Starting phenix.real_space_refine on Tue Aug 26 21:41:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_18603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_18603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_18603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_18603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqs_18603/08_2025/8qqs_18603.map" } resolution = 2.9 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= 0.007 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. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.19, per 1000 atoms: 0.17 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 - 3.00 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: 3.39 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 7.17 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: 10.28 Time building geometry restraints manager: 4.80 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: 0.00 - 10.26: 76776 10.26 - 20.52: 5 20.52 - 30.79: 1 30.79 - 41.05: 0 41.05 - 51.31: 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 Time spend for trying shortcut: 0.00 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: 3.630 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: 0.260 Extract box with map and model: 0.540 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 43.590 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.060 ------------------------------------------------------------------------------- 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= 0.182 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 359 TYR 0.012 0.001 TYR C 63 PHE 0.012 0.002 PHE B 196 TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00423 (21673) covalent geometry : angle 0.67417 (29528) hydrogen bonds : bond 0.16547 ( 1122) hydrogen bonds : angle 6.48553 ( 3177) *********************** 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 to be fit. rotamer outliers: 5 poor density : 513 time to evaluate : 0.998 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: 0.7700 (m-30) REVERT: A 159 MET cc_start: 0.9373 (mmt) cc_final: 0.8944 (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: 0.7831 (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: 0.7216 (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: 0.7078 (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: 1.6648 time to fit residues: 950.0603 Evaluate side-chains 258 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 106 GLN A 319 ASN A 464 GLN A 484 GLN B 46 ASN B 434 GLN B 531 GLN B 542 GLN C 94 GLN C 165 ASN C 327 GLN D 271 ASN D 531 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114546 restraints weight = 76552.770| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.90 r_work: 0.3231 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21673 Z= 0.147 Angle : 0.536 8.120 29528 Z= 0.296 Chirality : 0.042 0.174 3308 Planarity : 0.004 0.057 3659 Dihedral : 13.527 169.922 3496 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.74 % Allowed : 13.13 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.17), residues: 2508 helix: 2.38 (0.15), residues: 1186 sheet: -0.99 (0.25), residues: 390 loop : -1.05 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 206 TYR 0.010 0.001 TYR C 149 PHE 0.012 0.001 PHE B 262 TRP 0.005 0.001 TRP B 751 HIS 0.003 0.001 HIS D 679 Details of bonding type rmsd covalent geometry : bond 0.00331 (21673) covalent geometry : angle 0.53619 (29528) hydrogen bonds : bond 0.04428 ( 1122) hydrogen bonds : angle 4.99562 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 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 304 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 1.014 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: A 153 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: A 159 MET cc_start: 0.9257 (mmt) cc_final: 0.8694 (mmt) REVERT: A 231 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7625 (mp0) REVERT: A 416 GLN cc_start: 0.7743 (pp30) cc_final: 0.7514 (pp30) REVERT: A 487 GLU cc_start: 0.8033 (tp30) cc_final: 0.7516 (pt0) REVERT: B 21 LYS cc_start: 0.8605 (mttt) cc_final: 0.8235 (mmmt) REVERT: B 57 LYS cc_start: 0.8144 (tttm) cc_final: 0.7827 (tmtt) REVERT: B 69 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8213 (m) REVERT: B 169 PHE cc_start: 0.8043 (p90) cc_final: 0.7705 (p90) REVERT: B 218 TYR cc_start: 0.7188 (m-80) cc_final: 0.6941 (m-80) REVERT: B 242 TYR cc_start: 0.8475 (t80) cc_final: 0.8236 (t80) REVERT: B 253 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 265 ASN cc_start: 0.7966 (m-40) cc_final: 0.7734 (m-40) REVERT: B 346 LYS cc_start: 0.8003 (tttt) cc_final: 0.7781 (tttm) REVERT: B 439 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7896 (mmtm) REVERT: B 569 ASN cc_start: 0.8352 (m110) cc_final: 0.7387 (m110) REVERT: B 611 TYR cc_start: 0.8098 (m-80) cc_final: 0.7882 (m-80) REVERT: B 617 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7389 (tp30) REVERT: B 640 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8203 (mtmt) REVERT: B 702 GLU cc_start: 0.8087 (mm-30) cc_final: 0.6958 (mp0) REVERT: B 754 THR cc_start: 0.8279 (p) cc_final: 0.7529 (t) REVERT: B 793 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: C 141 GLU cc_start: 0.7942 (pt0) cc_final: 0.7244 (pp20) REVERT: C 401 PRO cc_start: 0.8377 (Cg_endo) cc_final: 0.8173 (Cg_exo) REVERT: C 487 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7067 (mp0) REVERT: D 13 LEU cc_start: 0.7364 (mt) cc_final: 0.7066 (tp) REVERT: D 257 GLN cc_start: 0.7098 (tt0) cc_final: 0.6590 (tp-100) REVERT: D 277 ASP cc_start: 0.7679 (m-30) cc_final: 0.7258 (t0) REVERT: D 344 GLU cc_start: 0.6818 (pm20) cc_final: 0.6438 (pm20) REVERT: D 359 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7087 (mm-30) REVERT: D 377 ASP cc_start: 0.8060 (t0) cc_final: 0.7543 (m-30) REVERT: D 474 LEU cc_start: 0.7964 (tp) cc_final: 0.7712 (tp) REVERT: D 640 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8328 (mmtt) REVERT: D 754 THR cc_start: 0.8338 (p) cc_final: 0.7763 (t) outliers start: 37 outliers final: 16 residues processed: 294 average time/residue: 1.4424 time to fit residues: 478.8773 Evaluate side-chains 249 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 73 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 341 GLN A 378 HIS B 46 ASN D 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109552 restraints weight = 76587.250| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21673 Z= 0.222 Angle : 0.559 6.474 29528 Z= 0.307 Chirality : 0.043 0.175 3308 Planarity : 0.004 0.044 3659 Dihedral : 13.579 167.415 3494 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.07 % Allowed : 14.16 % Favored : 83.76 % 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 aren not related in a simple way. whole: 0.81 (0.17), residues: 2508 helix: 2.31 (0.15), residues: 1190 sheet: -1.00 (0.26), residues: 390 loop : -1.15 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 206 TYR 0.011 0.001 TYR A 86 PHE 0.014 0.002 PHE D 196 TRP 0.014 0.001 TRP C 415 HIS 0.006 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00522 (21673) covalent geometry : angle 0.55872 (29528) hydrogen bonds : bond 0.04797 ( 1122) hydrogen bonds : angle 4.73574 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 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 288 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.683 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: A 120 MET cc_start: 0.8901 (ttm) cc_final: 0.8649 (ttp) REVERT: A 153 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: A 159 MET cc_start: 0.9289 (mmt) cc_final: 0.8761 (mmt) REVERT: A 231 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7641 (mp0) REVERT: A 395 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: A 416 GLN cc_start: 0.7904 (pp30) cc_final: 0.7626 (pp30) REVERT: B 21 LYS cc_start: 0.8617 (mttt) cc_final: 0.8286 (mmmt) REVERT: B 57 LYS cc_start: 0.8242 (tttm) cc_final: 0.7925 (tmtt) REVERT: B 169 PHE cc_start: 0.8148 (p90) cc_final: 0.7822 (p90) REVERT: B 253 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 265 ASN cc_start: 0.7962 (m-40) cc_final: 0.7583 (m-40) REVERT: B 439 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7895 (mmtm) REVERT: B 465 GLN cc_start: 0.7959 (mp-120) cc_final: 0.7700 (mp-120) REVERT: B 569 ASN cc_start: 0.8327 (m110) cc_final: 0.7374 (m110) REVERT: B 617 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7289 (tp30) REVERT: B 640 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8158 (mtmt) REVERT: B 702 GLU cc_start: 0.8127 (mm-30) cc_final: 0.6974 (mp0) REVERT: B 793 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: C 141 GLU cc_start: 0.8156 (pt0) cc_final: 0.7208 (pp20) REVERT: C 487 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7174 (mp0) REVERT: D 13 LEU cc_start: 0.7402 (mt) cc_final: 0.7098 (tp) REVERT: D 204 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6447 (ttt180) REVERT: D 252 VAL cc_start: 0.8384 (t) cc_final: 0.8174 (p) REVERT: D 277 ASP cc_start: 0.7648 (m-30) cc_final: 0.7307 (t0) REVERT: D 344 GLU cc_start: 0.6785 (pm20) cc_final: 0.6502 (pm20) REVERT: D 377 ASP cc_start: 0.8131 (t0) cc_final: 0.7559 (m-30) REVERT: D 474 LEU cc_start: 0.8017 (tp) cc_final: 0.7744 (tp) REVERT: D 640 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8284 (mmtt) REVERT: D 702 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: D 754 THR cc_start: 0.8635 (p) cc_final: 0.8068 (t) outliers start: 44 outliers final: 23 residues processed: 271 average time/residue: 1.3657 time to fit residues: 418.2345 Evaluate side-chains 244 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.150085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111093 restraints weight = 76614.968| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.89 r_work: 0.3191 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21673 Z= 0.199 Angle : 0.534 5.935 29528 Z= 0.294 Chirality : 0.042 0.158 3308 Planarity : 0.004 0.068 3659 Dihedral : 13.602 168.122 3494 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 14.78 % Favored : 82.73 % 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 aren not related in a simple way. whole: 0.80 (0.17), residues: 2508 helix: 2.33 (0.15), residues: 1188 sheet: -1.02 (0.25), residues: 399 loop : -1.16 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 413 TYR 0.011 0.001 TYR C 63 PHE 0.010 0.001 PHE D 196 TRP 0.010 0.001 TRP C 415 HIS 0.005 0.001 HIS B 652 Details of bonding type rmsd covalent geometry : bond 0.00469 (21673) covalent geometry : angle 0.53411 (29528) hydrogen bonds : bond 0.04397 ( 1122) hydrogen bonds : angle 4.60497 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 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 283 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.090 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: A 120 MET cc_start: 0.8874 (ttm) cc_final: 0.8628 (ttp) REVERT: A 153 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: A 159 MET cc_start: 0.9244 (mmt) cc_final: 0.8714 (mmt) REVERT: A 231 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7754 (mp0) REVERT: A 306 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: A 416 GLN cc_start: 0.7917 (pp30) cc_final: 0.7664 (pp30) REVERT: B 21 LYS cc_start: 0.8614 (mttt) cc_final: 0.8302 (mmmt) REVERT: B 57 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7932 (tmtt) REVERT: B 169 PHE cc_start: 0.8157 (p90) cc_final: 0.7857 (p90) REVERT: B 253 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 439 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7970 (mmtm) REVERT: B 569 ASN cc_start: 0.8349 (m110) cc_final: 0.7370 (m110) REVERT: B 617 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7274 (tp30) REVERT: B 640 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8219 (mtmt) REVERT: B 702 GLU cc_start: 0.8118 (mm-30) cc_final: 0.6751 (mp0) REVERT: B 793 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: C 106 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: C 141 GLU cc_start: 0.8126 (pt0) cc_final: 0.7258 (pp20) REVERT: C 487 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7164 (mp0) REVERT: D 13 LEU cc_start: 0.7411 (mt) cc_final: 0.7102 (tp) REVERT: D 131 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6623 (mp0) REVERT: D 166 MET cc_start: 0.6896 (tmt) cc_final: 0.6515 (tmt) REVERT: D 204 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6423 (ttt180) REVERT: D 277 ASP cc_start: 0.7683 (m-30) cc_final: 0.7391 (t0) REVERT: D 344 GLU cc_start: 0.6800 (pm20) cc_final: 0.6507 (pm20) REVERT: D 377 ASP cc_start: 0.8149 (t0) cc_final: 0.7553 (m-30) REVERT: D 474 LEU cc_start: 0.7980 (tp) cc_final: 0.7726 (tp) REVERT: D 702 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7043 (mp0) outliers start: 53 outliers final: 21 residues processed: 268 average time/residue: 1.5285 time to fit residues: 461.6509 Evaluate side-chains 242 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 146 optimal weight: 0.0980 chunk 150 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 202 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113698 restraints weight = 76357.200| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3234 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21673 Z= 0.114 Angle : 0.490 6.094 29528 Z= 0.269 Chirality : 0.040 0.148 3308 Planarity : 0.003 0.046 3659 Dihedral : 13.503 168.679 3494 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.69 % Allowed : 15.58 % Favored : 82.73 % 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 aren not related in a simple way. whole: 1.08 (0.17), residues: 2508 helix: 2.54 (0.15), residues: 1189 sheet: -0.93 (0.26), residues: 394 loop : -1.00 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.012 0.001 TYR D 228 PHE 0.021 0.001 PHE D 169 TRP 0.008 0.001 TRP C 415 HIS 0.004 0.001 HIS B 652 Details of bonding type rmsd covalent geometry : bond 0.00259 (21673) covalent geometry : angle 0.49021 (29528) hydrogen bonds : bond 0.03700 ( 1122) hydrogen bonds : angle 4.35263 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 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 267 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.075 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: A 120 MET cc_start: 0.8815 (ttm) cc_final: 0.8552 (ttp) REVERT: A 153 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: A 159 MET cc_start: 0.9243 (mmt) cc_final: 0.8733 (mmt) REVERT: A 231 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7727 (mp0) REVERT: A 306 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: A 416 GLN cc_start: 0.7946 (pp30) cc_final: 0.7704 (pp30) REVERT: A 487 GLU cc_start: 0.7943 (tp30) cc_final: 0.7601 (pt0) REVERT: B 21 LYS cc_start: 0.8621 (mttt) cc_final: 0.8311 (mmmt) REVERT: B 57 LYS cc_start: 0.8222 (tttm) cc_final: 0.7901 (tmtt) REVERT: B 169 PHE cc_start: 0.8097 (p90) cc_final: 0.7786 (p90) REVERT: B 253 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 265 ASN cc_start: 0.8052 (m-40) cc_final: 0.7685 (m-40) REVERT: B 383 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7647 (tp30) REVERT: B 426 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: B 562 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6484 (m-30) REVERT: B 569 ASN cc_start: 0.8330 (m110) cc_final: 0.7335 (m110) REVERT: B 640 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8210 (mtpt) REVERT: B 702 GLU cc_start: 0.8059 (mm-30) cc_final: 0.6691 (mp0) REVERT: B 793 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 141 GLU cc_start: 0.8046 (pt0) cc_final: 0.7245 (pp20) REVERT: D 13 LEU cc_start: 0.7401 (mt) cc_final: 0.7077 (tp) REVERT: D 131 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6726 (mp0) REVERT: D 204 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6527 (ttt180) REVERT: D 277 ASP cc_start: 0.7669 (m-30) cc_final: 0.7346 (t0) REVERT: D 344 GLU cc_start: 0.6771 (pm20) cc_final: 0.6510 (pm20) REVERT: D 377 ASP cc_start: 0.8093 (t0) cc_final: 0.7539 (m-30) REVERT: D 474 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7694 (tp) REVERT: D 702 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: D 754 THR cc_start: 0.8445 (p) cc_final: 0.8029 (t) outliers start: 36 outliers final: 19 residues processed: 257 average time/residue: 1.3707 time to fit residues: 400.2942 Evaluate side-chains 240 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 69 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS C 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109671 restraints weight = 76534.409| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.97 r_work: 0.3155 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21673 Z= 0.250 Angle : 0.566 6.237 29528 Z= 0.312 Chirality : 0.044 0.207 3308 Planarity : 0.004 0.064 3659 Dihedral : 13.695 167.186 3494 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.59 % Allowed : 15.29 % Favored : 82.12 % 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 aren not related in a simple way. whole: 0.83 (0.17), residues: 2508 helix: 2.33 (0.15), residues: 1187 sheet: -1.09 (0.25), residues: 390 loop : -1.09 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 291 TYR 0.015 0.001 TYR D 242 PHE 0.042 0.002 PHE D 169 TRP 0.014 0.001 TRP D 170 HIS 0.005 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00595 (21673) covalent geometry : angle 0.56608 (29528) hydrogen bonds : bond 0.04900 ( 1122) hydrogen bonds : angle 4.58789 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 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 275 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 1.174 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: A 120 MET cc_start: 0.8879 (ttm) cc_final: 0.8637 (ttp) REVERT: A 153 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: A 159 MET cc_start: 0.9228 (mmt) cc_final: 0.8768 (mmt) REVERT: A 306 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: A 416 GLN cc_start: 0.8004 (pp30) cc_final: 0.7767 (pp30) REVERT: B 17 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 21 LYS cc_start: 0.8610 (mttt) cc_final: 0.8366 (ttmm) REVERT: B 57 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7920 (tmtt) REVERT: B 169 PHE cc_start: 0.8116 (p90) cc_final: 0.7868 (p90) REVERT: B 253 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 426 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: B 569 ASN cc_start: 0.8421 (m110) cc_final: 0.7412 (m110) REVERT: B 640 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8333 (mtpt) REVERT: B 702 GLU cc_start: 0.8135 (mm-30) cc_final: 0.6732 (mp0) REVERT: B 754 THR cc_start: 0.8536 (p) cc_final: 0.8122 (t) REVERT: B 793 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 106 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: C 141 GLU cc_start: 0.8214 (pt0) cc_final: 0.7283 (pp20) REVERT: C 487 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7258 (mp0) REVERT: D 13 LEU cc_start: 0.7410 (mt) cc_final: 0.7070 (tp) REVERT: D 131 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6664 (mp0) REVERT: D 204 ARG cc_start: 0.7211 (mtp85) cc_final: 0.6599 (ttt180) REVERT: D 275 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.6379 (mp10) REVERT: D 277 ASP cc_start: 0.7648 (m-30) cc_final: 0.7389 (t0) REVERT: D 344 GLU cc_start: 0.6842 (pm20) cc_final: 0.6537 (pm20) REVERT: D 377 ASP cc_start: 0.8139 (t0) cc_final: 0.7577 (m-30) REVERT: D 474 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7733 (tp) REVERT: D 653 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7876 (t) REVERT: D 702 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: D 754 THR cc_start: 0.8770 (p) cc_final: 0.8206 (t) outliers start: 55 outliers final: 23 residues processed: 257 average time/residue: 1.5206 time to fit residues: 443.0364 Evaluate side-chains 242 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 281 HIS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 730 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 53.3825 > 50: distance: 155 - 212: 6.109 distance: 169 - 236: 6.364 distance: 184 - 250: 9.994 distance: 191 - 192: 4.706 distance: 191 - 203: 7.068 distance: 192 - 193: 4.858 distance: 192 - 204: 4.888 distance: 193 - 194: 7.679 distance: 193 - 212: 4.879 distance: 195 - 205: 3.955 distance: 195 - 206: 5.225 distance: 196 - 198: 3.736 distance: 197 - 199: 4.768 distance: 198 - 208: 3.071 distance: 200 - 201: 3.497 distance: 202 - 211: 4.644 distance: 213 - 216: 3.116 distance: 213 - 224: 4.431 distance: 216 - 225: 3.923 distance: 216 - 226: 3.506 distance: 217 - 218: 3.120 distance: 217 - 228: 3.834 distance: 218 - 219: 4.227 distance: 218 - 229: 3.995 distance: 218 - 230: 3.281 distance: 219 - 220: 15.400 distance: 219 - 231: 5.955 distance: 220 - 221: 7.620 distance: 220 - 222: 6.370 distance: 221 - 233: 6.232 distance: 222 - 234: 4.041 distance: 222 - 235: 5.828 distance: 236 - 237: 9.457 distance: 236 - 243: 4.031 distance: 237 - 238: 3.878 distance: 237 - 240: 5.952 distance: 237 - 244: 4.450 distance: 238 - 239: 20.137 distance: 238 - 250: 7.820 distance: 240 - 241: 4.858 distance: 240 - 242: 6.587 distance: 240 - 245: 8.445 distance: 241 - 246: 16.144 distance: 242 - 247: 6.171 distance: 242 - 248: 3.407 distance: 242 - 249: 3.337 distance: 250 - 251: 4.456 distance: 250 - 254: 11.554 distance: 251 - 255: 5.074 distance: 251 - 256: 5.743 distance: 252 - 253: 4.430 distance: 252 - 257: 7.843 distance: 257 - 258: 4.222 distance: 257 - 268: 9.059 distance: 258 - 261: 3.921 distance: 258 - 269: 4.769 distance: 259 - 260: 4.947 distance: 259 - 281: 3.617 distance: 261 - 262: 3.587 distance: 261 - 270: 7.860 distance: 261 - 271: 7.517 distance: 262 - 272: 4.914 distance: 263 - 274: 4.146 distance: 263 - 275: 3.577 distance: 281 - 282: 6.105 distance: 281 - 468: 4.437 distance: 282 - 283: 7.176 distance: 282 - 286: 9.281 distance: 282 - 287: 7.481 distance: 283 - 284: 13.822 distance: 283 - 288: 3.051 distance: 284 - 465: 11.382 distance: 288 - 289: 5.262 distance: 288 - 297: 3.152 distance: 289 - 290: 15.539 distance: 289 - 292: 11.256 distance: 289 - 298: 13.966 distance: 290 - 291: 17.632 distance: 290 - 310: 18.726 distance: 292 - 293: 6.636 distance: 292 - 299: 4.641 distance: 292 - 300: 4.406 distance: 293 - 294: 4.162 distance: 293 - 301: 3.622 distance: 293 - 302: 6.972 distance: 294 - 295: 6.798 distance: 294 - 304: 3.146 distance: 295 - 296: 5.253 distance: 295 - 306: 3.505 distance: 296 - 308: 3.791 distance: 310 - 311: 4.431 distance: 310 - 317: 17.768 distance: 310 - 446: 3.952 distance: 311 - 312: 9.990 distance: 311 - 314: 8.650 distance: 311 - 318: 6.080 distance: 312 - 313: 10.037 distance: 312 - 326: 7.212 distance: 314 - 315: 3.680 distance: 314 - 316: 6.316 distance: 314 - 319: 6.597 distance: 315 - 320: 6.174 distance: 315 - 321: 8.926 distance: 315 - 322: 9.968 distance: 316 - 323: 14.281 distance: 316 - 324: 8.217 distance: 316 - 325: 12.579 distance: 326 - 327: 8.688 distance: 326 - 338: 5.445 distance: 327 - 328: 4.195 distance: 327 - 330: 9.127 distance: 327 - 339: 6.394 distance: 328 - 329: 5.582 distance: 330 - 331: 3.610 distance: 330 - 340: 6.052 distance: 330 - 341: 10.527 distance: 331 - 332: 8.342 distance: 331 - 333: 7.619 distance: 332 - 342: 5.195 distance: 333 - 343: 6.179 distance: 334 - 336: 10.124 distance: 334 - 344: 5.823 distance: 335 - 336: 5.104 distance: 335 - 345: 7.695 distance: 336 - 337: 5.814 distance: 337 - 346: 5.336 distance: 347 - 355: 4.849 distance: 347 - 422: 4.692 distance: 351 - 357: 5.828 distance: 352 - 354: 4.755 distance: 353 - 362: 4.706 distance: 354 - 363: 4.249 distance: 354 - 364: 5.612 distance: 354 - 365: 6.752