Starting phenix.real_space_refine on Wed Jan 14 02:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296.map" model { file = "/net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fml_29296/01_2026/8fml_29296_neut.cif" } resolution = 2.93 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= 0.001 sd= 0.019 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 64 5.16 5 C 7352 2.51 5 N 1950 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11528 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10880 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1297} Chain breaks: 1 Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 648 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain breaks: 1 Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11528 At special positions: 0 Unit cell: (92.4, 87.12, 147.312, 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 64 16.00 O 2162 8.00 N 1950 7.00 C 7352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 124 " distance=2.04 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: 0.93 Conformation dependent library (CDL) restraints added in 571.3 milliseconds 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 46.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.541A pdb=" N LEU A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.668A pdb=" N ARG A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.058A pdb=" N ARG A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.891A pdb=" N GLY A 129 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.639A pdb=" N ARG A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.095A pdb=" N ASP A 168 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.913A pdb=" N HIS A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.527A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.632A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.824A pdb=" N VAL A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.833A pdb=" N LEU A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.771A pdb=" N SER A 427 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 428 " --> pdb=" O CYS A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.186A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 586 through 591 removed outlier: 4.273A pdb=" N LEU A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.550A pdb=" N THR A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 632 removed outlier: 3.809A pdb=" N VAL A 622 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 4.602A pdb=" N GLY A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A 639 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.586A pdb=" N ALA A 656 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 Processing helix chain 'A' and resid 682 through 702 removed outlier: 3.576A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.681A pdb=" N THR A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 726 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 727 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 762 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.867A pdb=" N GLN A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.540A pdb=" N ALA A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 4.029A pdb=" N HIS A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 removed outlier: 4.054A pdb=" N THR A 807 " --> pdb=" O LYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.724A pdb=" N MET A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 852 removed outlier: 3.659A pdb=" N PHE A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 Processing helix chain 'A' and resid 877 through 890 Proline residue: A 883 - end of helix Processing helix chain 'A' and resid 896 through 905 removed outlier: 3.528A pdb=" N LEU A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 903 " --> pdb=" O ASN A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 957 through 977 removed outlier: 4.139A pdb=" N ILE A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.966A pdb=" N GLN A1018 " --> pdb=" O GLN A1014 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A1025 " --> pdb=" O MET A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1044 removed outlier: 3.810A pdb=" N SER A1043 " --> pdb=" O GLY A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1051 removed outlier: 4.015A pdb=" N LEU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A1051 " --> pdb=" O ALA A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1075 removed outlier: 4.021A pdb=" N GLU A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU A1072 " --> pdb=" O ALA A1068 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1147 Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 3.597A pdb=" N GLN A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1178 Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1248 through 1260 removed outlier: 4.789A pdb=" N LEU A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1285 removed outlier: 4.433A pdb=" N ARG A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1315 removed outlier: 3.721A pdb=" N PHE A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1351 removed outlier: 4.045A pdb=" N THR A1341 " --> pdb=" O GLN A1337 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A1348 " --> pdb=" O LYS A1344 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A1349 " --> pdb=" O ALA A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1379 removed outlier: 3.810A pdb=" N LYS A1372 " --> pdb=" O GLU A1368 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1373 " --> pdb=" O GLU A1369 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 31 through 37 removed outlier: 4.182A pdb=" N ARG B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 483 Processing helix chain 'B' and resid 485 through 495 removed outlier: 3.999A pdb=" N ASN B 489 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA3, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.540A pdb=" N GLY A 470 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 548 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 580 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 550 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N HIS A 582 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 730 through 733 Processing sheet with id=AA6, first strand: chain 'A' and resid 945 through 946 Processing sheet with id=AA7, first strand: chain 'A' and resid 954 through 956 removed outlier: 5.781A pdb=" N GLU A 955 " --> pdb=" O VAL A1395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 999 through 1001 removed outlier: 8.024A pdb=" N ILE A 999 " --> pdb=" O GLN A1028 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A1030 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LYS A1001 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N PHE A1032 " --> pdb=" O LYS A1001 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N GLN A1028 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS A1057 " --> pdb=" O GLN A1028 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A1030 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER A1059 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A1032 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N SER A1061 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A1034 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU A1083 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS A1058 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER A1085 " --> pdb=" O CYS A1058 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N MET A1060 " --> pdb=" O SER A1085 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1133 through 1134 Processing sheet with id=AB1, first strand: chain 'A' and resid 1267 through 1268 367 hydrogen bonds defined for protein. 1011 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: 1.95 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3777 1.35 - 1.47: 2753 1.47 - 1.60: 5149 1.60 - 1.72: 1 1.72 - 1.84: 90 Bond restraints: 11770 Sorted by residual: bond pdb=" CB PRO A 78 " pdb=" CG PRO A 78 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.17e+00 bond pdb=" CG PRO A 178 " pdb=" CD PRO A 178 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.48e+00 bond pdb=" CG PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 1.503 1.463 0.040 3.40e-02 8.65e+02 1.40e+00 bond pdb=" CG GLN B 474 " pdb=" CD GLN B 474 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CB GLU A 909 " pdb=" CG GLU A 909 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 11765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 15779 3.02 - 6.05: 114 6.05 - 9.07: 17 9.07 - 12.10: 0 12.10 - 15.12: 4 Bond angle restraints: 15914 Sorted by residual: angle pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 112.00 103.55 8.45 1.40e+00 5.10e-01 3.64e+01 angle pdb=" C LEU A1320 " pdb=" CA LEU A1320 " pdb=" CB LEU A1320 " ideal model delta sigma weight residual 110.65 115.36 -4.71 1.04e+00 9.25e-01 2.05e+01 angle pdb=" CA LEU A1320 " pdb=" CB LEU A1320 " pdb=" CG LEU A1320 " ideal model delta sigma weight residual 116.30 131.42 -15.12 3.50e+00 8.16e-02 1.87e+01 angle pdb=" CB MET A 282 " pdb=" CG MET A 282 " pdb=" SD MET A 282 " ideal model delta sigma weight residual 112.70 125.46 -12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CA LEU A 850 " pdb=" CB LEU A 850 " pdb=" CG LEU A 850 " ideal model delta sigma weight residual 116.30 131.11 -14.81 3.50e+00 8.16e-02 1.79e+01 ... (remaining 15909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5888 17.82 - 35.63: 913 35.63 - 53.45: 284 53.45 - 71.26: 46 71.26 - 89.08: 14 Dihedral angle restraints: 7145 sinusoidal: 2918 harmonic: 4227 Sorted by residual: dihedral pdb=" CA HIS A1271 " pdb=" C HIS A1271 " pdb=" N ASP A1272 " pdb=" CA ASP A1272 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLY A 988 " pdb=" C GLY A 988 " pdb=" N TYR A 989 " pdb=" CA TYR A 989 " ideal model delta harmonic sigma weight residual 180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA SER A1363 " pdb=" C SER A1363 " pdb=" N TRP A1364 " pdb=" CA TRP A1364 " ideal model delta harmonic sigma weight residual 180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1426 0.053 - 0.107: 317 0.107 - 0.160: 34 0.160 - 0.214: 2 0.214 - 0.267: 1 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CB VAL A1159 " pdb=" CA VAL A1159 " pdb=" CG1 VAL A1159 " pdb=" CG2 VAL A1159 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A1299 " pdb=" CA ILE A1299 " pdb=" CG1 ILE A1299 " pdb=" CG2 ILE A1299 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU A1072 " pdb=" CB LEU A1072 " pdb=" CD1 LEU A1072 " pdb=" CD2 LEU A1072 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 1777 not shown) Planarity restraints: 2050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 177 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO A 178 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 77 " -0.061 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO A 78 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 909 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CD GLU A 909 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 909 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A 909 " -0.016 2.00e-02 2.50e+03 ... (remaining 2047 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 397 2.70 - 3.25: 11797 3.25 - 3.80: 19056 3.80 - 4.35: 24466 4.35 - 4.90: 39273 Nonbonded interactions: 94989 Sorted by model distance: nonbonded pdb=" O PHE A 871 " pdb=" OG SER A 875 " model vdw 2.150 3.040 nonbonded pdb=" O GLU A1132 " pdb=" N HIS A1158 " model vdw 2.185 3.120 nonbonded pdb=" O HIS A 564 " pdb=" OG1 THR A 568 " model vdw 2.194 3.040 nonbonded pdb=" O TRP A 396 " pdb=" OG SER A 538 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU A 750 " pdb=" OH TYR A 831 " model vdw 2.220 3.040 ... (remaining 94984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 17.630 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: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.680 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 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 0.114 11771 Z= 0.139 Angle : 0.722 15.122 15916 Z= 0.362 Chirality : 0.044 0.267 1780 Planarity : 0.005 0.106 2050 Dihedral : 18.965 89.078 4388 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.00 % Favored : 86.86 % Rotamer: Outliers : 4.48 % Allowed : 33.15 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.38 (0.22), residues: 1431 helix: -0.08 (0.23), residues: 545 sheet: -2.60 (0.57), residues: 73 loop : -2.68 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 962 TYR 0.014 0.001 TYR A 950 PHE 0.028 0.001 PHE A 479 TRP 0.011 0.001 TRP A1364 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00320 (11770) covalent geometry : angle 0.72117 (15914) SS BOND : bond 0.01122 ( 1) SS BOND : angle 2.91494 ( 2) hydrogen bonds : bond 0.14271 ( 367) hydrogen bonds : angle 5.98628 ( 1011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 121 time to evaluate : 0.461 Fit side-chains outliers start: 58 outliers final: 47 residues processed: 175 average time/residue: 0.4243 time to fit residues: 83.0979 Evaluate side-chains 164 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 TYR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1158 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1329 CYS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1341 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 489 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 973 ASN ** A1229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.221187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.202089 restraints weight = 16459.511| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.23 r_work: 0.4438 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11771 Z= 0.175 Angle : 0.699 14.821 15916 Z= 0.354 Chirality : 0.045 0.212 1780 Planarity : 0.005 0.071 2050 Dihedral : 8.666 78.090 1625 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.28 % Favored : 86.58 % Rotamer: Outliers : 6.88 % Allowed : 30.22 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.49 (0.22), residues: 1431 helix: -0.25 (0.22), residues: 553 sheet: -2.35 (0.64), residues: 61 loop : -2.75 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 962 TYR 0.016 0.002 TYR A 605 PHE 0.018 0.001 PHE A 305 TRP 0.007 0.001 TRP A 960 HIS 0.010 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00394 (11770) covalent geometry : angle 0.69643 (15914) SS BOND : bond 0.01609 ( 1) SS BOND : angle 4.91210 ( 2) hydrogen bonds : bond 0.04605 ( 367) hydrogen bonds : angle 5.64834 ( 1011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 131 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 322 LEU cc_start: 0.3766 (OUTLIER) cc_final: 0.3482 (mp) REVERT: A 524 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5295 (mt) REVERT: A 729 MET cc_start: 0.1712 (tmm) cc_final: 0.1309 (tmm) REVERT: A 773 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5939 (tt) REVERT: A 820 GLU cc_start: 0.2999 (OUTLIER) cc_final: 0.2766 (pm20) REVERT: A 1174 MET cc_start: 0.3544 (tpp) cc_final: 0.2978 (tpp) REVERT: A 1371 MET cc_start: 0.4147 (mmp) cc_final: 0.3519 (mmp) REVERT: B 455 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.4369 (pp20) outliers start: 89 outliers final: 41 residues processed: 200 average time/residue: 0.4251 time to fit residues: 95.2300 Evaluate side-chains 168 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 820 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 950 TYR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1329 CYS Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1373 VAL Chi-restraints excluded: chain A residue 1374 ILE Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 455 GLU Chi-restraints excluded: chain B residue 489 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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: 51.4253 > 50: distance: 38 - 56: 11.937 distance: 42 - 62: 27.635 distance: 46 - 67: 29.115 distance: 50 - 56: 11.107 distance: 51 - 76: 16.887 distance: 56 - 57: 26.667 distance: 57 - 58: 28.047 distance: 57 - 60: 8.087 distance: 58 - 59: 13.570 distance: 58 - 62: 28.488 distance: 60 - 61: 16.056 distance: 62 - 63: 22.811 distance: 63 - 64: 22.220 distance: 63 - 66: 10.452 distance: 64 - 65: 7.775 distance: 64 - 67: 27.309 distance: 67 - 68: 8.427 distance: 68 - 71: 8.156 distance: 69 - 70: 18.598 distance: 69 - 76: 16.001 distance: 71 - 72: 7.070 distance: 72 - 73: 11.663 distance: 73 - 75: 12.746 distance: 76 - 77: 15.089 distance: 77 - 78: 7.597 distance: 77 - 80: 14.889 distance: 78 - 79: 9.615 distance: 78 - 84: 10.033 distance: 80 - 81: 21.067 distance: 81 - 82: 12.596 distance: 81 - 83: 10.293 distance: 84 - 85: 7.168 distance: 85 - 86: 10.179 distance: 85 - 88: 7.394 distance: 86 - 87: 6.991 distance: 86 - 92: 4.705 distance: 87 - 101: 29.585 distance: 88 - 89: 8.160 distance: 89 - 90: 10.237 distance: 89 - 91: 14.273 distance: 92 - 93: 20.038 distance: 93 - 94: 18.352 distance: 94 - 95: 27.034 distance: 94 - 96: 12.991 distance: 96 - 97: 11.396 distance: 97 - 98: 12.397 distance: 97 - 100: 5.588 distance: 98 - 99: 15.297 distance: 98 - 101: 12.621 distance: 101 - 102: 17.914 distance: 102 - 103: 18.380 distance: 103 - 104: 9.261 distance: 103 - 105: 4.220 distance: 105 - 106: 10.907 distance: 106 - 107: 38.747 distance: 107 - 108: 12.415 distance: 107 - 109: 32.300 distance: 109 - 110: 6.952 distance: 110 - 111: 19.236 distance: 110 - 113: 19.395 distance: 111 - 112: 13.375 distance: 111 - 115: 20.413 distance: 113 - 114: 11.378