb=" N VAL A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 708 " --> pdb=" O THR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.523A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 724 " --> pdb=" O PHE A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 737 removed outlier: 3.596A pdb=" N ASN A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.608A pdb=" N PHE A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.571A pdb=" N THR A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.747A pdb=" N ALA A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.602A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.622A pdb=" N ASN A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 882 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 874 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 removed outlier: 3.716A pdb=" N LEU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 893 " --> pdb=" O GLN A 889 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 929 through 941 removed outlier: 3.614A pdb=" N LEU A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 941 " --> pdb=" O LEU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 removed outlier: 3.649A pdb=" N LEU A 958 " --> pdb=" O LEU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 984 removed outlier: 3.590A pdb=" N ILE A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.799A pdb=" N ARG A 988 " --> pdb=" O GLN A 985 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1021 removed outlier: 3.860A pdb=" N ARG A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1044 removed outlier: 3.524A pdb=" N LEU A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1074 removed outlier: 3.658A pdb=" N ILE A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A1074 " --> pdb=" O THR A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1089 through 1103 Processing helix chain 'A' and resid 1109 through 1120 Processing helix chain 'A' and resid 1138 through 1154 removed outlier: 4.067A pdb=" N VAL A1153 " --> pdb=" O MET A1149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A1154 " --> pdb=" O HIS A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 3.591A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A1167 " --> pdb=" O ARG A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1188 removed outlier: 4.136A pdb=" N ALA A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1210 removed outlier: 3.534A pdb=" N ALA A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A1210 " --> pdb=" O ASP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1234 removed outlier: 3.585A pdb=" N SER A1234 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 3.590A pdb=" N ALA A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A1248 " --> pdb=" O HIS A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1269 removed outlier: 3.798A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1292 Processing helix chain 'B' and resid 172 through 237 removed outlier: 4.310A pdb=" N LYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 237 removed outlier: 3.997A pdb=" N SER E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1524 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: 2.06 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2473 1.34 - 1.46: 1120 1.46 - 1.58: 3958 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7613 Sorted by residual: bond pdb=" CB MET E 218 " pdb=" CG MET E 218 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ILE B 222 " pdb=" CG2 ILE B 222 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB ARG B 233 " pdb=" CG ARG B 233 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CB GLN B 226 " pdb=" CG GLN B 226 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CG1 ILE A 855 " pdb=" CD1 ILE A 855 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 ... (remaining 7608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 10175 2.26 - 4.52: 101 4.52 - 6.79: 14 6.79 - 9.05: 3 9.05 - 11.31: 1 Bond angle restraints: 10294 Sorted by residual: angle pdb=" CA LEU E 229 " pdb=" CB LEU E 229 " pdb=" CG LEU E 229 " ideal model delta sigma weight residual 116.30 127.61 -11.31 3.50e+00 8.16e-02 1.04e+01 angle pdb=" C PRO A 668 " pdb=" N TYR A 669 " pdb=" CA TYR A 669 " ideal model delta sigma weight residual 120.09 123.97 -3.88 1.25e+00 6.40e-01 9.65e+00 angle pdb=" N GLN B 210 " pdb=" CA GLN B 210 " pdb=" CB GLN B 210 " ideal model delta sigma weight residual 110.28 114.70 -4.42 1.55e+00 4.16e-01 8.13e+00 angle pdb=" N GLU B 216 " pdb=" CA GLU B 216 " pdb=" CB GLU B 216 " ideal model delta sigma weight residual 110.28 114.65 -4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C VAL B 215 " pdb=" N GLU B 216 " pdb=" CA GLU B 216 " ideal model delta sigma weight residual 120.31 116.04 4.27 1.52e+00 4.33e-01 7.90e+00 ... (remaining 10289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4136 18.00 - 35.99: 427 35.99 - 53.99: 81 53.99 - 71.98: 23 71.98 - 89.98: 13 Dihedral angle restraints: 4680 sinusoidal: 1898 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU E 196 " pdb=" C GLU E 196 " pdb=" N LEU E 197 " pdb=" CA LEU E 197 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A1258 " pdb=" CG GLU A1258 " pdb=" CD GLU A1258 " pdb=" OE1 GLU A1258 " ideal model delta sinusoidal sigma weight residual 0.00 89.98 -89.98 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CG ARG A 396 " pdb=" CD ARG A 396 " pdb=" NE ARG A 396 " pdb=" CZ ARG A 396 " ideal model delta sinusoidal sigma weight residual -90.00 -134.46 44.46 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 945 0.039 - 0.079: 251 0.079 - 0.118: 43 0.118 - 0.158: 8 0.158 - 0.197: 2 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CA GLU E 196 " pdb=" N GLU E 196 " pdb=" C GLU E 196 " pdb=" CB GLU E 196 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA ILE A 691 " pdb=" N ILE A 691 " pdb=" C ILE A 691 " pdb=" CB ILE A 691 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA GLN B 210 " pdb=" N GLN B 210 " pdb=" C GLN B 210 " pdb=" CB GLN B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1246 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1105 " 0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A1106 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A1106 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1106 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 691 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO A 692 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 692 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 692 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 216 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" CD GLU B 216 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU B 216 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 216 " -0.013 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 119 2.70 - 3.25: 7578 3.25 - 3.80: 11361 3.80 - 4.35: 14990 4.35 - 4.90: 24770 Nonbonded interactions: 58818 Sorted by model distance: nonbonded pdb=" NZ LYS B 198 " pdb=" OG SER E 194 " model vdw 2.147 3.120 nonbonded pdb=" O ILE A 511 " pdb=" OH TYR A 675 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG B 233 " pdb=" OE1 GLN E 228 " model vdw 2.262 3.120 nonbonded pdb=" O LEU A1122 " pdb=" NH2 ARG A1144 " model vdw 2.268 3.120 nonbonded pdb=" O GLU A 883 " pdb=" NE2 GLN A 889 " model vdw 2.324 3.120 ... (remaining 58813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' 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: 1.250 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.003 0.050 7613 Z= 0.222 Angle : 0.584 11.309 10294 Z= 0.307 Chirality : 0.037 0.197 1249 Planarity : 0.005 0.090 1296 Dihedral : 15.981 89.976 2858 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.41 (0.28), residues: 933 helix: 0.85 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 760 HIS 0.006 0.001 HIS A 737 PHE 0.011 0.001 PHE A 775 TYR 0.010 0.001 TYR B 193 ARG 0.002 0.000 ARG A1163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.860 Fit side-chains REVERT: A 524 ARG cc_start: 0.5525 (mpp-170) cc_final: 0.5169 (mpp-170) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1825 time to fit residues: 22.1245 Evaluate side-chains 74 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 ASN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7613 Z= 0.193 Angle : 0.566 13.123 10294 Z= 0.286 Chirality : 0.036 0.138 1249 Planarity : 0.005 0.063 1296 Dihedral : 3.776 14.827 999 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.59 % Allowed : 7.29 % Favored : 92.13 % 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: 1.02 (0.27), residues: 933 helix: 1.25 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1091 HIS 0.004 0.001 HIS A 643 PHE 0.008 0.001 PHE A1110 TYR 0.014 0.001 TYR B 193 ARG 0.002 0.000 ARG A 935 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 524 ARG cc_start: 0.5554 (mpp-170) cc_final: 0.5191 (mpp-170) REVERT: A 1001 THR cc_start: 0.7990 (m) cc_final: 0.7625 (p) REVERT: A 1176 MET cc_start: 0.6750 (mmp) cc_final: 0.6430 (mmm) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.1918 time to fit residues: 23.8881 Evaluate side-chains 81 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 1156 LYS Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 0.0060 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7613 Z= 0.143 Angle : 0.503 10.834 10294 Z= 0.251 Chirality : 0.035 0.126 1249 Planarity : 0.004 0.056 1296 Dihedral : 3.567 13.827 999 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 9.87 % Favored : 88.95 % 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: 1.57 (0.28), residues: 933 helix: 1.68 (0.20), residues: 744 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1091 HIS 0.003 0.001 HIS A 998 PHE 0.006 0.001 PHE A1109 TYR 0.009 0.001 TYR B 193 ARG 0.003 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8526 (m) cc_final: 0.8261 (p) REVERT: A 524 ARG cc_start: 0.5517 (mpp-170) cc_final: 0.5140 (mpp-170) REVERT: B 227 GLN cc_start: 0.7638 (mt0) cc_final: 0.7337 (mt0) REVERT: E 229 LEU cc_start: 0.7599 (mt) cc_final: 0.7336 (mt) outliers start: 10 outliers final: 3 residues processed: 96 average time/residue: 0.1861 time to fit residues: 24.9386 Evaluate side-chains 86 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7613 Z= 0.151 Angle : 0.490 11.254 10294 Z= 0.246 Chirality : 0.035 0.131 1249 Planarity : 0.004 0.051 1296 Dihedral : 3.483 13.903 999 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.53 % Allowed : 10.93 % Favored : 87.54 % 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: 1.75 (0.28), residues: 933 helix: 1.81 (0.20), residues: 746 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1091 HIS 0.002 0.000 HIS A 814 PHE 0.010 0.001 PHE A1109 TYR 0.011 0.001 TYR B 193 ARG 0.004 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.8527 (m) cc_final: 0.8283 (p) REVERT: A 524 ARG cc_start: 0.5543 (mpp-170) cc_final: 0.5168 (mpp-170) REVERT: B 227 GLN cc_start: 0.7634 (mt0) cc_final: 0.7373 (mt0) REVERT: B 228 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6931 (tm-30) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.1756 time to fit residues: 23.5624 Evaluate side-chains 88 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 221 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 57.4076 > 50: distance: 37 - 41: 22.698 distance: 41 - 42: 25.278 distance: 42 - 43: 28.095 distance: 42 - 45: 15.852 distance: 43 - 44: 32.281 distance: 43 - 47: 20.078 distance: 45 - 46: 11.962 distance: 47 - 48: 36.432 distance: 48 - 49: 9.434 distance: 48 - 51: 15.278 distance: 49 - 50: 11.165 distance: 49 - 58: 16.398 distance: 51 - 52: 11.673 distance: 52 - 53: 16.210 distance: 52 - 54: 9.907 distance: 53 - 55: 16.017 distance: 54 - 56: 13.606 distance: 55 - 57: 13.976 distance: 56 - 57: 15.640 distance: 58 - 59: 16.921 distance: 58 - 64: 11.349 distance: 59 - 60: 34.766 distance: 59 - 62: 16.729 distance: 60 - 61: 28.882 distance: 60 - 65: 18.650 distance: 62 - 63: 3.419 distance: 63 - 64: 37.024 distance: 65 - 66: 24.632 distance: 66 - 67: 16.819 distance: 66 - 69: 26.014 distance: 67 - 68: 21.985 distance: 67 - 72: 34.971 distance: 69 - 70: 19.287 distance: 69 - 71: 26.291 distance: 72 - 73: 8.494 distance: 73 - 74: 23.928 distance: 73 - 76: 19.968 distance: 74 - 75: 33.998 distance: 74 - 80: 13.952 distance: 76 - 77: 12.777 distance: 77 - 78: 10.011 distance: 78 - 79: 6.635 distance: 80 - 81: 17.148 distance: 81 - 82: 32.385 distance: 81 - 84: 35.497 distance: 82 - 83: 31.609 distance: 82 - 85: 15.778 distance: 85 - 86: 15.125 distance: 86 - 87: 24.378 distance: 86 - 89: 21.943 distance: 87 - 88: 36.461 distance: 87 - 96: 25.581 distance: 89 - 90: 31.233 distance: 90 - 91: 5.713 distance: 91 - 92: 18.776 distance: 92 - 93: 5.592 distance: 96 - 97: 16.481 distance: 97 - 100: 25.633 distance: 98 - 99: 29.091 distance: 98 - 104: 16.279 distance: 100 - 101: 7.496 distance: 100 - 102: 11.073 distance: 101 - 103: 13.183 distance: 104 - 105: 17.192 distance: 105 - 106: 23.743 distance: 106 - 107: 27.778 distance: 106 - 111: 8.477 distance: 108 - 109: 9.033 distance: 108 - 110: 12.077 distance: 111 - 112: 30.698 distance: 113 - 114: 9.461 distance: 113 - 115: 4.371