Starting phenix.real_space_refine on Thu Apr 11 22:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soa_40651/04_2024/8soa_40651_trim_updated.pdb" } resolution = 3.32 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 61 5.16 5 C 7684 2.51 5 N 2045 2.21 5 O 2180 1.98 5 H 12066 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24039 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 16081 Classifications: {'peptide': 984} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7927 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 8 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.59, per 1000 atoms: 0.48 Number of scatterers: 24039 At special positions: 0 Unit cell: (103.68, 101.52, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 3 15.00 O 2180 8.00 N 2045 7.00 C 7684 6.00 H 12066 1.00 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: 19.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 14 sheets defined 43.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 172 through 190 removed outlier: 4.158A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.567A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.848A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 569 through 577 Processing helix chain 'A' and resid 586 through 592 removed outlier: 3.642A pdb=" N TYR A 589 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Proline residue: A 590 - end of helix No H-bonds generated for 'chain 'A' and resid 586 through 592' Processing helix chain 'A' and resid 601 through 611 Processing helix chain 'A' and resid 624 through 631 removed outlier: 4.360A pdb=" N LEU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.673A pdb=" N ALA A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 removed outlier: 3.785A pdb=" N HIS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.503A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N PHE A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 689 through 705 removed outlier: 3.510A pdb=" N PHE A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 721 removed outlier: 3.620A pdb=" N GLN A 710 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN A 711 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 712 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 751 removed outlier: 3.531A pdb=" N GLN A 735 " --> pdb=" O ASP A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 776 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 888 through 891 No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 904 through 914 removed outlier: 4.055A pdb=" N LEU A 907 " --> pdb=" O ASP A 904 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 908 " --> pdb=" O GLU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 941 removed outlier: 3.543A pdb=" N ARG A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 934 " --> pdb=" O TYR A 930 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 989 through 995 removed outlier: 3.632A pdb=" N MET A 995 " --> pdb=" O PHE A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1037 removed outlier: 3.668A pdb=" N LYS A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1024 " --> pdb=" O LEU A1020 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A1026 " --> pdb=" O HIS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1053 removed outlier: 3.530A pdb=" N ILE A1051 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A1053 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1067 through 1078 Processing helix chain 'A' and resid 1082 through 1091 Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 52 through 72 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.624A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 119 through 135 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 189 through 208 removed outlier: 3.739A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.733A pdb=" N GLY B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 264 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 525 through 542 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'B' and resid 696 through 701 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.658A pdb=" N VAL A 137 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 235 removed outlier: 6.619A pdb=" N ILE A 303 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A 225 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 305 " --> pdb=" O HIS A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 351 through 353 No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 362 through 365 Processing sheet with id= E, first strand: chain 'A' and resid 367 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 392 through 396 removed outlier: 6.703A pdb=" N ILE A 387 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A 396 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA A 385 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 462 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS A 435 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 460 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 478 through 483 Processing sheet with id= H, first strand: chain 'A' and resid 830 through 834 Processing sheet with id= I, first strand: chain 'A' and resid 885 through 887 Processing sheet with id= J, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.143A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 162 through 165 removed outlier: 8.305A pdb=" N VAL B 163 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG B 516 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 165 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 518 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 551 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL B 517 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 553 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL B 519 " --> pdb=" O GLN B 553 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 555 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY B 521 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 557 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.733A pdb=" N ILE B 869 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 683 through 688 removed outlier: 3.911A pdb=" N LYS B 732 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.307A pdb=" N ALA B 813 " --> pdb=" O GLY B 695 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 695 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 795 " --> pdb=" O LEU B 774 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1245 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: 9.53 Time building geometry restraints manager: 19.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12030 1.03 - 1.23: 41 1.23 - 1.42: 5037 1.42 - 1.62: 7105 1.62 - 1.81: 86 Bond restraints: 24299 Sorted by residual: bond pdb=" N THR B 7 " pdb=" CA THR B 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU A 37 " pdb=" CA LEU A 37 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N THR B 7 " pdb=" H THR B 7 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" N LEU A 37 " pdb=" H LEU A 37 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" CB PRO B 868 " pdb=" CG PRO B 868 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.35e+00 ... (remaining 24294 not shown) Histogram of bond angle deviations from ideal: 100.27 - 108.17: 5635 108.17 - 116.07: 26047 116.07 - 123.98: 10561 123.98 - 131.88: 1729 131.88 - 139.78: 28 Bond angle restraints: 44000 Sorted by residual: angle pdb=" N VAL B 529 " pdb=" CA VAL B 529 " pdb=" C VAL B 529 " ideal model delta sigma weight residual 110.30 103.59 6.71 9.70e-01 1.06e+00 4.78e+01 angle pdb=" N ILE A 891 " pdb=" CA ILE A 891 " pdb=" C ILE A 891 " ideal model delta sigma weight residual 112.98 107.83 5.15 1.25e+00 6.40e-01 1.70e+01 angle pdb=" CA VAL A 983 " pdb=" C VAL A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.35e+00 angle pdb=" N ARG B 538 " pdb=" CA ARG B 538 " pdb=" C ARG B 538 " ideal model delta sigma weight residual 112.89 109.50 3.39 1.24e+00 6.50e-01 7.47e+00 angle pdb=" N VAL B 517 " pdb=" CA VAL B 517 " pdb=" C VAL B 517 " ideal model delta sigma weight residual 108.36 104.48 3.88 1.43e+00 4.89e-01 7.37e+00 ... (remaining 43995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10646 17.58 - 35.15: 489 35.15 - 52.73: 184 52.73 - 70.30: 63 70.30 - 87.88: 7 Dihedral angle restraints: 11389 sinusoidal: 6239 harmonic: 5150 Sorted by residual: dihedral pdb=" CD ARG A 700 " pdb=" NE ARG A 700 " pdb=" CZ ARG A 700 " pdb=" NH1 ARG A 700 " ideal model delta sinusoidal sigma weight residual 0.00 43.40 -43.40 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CA VAL B 519 " pdb=" C VAL B 519 " pdb=" N PHE B 520 " pdb=" CA PHE B 520 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL A1057 " pdb=" C VAL A1057 " pdb=" N GLY A1058 " pdb=" CA GLY A1058 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 11386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1649 0.060 - 0.120: 207 0.120 - 0.179: 31 0.179 - 0.239: 1 0.239 - 0.299: 2 Chirality restraints: 1890 Sorted by residual: chirality pdb=" C2' ATP A1201 " pdb=" C1' ATP A1201 " pdb=" C3' ATP A1201 " pdb=" O2' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A1201 " pdb=" C2' ATP A1201 " pdb=" C4' ATP A1201 " pdb=" O3' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4' ATP A1201 " pdb=" C3' ATP A1201 " pdb=" C5' ATP A1201 " pdb=" O4' ATP A1201 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1887 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 700 " -0.633 9.50e-02 1.11e+02 2.12e-01 5.59e+01 pdb=" NE ARG A 700 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 700 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 700 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 700 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG A 700 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 700 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 700 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 700 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 155 " -0.021 2.00e-02 2.50e+03 2.53e-02 9.63e+00 pdb=" CG ASN A 155 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 155 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 155 " 0.040 2.00e-02 2.50e+03 pdb="HD21 ASN A 155 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 155 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 151 " 0.021 2.00e-02 2.50e+03 2.50e-02 9.38e+00 pdb=" CD GLN A 151 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 151 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN A 151 " -0.040 2.00e-02 2.50e+03 pdb="HE21 GLN A 151 " -0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 151 " 0.038 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1155 2.18 - 2.79: 49327 2.79 - 3.39: 63555 3.39 - 4.00: 82486 4.00 - 4.60: 130904 Nonbonded interactions: 327427 Sorted by model distance: nonbonded pdb=" OD1 ASN A 66 " pdb=" H GLN A 69 " model vdw 1.576 1.850 nonbonded pdb="HH21 ARG A 178 " pdb=" O PRO A 324 " model vdw 1.605 1.850 nonbonded pdb=" OD2 ASP A 674 " pdb="HH21 ARG A 679 " model vdw 1.608 1.850 nonbonded pdb=" OD2 ASP B 245 " pdb=" H GLU B 248 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLU A 337 " pdb="HH21 ARG A 533 " model vdw 1.609 1.850 ... (remaining 327422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.940 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: 0.390 Extract box with map and model: 8.270 Check model and map are aligned: 0.400 Set scattering table: 0.200 Process input model: 78.890 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.004 0.058 12233 Z= 0.255 Angle : 0.634 9.190 16577 Z= 0.346 Chirality : 0.043 0.299 1890 Planarity : 0.007 0.271 2085 Dihedral : 13.198 87.876 4561 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.37 % Favored : 93.36 % Rotamer: Outliers : 4.83 % Allowed : 7.01 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.21 (0.22), residues: 1445 helix: -0.31 (0.21), residues: 646 sheet: -1.28 (0.33), residues: 237 loop : -0.97 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 812 HIS 0.007 0.001 HIS A 169 PHE 0.029 0.002 PHE A1009 TYR 0.025 0.002 TYR A 389 ARG 0.048 0.001 ARG A 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 226 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 431 LEU cc_start: 0.8139 (mt) cc_final: 0.7682 (mt) REVERT: A 498 ASN cc_start: 0.7924 (t0) cc_final: 0.7682 (t0) REVERT: A 581 GLU cc_start: 0.6076 (tp30) cc_final: 0.5709 (mp0) REVERT: A 993 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: A 1055 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6927 (tt) REVERT: A 1062 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: B 239 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9073 (tt) REVERT: B 516 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6691 (mtm180) REVERT: B 611 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6022 (pmm) outliers start: 64 outliers final: 31 residues processed: 275 average time/residue: 0.7166 time to fit residues: 266.6710 Evaluate side-chains 161 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 516 ARG Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 773 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 265 GLN A 391 GLN A 959 ASN B 70 GLN B 156 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12233 Z= 0.173 Angle : 0.560 5.337 16577 Z= 0.290 Chirality : 0.041 0.174 1890 Planarity : 0.004 0.039 2085 Dihedral : 8.672 80.125 1693 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.02 % Allowed : 11.84 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.83 (0.22), residues: 1445 helix: 0.03 (0.20), residues: 656 sheet: -1.17 (0.33), residues: 235 loop : -0.78 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1080 HIS 0.008 0.001 HIS A 693 PHE 0.018 0.002 PHE A 248 TYR 0.014 0.001 TYR A 935 ARG 0.005 0.000 ARG A 700 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7745 (m-10) cc_final: 0.7417 (m-10) REVERT: A 249 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 428 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 581 GLU cc_start: 0.5976 (tp30) cc_final: 0.5679 (mp0) REVERT: A 851 MET cc_start: 0.7382 (mtp) cc_final: 0.7087 (mtp) REVERT: A 964 ASP cc_start: 0.6939 (t0) cc_final: 0.6690 (t0) REVERT: A 993 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 998 SER cc_start: 0.7373 (p) cc_final: 0.7165 (m) REVERT: A 1055 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6825 (tt) REVERT: A 1078 LYS cc_start: 0.6434 (mmmt) cc_final: 0.6210 (pttt) REVERT: A 1084 PHE cc_start: 0.8230 (t80) cc_final: 0.7655 (t80) REVERT: B 148 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7458 (mt-10) REVERT: B 239 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 730 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6681 (p90) outliers start: 40 outliers final: 27 residues processed: 161 average time/residue: 0.6419 time to fit residues: 143.7395 Evaluate side-chains 139 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1089 HIS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 739 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 50.8231 > 50: distance: 22 - 58: 3.058 distance: 154 - 166: 3.572 distance: 166 - 172: 5.664 distance: 167 - 168: 4.965 distance: 167 - 170: 3.958 distance: 167 - 173: 6.456 distance: 168 - 169: 8.649 distance: 168 - 177: 6.442 distance: 170 - 171: 5.082 distance: 170 - 174: 7.011 distance: 170 - 175: 4.662 distance: 171 - 176: 4.339 distance: 177 - 178: 7.748 distance: 177 - 185: 10.116 distance: 178 - 179: 12.913 distance: 178 - 181: 8.936 distance: 178 - 186: 6.155 distance: 179 - 180: 18.379 distance: 179 - 196: 12.120 distance: 181 - 182: 8.858 distance: 181 - 187: 5.728 distance: 181 - 188: 5.491 distance: 182 - 183: 4.236 distance: 182 - 184: 9.685 distance: 182 - 189: 3.732 distance: 183 - 191: 6.216 distance: 184 - 193: 7.172 distance: 184 - 194: 7.507 distance: 184 - 195: 7.088 distance: 196 - 197: 5.985 distance: 196 - 206: 23.728 distance: 197 - 198: 8.234 distance: 197 - 207: 5.576 distance: 198 - 199: 6.647 distance: 199 - 272: 8.915 distance: 200 - 201: 5.001 distance: 200 - 208: 4.707 distance: 200 - 209: 5.042 distance: 201 - 202: 5.341 distance: 201 - 203: 3.976 distance: 202 - 204: 5.279 distance: 203 - 205: 7.915 distance: 204 - 211: 4.148 distance: 205 - 212: 4.132 distance: 214 - 215: 5.778 distance: 214 - 217: 3.005 distance: 214 - 225: 6.038 distance: 215 - 216: 4.805 distance: 215 - 233: 5.355 distance: 216 - 292: 12.939 distance: 217 - 226: 4.685 distance: 217 - 227: 4.032 distance: 218 - 219: 3.245 distance: 219 - 221: 3.536 distance: 220 - 222: 4.012 distance: 221 - 223: 3.618 distance: 233 - 234: 4.296 distance: 233 - 242: 6.290 distance: 234 - 235: 3.452 distance: 235 - 236: 4.040 distance: 235 - 250: 6.667 distance: 237 - 238: 3.180 distance: 237 - 244: 5.280 distance: 238 - 239: 3.110 distance: 238 - 246: 3.489 distance: 238 - 247: 3.741 distance: 239 - 240: 4.925 distance: 239 - 241: 4.092 distance: 241 - 248: 3.260 distance: 250 - 251: 3.227 distance: 251 - 252: 3.610 distance: 252 - 253: 8.558 distance: 252 - 272: 5.388 distance: 253 - 321: 10.573 distance: 254 - 255: 4.924 distance: 254 - 261: 6.629 distance: 255 - 264: 3.820 distance: 257 - 258: 3.992 distance: 272 - 273: 3.188 distance: 272 - 283: 4.264 distance: 273 - 274: 4.199 distance: 273 - 284: 4.012 distance: 274 - 275: 6.860 distance: 274 - 292: 4.985 distance: 275 - 337: 7.228 distance: 276 - 285: 6.042 distance: 278 - 287: 3.270 distance: 292 - 301: 8.018 distance: 293 - 302: 6.949 distance: 294 - 295: 7.535 distance: 294 - 309: 4.799 distance: 295 - 348: 8.989 distance: 296 - 297: 6.470 distance: 296 - 304: 9.580 distance: 297 - 305: 9.573 distance: 297 - 306: 6.647 distance: 298 - 299: 7.970 distance: 298 - 300: 3.579 distance: 300 - 307: 5.355 distance: 300 - 308: 4.651 distance: 310 - 311: 4.117 distance: 311 - 321: 4.144 distance: 312 - 363: 5.375 distance: 313 - 314: 3.806 distance: 313 - 320: 3.200 distance: 314 - 315: 4.264 distance: 314 - 316: 4.278 distance: 321 - 328: 3.165 distance: 323 - 324: 3.675 distance: 325 - 330: 3.364 distance: 327 - 334: 4.711