Starting phenix.real_space_refine on Sun Jul 28 02:01:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqs_18603/07_2024/8qqs_18603.cif" } resolution = 2.9 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= 0.007 sd= 0.186 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 60 5.49 5 S 76 5.16 5 C 13134 2.51 5 N 3770 2.21 5 O 4157 1.98 5 H 20715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 41912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 8280 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain: "B" Number of atoms: 11766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 11766 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 25, 'TRANS': 717} Chain breaks: 2 Chain: "C" Number of atoms: 8261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 8261 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain: "D" Number of atoms: 11715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 11715 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 25, 'TRANS': 714} Chain breaks: 2 Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 930 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 960 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Time building chain proxies: 19.24, per 1000 atoms: 0.46 Number of scatterers: 41912 At special positions: 0 Unit cell: (133.61, 143.954, 149.126, 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 76 16.00 P 60 15.00 O 4157 8.00 N 3770 7.00 C 13134 6.00 H 20715 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: 34.38 Conformation dependent library (CDL) restraints added in 4.0 seconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4706 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 28 sheets defined 50.0% alpha, 14.4% beta 30 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 18.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.816A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.655A pdb=" N HIS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 136 No H-bonds generated for 'chain 'A' and resid 135 through 136' Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.940A pdb=" N GLU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 417 through 425 removed outlier: 4.150A pdb=" N ALA A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.784A pdb=" N HIS A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.602A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.897A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 removed outlier: 3.693A pdb=" N TYR B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.676A pdb=" N HIS B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.527A pdb=" N ALA B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.866A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 343 through 364 removed outlier: 4.517A pdb=" N SER B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 386 removed outlier: 3.698A pdb=" N ALA B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.610A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.626A pdb=" N THR B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.644A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 576 through 597 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.767A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 removed outlier: 3.546A pdb=" N LEU B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 621 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 622' Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.728A pdb=" N THR B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 718 through 731 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 785 through 801 Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 128 through 134 removed outlier: 3.692A pdb=" N HIS C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.517A pdb=" N LEU C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.713A pdb=" N ALA C 427 " --> pdb=" O MET C 423 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 467 through 494 removed outlier: 3.789A pdb=" N HIS C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.761A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.719A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.771A pdb=" N TYR D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 removed outlier: 3.502A pdb=" N HIS D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 183 through 198 removed outlier: 3.704A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 231 Processing helix chain 'D' and resid 279 through 301 Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.552A pdb=" N LYS D 305 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 364 removed outlier: 3.897A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 386 removed outlier: 3.610A pdb=" N ILE D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.549A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 3.634A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 576 through 597 Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.722A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 3.555A pdb=" N LEU D 620 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 622' Processing helix chain 'D' and resid 622 through 640 removed outlier: 3.550A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 removed outlier: 3.685A pdb=" N THR D 683 " --> pdb=" O HIS D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.773A pdb=" N MET D 755 " --> pdb=" O TRP D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 785 through 801 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.543A pdb=" N THR A 9 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR B 766 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 423 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 250 removed outlier: 4.566A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 444 removed outlier: 3.578A pdb=" N LEU A 447 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 139 through 145 removed outlier: 3.579A pdb=" N LYS B 129 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 168 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 169 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 69 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 60 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 59 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ARG B 206 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 61 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.529A pdb=" N PHE B 243 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 254 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 247 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.529A pdb=" N PHE B 243 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 254 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 322 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 321 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AB5, first strand: chain 'B' and resid 647 through 654 removed outlier: 3.796A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 8 through 12 removed outlier: 5.595A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 495 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 423 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB9, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 333 Processing sheet with id=AC2, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.575A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 303 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 292 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 306 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC4, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'D' and resid 139 through 145 removed outlier: 6.735A pdb=" N TRP D 170 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU D 130 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG D 168 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU D 132 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET D 166 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 69 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE D 60 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.761A pdb=" N LYS D 247 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 241 through 243 removed outlier: 3.725A pdb=" N GLY D 251 " --> pdb=" O LYS D 326 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 265 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL D 323 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR D 267 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL D 325 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE D 269 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS D 268 " --> pdb=" O GLN D 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC9, first strand: chain 'D' and resid 565 through 567 Processing sheet with id=AD1, first strand: chain 'D' and resid 646 through 654 removed outlier: 3.536A pdb=" N LEU D 659 " --> pdb=" O ASN D 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 675 " --> pdb=" O VAL D 664 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3057 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 17.25 Time building geometry restraints manager: 36.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 6927 1.05 - 1.24: 16468 1.24 - 1.43: 6319 1.43 - 1.62: 12534 1.62 - 1.81: 140 Bond restraints: 42388 Sorted by residual: bond pdb=" NE1 TRP C 436 " pdb=" HE1 TRP C 436 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP B 751 " pdb=" HE1 TRP B 751 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP B 258 " pdb=" HE1 TRP B 258 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP B 170 " pdb=" HE1 TRP B 170 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP D 258 " pdb=" HE1 TRP D 258 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 42383 not shown) Histogram of bond angle deviations from ideal: 90.54 - 105.49: 867 105.49 - 120.44: 64719 120.44 - 135.40: 11195 135.40 - 150.35: 1 150.35 - 165.31: 2 Bond angle restraints: 76784 Sorted by residual: angle pdb=" CA SER D 121 " pdb=" N SER D 121 " pdb=" H SER D 121 " ideal model delta sigma weight residual 114.00 165.31 -51.31 3.00e+00 1.11e-01 2.93e+02 angle pdb=" CA THR D 163 " pdb=" N THR D 163 " pdb=" H THR D 163 " ideal model delta sigma weight residual 114.00 156.34 -42.34 3.00e+00 1.11e-01 1.99e+02 angle pdb=" N VAL D 167 " pdb=" CA VAL D 167 " pdb=" C VAL D 167 " ideal model delta sigma weight residual 108.11 90.54 17.57 1.40e+00 5.10e-01 1.58e+02 angle pdb=" CA THR B 163 " pdb=" N THR B 163 " pdb=" H THR B 163 " ideal model delta sigma weight residual 114.00 143.64 -29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C VAL D 167 " pdb=" CA VAL D 167 " pdb=" CB VAL D 167 " ideal model delta sigma weight residual 110.63 121.91 -11.28 1.48e+00 4.57e-01 5.81e+01 ... (remaining 76779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 18945 33.79 - 67.57: 605 67.57 - 101.36: 2 101.36 - 135.14: 0 135.14 - 168.93: 2 Dihedral angle restraints: 19554 sinusoidal: 11308 harmonic: 8246 Sorted by residual: dihedral pdb=" CA GLY C 31 " pdb=" C GLY C 31 " pdb=" N ARG C 32 " pdb=" CA ARG C 32 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" C4' DT E 28 " pdb=" C3' DT E 28 " pdb=" O3' DT E 28 " pdb=" P DT E 29 " ideal model delta sinusoidal sigma weight residual 220.00 51.07 168.93 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA F 1 " pdb=" C3' DA F 1 " pdb=" O3' DA F 1 " pdb=" P DA F 2 " ideal model delta sinusoidal sigma weight residual 220.00 62.78 157.22 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 19551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2297 0.039 - 0.079: 727 0.079 - 0.118: 172 0.118 - 0.157: 101 0.157 - 0.196: 11 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 3305 not shown) Planarity restraints: 6113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT E 6 " 0.014 2.00e-02 2.50e+03 1.38e-02 5.26e+00 pdb=" N1 DT E 6 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DT E 6 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT E 6 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT E 6 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT E 6 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DT E 6 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT E 6 " -0.005 2.00e-02 2.50e+03 pdb=" H6 DT E 6 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 163 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 164 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 163 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 164 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.030 5.00e-02 4.00e+02 ... (remaining 6110 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.99: 314 1.99 - 2.64: 51860 2.64 - 3.29: 123738 3.29 - 3.95: 157769 3.95 - 4.60: 247733 Nonbonded interactions: 581414 Sorted by model distance: nonbonded pdb=" HG1 THR B 292 " pdb="HD23 LEU B 357 " model vdw 1.332 2.270 nonbonded pdb=" HG SER C 27 " pdb="HG21 VAL D 501 " model vdw 1.391 2.270 nonbonded pdb=" HG SER A 27 " pdb="HG21 VAL B 501 " model vdw 1.409 2.270 nonbonded pdb=" HG1 THR D 292 " pdb="HD23 LEU D 357 " model vdw 1.507 2.270 nonbonded pdb=" HZ2 LYS B 449 " pdb=" HD1 HIS B 505 " model vdw 1.538 2.100 ... (remaining 581409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 524) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 11 through 76 or resid 121 through 802)) selection = (chain 'D' and (resid 11 through 76 or resid 121 through 802)) } 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: 5.580 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: 0.620 Extract box with map and model: 1.690 Check model and map are aligned: 0.330 Set scattering table: 0.450 Process input model: 145.340 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 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:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.070 21673 Z= 0.271 Angle : 0.674 17.575 29528 Z= 0.372 Chirality : 0.045 0.196 3308 Planarity : 0.004 0.055 3659 Dihedral : 13.220 168.928 8464 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.42 % 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: 0.40 (0.16), residues: 2508 helix: 1.83 (0.14), residues: 1156 sheet: -0.91 (0.26), residues: 406 loop : -1.16 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS A 378 PHE 0.012 0.002 PHE B 196 TYR 0.012 0.001 TYR C 63 ARG 0.004 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 513 time to evaluate : 2.912 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: A 23 ASP cc_start: 0.7984 (t0) cc_final: 0.7694 (m-30) REVERT: A 159 MET cc_start: 0.9373 (mmt) cc_final: 0.8945 (mmt) REVERT: A 231 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7364 (mp0) REVERT: A 487 GLU cc_start: 0.7793 (tp30) cc_final: 0.7418 (pt0) REVERT: A 508 LEU cc_start: 0.8744 (tp) cc_final: 0.8542 (tp) REVERT: B 21 LYS cc_start: 0.8542 (mttt) cc_final: 0.8167 (mmmt) REVERT: B 218 TYR cc_start: 0.7184 (m-80) cc_final: 0.6831 (m-80) REVERT: B 222 ILE cc_start: 0.7981 (mm) cc_final: 0.7748 (mp) REVERT: B 242 TYR cc_start: 0.8345 (t80) cc_final: 0.7832 (t80) REVERT: B 253 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 265 ASN cc_start: 0.7544 (m-40) cc_final: 0.7218 (m-40) REVERT: B 439 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7692 (mmtm) REVERT: B 474 LEU cc_start: 0.8223 (tp) cc_final: 0.7997 (tt) REVERT: B 569 ASN cc_start: 0.8054 (m110) cc_final: 0.7219 (m110) REVERT: B 640 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8307 (mtmt) REVERT: B 702 GLU cc_start: 0.7936 (mm-30) cc_final: 0.6864 (mp0) REVERT: B 754 THR cc_start: 0.8229 (p) cc_final: 0.7079 (t) REVERT: C 141 GLU cc_start: 0.7899 (pt0) cc_final: 0.7301 (pp20) REVERT: C 371 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7466 (ttm110) REVERT: D 13 LEU cc_start: 0.7296 (mt) cc_final: 0.7035 (tp) REVERT: D 41 PHE cc_start: 0.7117 (m-10) cc_final: 0.6582 (m-10) REVERT: D 277 ASP cc_start: 0.7587 (m-30) cc_final: 0.7043 (t0) REVERT: D 359 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7271 (mm-30) REVERT: D 377 ASP cc_start: 0.7968 (t0) cc_final: 0.7574 (m-30) REVERT: D 439 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8081 (ttmp) REVERT: D 474 LEU cc_start: 0.7896 (tp) cc_final: 0.7602 (tp) REVERT: D 556 GLN cc_start: 0.7586 (mt0) cc_final: 0.7246 (mt0) REVERT: D 754 THR cc_start: 0.8417 (p) cc_final: 0.7573 (t) outliers start: 5 outliers final: 1 residues processed: 515 average time/residue: 3.3673 time to fit residues: 1933.3905 Evaluate side-chains 258 residues out of total 2125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1705 > 50: distance: 60 - 79: 6.874 distance: 79 - 87: 14.055 distance: 80 - 81: 3.840 distance: 80 - 88: 3.682 distance: 81 - 82: 17.137 distance: 81 - 93: 7.497 distance: 83 - 84: 4.533 distance: 84 - 85: 4.378 distance: 93 - 94: 5.456 distance: 93 - 102: 20.953 distance: 94 - 95: 4.422 distance: 94 - 97: 6.376 distance: 94 - 103: 11.031 distance: 95 - 96: 7.745 distance: 97 - 98: 8.593 distance: 97 - 104: 10.398 distance: 97 - 105: 15.630 distance: 98 - 99: 3.813 distance: 98 - 106: 4.066 distance: 98 - 107: 8.306 distance: 99 - 108: 5.698 distance: 99 - 109: 3.824 distance: 100 - 101: 3.669 distance: 100 - 110: 4.057 distance: 100 - 111: 4.965 distance: 115 - 122: 3.915 distance: 116 - 117: 3.324 distance: 116 - 119: 5.647 distance: 116 - 123: 3.885 distance: 117 - 129: 5.499 distance: 119 - 120: 3.637 distance: 119 - 121: 6.133 distance: 120 - 125: 7.032 distance: 129 - 135: 3.015 distance: 130 - 131: 4.304 distance: 130 - 136: 6.807 distance: 131 - 132: 16.681 distance: 131 - 143: 8.014 distance: 133 - 137: 4.270 distance: 133 - 138: 4.891 distance: 134 - 135: 3.804 distance: 134 - 140: 8.246 distance: 135 - 141: 8.648 distance: 135 - 142: 5.357 distance: 143 - 144: 6.001 distance: 143 - 151: 10.315 distance: 144 - 145: 9.649 distance: 144 - 147: 3.716 distance: 144 - 152: 5.933 distance: 145 - 146: 13.574 distance: 145 - 162: 14.063 distance: 147 - 148: 3.131 distance: 147 - 153: 6.699 distance: 148 - 150: 3.020 distance: 148 - 155: 4.154 distance: 149 - 156: 3.091 distance: 149 - 158: 4.309 distance: 150 - 159: 5.187 distance: 150 - 160: 8.670 distance: 150 - 161: 5.035 distance: 162 - 163: 4.200 distance: 162 - 172: 3.604 distance: 163 - 164: 14.377 distance: 163 - 166: 8.917 distance: 163 - 173: 11.033 distance: 164 - 165: 22.587 distance: 164 - 179: 13.006 distance: 166 - 167: 6.423 distance: 166 - 174: 7.092 distance: 166 - 175: 5.801 distance: 167 - 169: 5.527 distance: 168 - 170: 5.973 distance: 169 - 171: 3.380 distance: 170 - 171: 3.316 distance: 171 - 178: 3.745 distance: 179 - 180: 4.175 distance: 179 - 185: 6.638 distance: 180 - 181: 5.380 distance: 180 - 183: 10.287 distance: 180 - 186: 7.127 distance: 181 - 182: 26.472 distance: 181 - 193: 11.250 distance: 183 - 184: 6.473 distance: 183 - 187: 12.821 distance: 183 - 188: 11.693 distance: 184 - 185: 11.597 distance: 184 - 189: 8.350 distance: 184 - 190: 4.339 distance: 185 - 191: 13.173 distance: 185 - 192: 6.092 distance: 193 - 194: 9.780 distance: 193 - 201: 14.259 distance: 194 - 197: 10.450 distance: 194 - 202: 5.240 distance: 195 - 207: 4.163 distance: 197 - 198: 5.510 distance: 197 - 203: 9.694 distance: 197 - 204: 3.761 distance: 198 - 199: 4.115 distance: 198 - 200: 7.071 distance: 200 - 205: 3.180 distance: 207 - 208: 5.778 distance: 207 - 215: 3.154 distance: 208 - 209: 9.622 distance: 208 - 211: 5.348 distance: 208 - 216: 8.748 distance: 209 - 210: 19.903 distance: 209 - 226: 8.591 distance: 211 - 213: 10.340 distance: 211 - 217: 5.127 distance: 212 - 214: 7.819 distance: 212 - 218: 4.242 distance: 212 - 219: 6.640 distance: 213 - 220: 8.131 distance: 213 - 221: 9.066 distance: 213 - 222: 5.179 distance: 214 - 223: 6.666 distance: 214 - 224: 3.510 distance: 214 - 225: 3.197 distance: 226 - 227: 7.695 distance: 226 - 237: 14.596 distance: 226 - 287: 4.074 distance: 227 - 228: 3.147 distance: 227 - 238: 4.173 distance: 228 - 229: 5.476 distance: 229 - 284: 7.898 distance: 230 - 231: 5.161 distance: 230 - 239: 5.542 distance: 230 - 240: 4.421 distance: 231 - 232: 4.420 distance: 231 - 233: 3.509 distance: 232 - 234: 3.525 distance: 232 - 241: 6.226 distance: 233 - 235: 3.658 distance: 233 - 242: 3.355 distance: 234 - 236: 3.307 distance: 234 - 243: 3.362 distance: 235 - 244: 3.718 distance: 236 - 245: 3.661 distance: 257 - 269: 3.462