Starting phenix.real_space_refine on Sat Dec 9 10:30:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/12_2023/8a7d_15220.pdb" } resolution = 3.06 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 1 6.06 5 S 100 5.16 5 C 6728 2.51 5 N 1861 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10771 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7256 Classifications: {'peptide': 921} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 863} Chain: "P" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1309 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain: "Q" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2085 Classifications: {'peptide': 273} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Unusual residues: {' CA': 7, ' ZN': 1, 'NAG': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.07, per 1000 atoms: 0.56 Number of scatterers: 10771 At special positions: 0 Unit cell: (125.736, 98.358, 137.904, 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) Zn 1 29.99 Ca 8 19.99 S 100 16.00 O 2073 8.00 N 1861 7.00 C 6728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 235 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 440 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 622 " distance=2.04 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 643 " distance=2.03 Simple disulfide: pdb=" SG CYS C 710 " - pdb=" SG CYS C 881 " distance=2.02 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 878 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS P 120 " distance=2.03 Simple disulfide: pdb=" SG CYS C 753 " - pdb=" SG CYS C 835 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 781 " distance=2.03 Simple disulfide: pdb=" SG CYS C 947 " - pdb=" SG CYS C 975 " distance=2.03 Simple disulfide: pdb=" SG CYS C 960 " - pdb=" SG CYS C 971 " distance=2.03 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 990 " distance=2.03 Simple disulfide: pdb=" SG CYS C 999 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 65 " - pdb=" SG CYS P 85 " distance=2.02 Simple disulfide: pdb=" SG CYS P 76 " - pdb=" SG CYS P 125 " distance=2.03 Simple disulfide: pdb=" SG CYS P 109 " - pdb=" SG CYS P 139 " distance=2.04 Simple disulfide: pdb=" SG CYS P 146 " - pdb=" SG CYS P 181 " distance=2.03 Simple disulfide: pdb=" SG CYS P 197 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1285 " - pdb=" SG CYS Q1329 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1300 " - pdb=" SG CYS Q1310 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1314 " - pdb=" SG CYS Q1342 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1346 " - pdb=" SG CYS Q1399 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1362 " - pdb=" SG CYS Q1373 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1377 " - pdb=" SG CYS Q1410 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1478 " - pdb=" SG CYS Q1539 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1492 " - pdb=" SG CYS Q1502 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1506 " - pdb=" SG CYS Q1554 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1558 " - pdb=" SG CYS Q1576 " distance=2.02 Simple disulfide: pdb=" SG CYS Q1567 " - pdb=" SG CYS Q1583 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1584 " - pdb=" SG CYS Q1608 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1600 " - pdb=" SG CYS Q1606 " distance=2.03 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 Links applied NAG-ASN " NAG C1701 " - " ASN C 725 " " NAG C1702 " - " ASN C 480 " " NAG C1703 " - " ASN C 429 " " NAG C1704 " - " ASN C 402 " " NAG C1705 " - " ASN C 390 " " NAG C1706 " - " ASN C 601 " " NAG C1707 " - " ASN C 825 " " NAG Q1701 " - " ASN Q1323 " Time building additional restraints: 4.40 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1708 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 566 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 572 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 562 " 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 18 sheets defined 26.1% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'C' and resid 229 through 234 removed outlier: 4.665A pdb=" N LYS C 234 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 removed outlier: 3.848A pdb=" N HIS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 4.007A pdb=" N ALA C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 296' Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 344 removed outlier: 3.634A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 removed outlier: 4.595A pdb=" N GLN C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.621A pdb=" N VAL C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 534 through 538 removed outlier: 3.611A pdb=" N ALA C 537 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 538' Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.511A pdb=" N TYR C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.967A pdb=" N ILE C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 562 " --> pdb=" O HIS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 762 through 766 Processing helix chain 'C' and resid 776 through 780 removed outlier: 4.061A pdb=" N GLN C 779 " --> pdb=" O PRO C 776 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 780 " --> pdb=" O GLU C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 780' Processing helix chain 'C' and resid 875 through 879 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 1007 through 1012 Processing helix chain 'P' and resid 46 through 60 removed outlier: 3.618A pdb=" N VAL P 58 " --> pdb=" O GLN P 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN P 59 " --> pdb=" O HIS P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 72 removed outlier: 4.017A pdb=" N CYS P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU P 72 " --> pdb=" O PHE P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 92 Processing helix chain 'P' and resid 93 through 95 No H-bonds generated for 'chain 'P' and resid 93 through 95' Processing helix chain 'P' and resid 96 through 118 removed outlier: 3.740A pdb=" N LEU P 107 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS P 108 " --> pdb=" O LYS P 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE P 118 " --> pdb=" O LEU P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 143 Processing helix chain 'P' and resid 144 through 152 removed outlier: 3.814A pdb=" N ALA P 148 " --> pdb=" O ASP P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 160 Processing helix chain 'P' and resid 161 through 168 Processing helix chain 'P' and resid 168 through 180 removed outlier: 3.560A pdb=" N VAL P 172 " --> pdb=" O HIS P 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 202 Processing helix chain 'P' and resid 202 through 209 removed outlier: 3.946A pdb=" N SER P 206 " --> pdb=" O GLY P 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1359 through 1364 Processing helix chain 'Q' and resid 1521 through 1525 removed outlier: 4.215A pdb=" N ILE Q1525 " --> pdb=" O VAL Q1522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1548 through 1552 Processing helix chain 'Q' and resid 1573 through 1575 No H-bonds generated for 'chain 'Q' and resid 1573 through 1575' Processing helix chain 'Q' and resid 1576 through 1581 removed outlier: 4.061A pdb=" N GLY Q1580 " --> pdb=" O CYS Q1576 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1613 through 1617 Processing sheet with id=AA1, first strand: chain 'C' and resid 215 through 220 removed outlier: 5.635A pdb=" N GLN C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 212 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 120 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 258 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN C 122 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 256 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 215 through 220 removed outlier: 5.635A pdb=" N GLN C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 212 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 120 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 258 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN C 122 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 256 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS C 255 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N ARG C 95 " --> pdb=" O HIS C 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 186 removed outlier: 3.774A pdb=" N ASP C 167 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 157 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL C 136 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 238 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 401 removed outlier: 6.329A pdb=" N LYS C 351 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 394 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 353 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 396 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 355 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 398 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL C 357 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 400 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN C 359 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N LEU C 513 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG C 354 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE C 515 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 356 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 517 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 358 " --> pdb=" O PHE C 517 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN C 514 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU C 546 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 516 " --> pdb=" O LEU C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 409 through 411 removed outlier: 5.992A pdb=" N LEU C 409 " --> pdb=" O LEU C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 680 through 684 removed outlier: 5.056A pdb=" N VAL C 681 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU C 692 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY C 683 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 713 through 714 removed outlier: 3.658A pdb=" N ILE C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 719 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU C 863 " --> pdb=" O THR C 801 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP C 799 " --> pdb=" O ASP C 865 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA C 867 " --> pdb=" O THR C 797 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR C 797 " --> pdb=" O ALA C 867 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 869 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 795 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER C 871 " --> pdb=" O PRO C 793 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 781 through 791 removed outlier: 6.200A pdb=" N TYR C 851 " --> pdb=" O PHE C 787 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 852 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 815 " --> pdb=" O TYR C 856 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 885 through 891 removed outlier: 3.680A pdb=" N GLU C 930 " --> pdb=" O SER C 927 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 885 through 891 Processing sheet with id=AB2, first strand: chain 'C' and resid 981 through 984 Processing sheet with id=AB3, first strand: chain 'Q' and resid 1296 through 1299 Processing sheet with id=AB4, first strand: chain 'Q' and resid 1319 through 1321 Processing sheet with id=AB5, first strand: chain 'Q' and resid 1345 through 1346 Processing sheet with id=AB6, first strand: chain 'Q' and resid 1355 through 1357 Processing sheet with id=AB7, first strand: chain 'Q' and resid 1488 through 1491 Processing sheet with id=AB8, first strand: chain 'Q' and resid 1532 through 1533 removed outlier: 3.834A pdb=" N THR Q1532 " --> pdb=" O ILE Q1515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE Q1515 " --> pdb=" O THR Q1532 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE Q1514 " --> pdb=" O HIS Q1553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 1566 through 1568 removed outlier: 6.081A pdb=" N CYS Q1567 " --> pdb=" O PHE Q1596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 334 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3584 1.34 - 1.46: 2457 1.46 - 1.58: 4871 1.58 - 1.70: 1 1.70 - 1.83: 124 Bond restraints: 11037 Sorted by residual: bond pdb=" N ASP C 458 " pdb=" CA ASP C 458 " ideal model delta sigma weight residual 1.457 1.618 -0.161 1.29e-02 6.01e+03 1.55e+02 bond pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 1.332 1.427 -0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" N VAL Q1411 " pdb=" CA VAL Q1411 " ideal model delta sigma weight residual 1.465 1.495 -0.030 1.02e-02 9.61e+03 8.82e+00 bond pdb=" CA ASP C 458 " pdb=" C ASP C 458 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.34e-02 5.57e+03 7.87e+00 bond pdb=" C ASP C 458 " pdb=" N MET C 459 " ideal model delta sigma weight residual 1.332 1.363 -0.030 1.40e-02 5.10e+03 4.69e+00 ... (remaining 11032 not shown) Histogram of bond angle deviations from ideal: 89.10 - 100.96: 16 100.96 - 112.81: 6132 112.81 - 124.66: 8595 124.66 - 136.51: 251 136.51 - 148.36: 1 Bond angle restraints: 14995 Sorted by residual: angle pdb=" O CYS C 457 " pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 122.81 89.10 33.71 1.23e+00 6.61e-01 7.51e+02 angle pdb=" CA CYS C 457 " pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 115.56 148.36 -32.80 1.30e+00 5.92e-01 6.37e+02 angle pdb=" C ASP C 458 " pdb=" N MET C 459 " pdb=" CA MET C 459 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C CYS C 457 " pdb=" N ASP C 458 " pdb=" CA ASP C 458 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N HIS C 430 " pdb=" CA HIS C 430 " pdb=" C HIS C 430 " ideal model delta sigma weight residual 110.80 119.79 -8.99 2.13e+00 2.20e-01 1.78e+01 ... (remaining 14990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6085 17.78 - 35.56: 547 35.56 - 53.34: 125 53.34 - 71.12: 30 71.12 - 88.90: 18 Dihedral angle restraints: 6805 sinusoidal: 2871 harmonic: 3934 Sorted by residual: dihedral pdb=" CA GLU C 777 " pdb=" C GLU C 777 " pdb=" N PRO C 778 " pdb=" CA PRO C 778 " ideal model delta harmonic sigma weight residual -180.00 -126.45 -53.55 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS Q1558 " pdb=" SG CYS Q1558 " pdb=" SG CYS Q1576 " pdb=" CB CYS Q1576 " ideal model delta sinusoidal sigma weight residual -86.00 -152.08 66.08 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 327 " pdb=" SG CYS C 327 " pdb=" SG CYS C 587 " pdb=" CB CYS C 587 " ideal model delta sinusoidal sigma weight residual 93.00 145.22 -52.22 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 6802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1475 0.078 - 0.156: 150 0.156 - 0.233: 2 0.233 - 0.311: 4 0.311 - 0.389: 1 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 NAG C1704 " pdb=" ND2 ASN C 402 " pdb=" C2 NAG C1704 " pdb=" O5 NAG C1704 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA ASP C 458 " pdb=" N ASP C 458 " pdb=" C ASP C 458 " pdb=" CB ASP C 458 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA HIS C 430 " pdb=" N HIS C 430 " pdb=" C HIS C 430 " pdb=" CB HIS C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1629 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1703 " 0.046 2.00e-02 2.50e+03 4.35e-02 2.36e+01 pdb=" C7 NAG C1703 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG C1703 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG C1703 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG C1703 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 457 " 0.026 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C CYS C 457 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS C 457 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 458 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 777 " 0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO C 778 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 778 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 778 " 0.044 5.00e-02 4.00e+02 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 215 2.67 - 3.23: 10528 3.23 - 3.79: 16708 3.79 - 4.34: 23308 4.34 - 4.90: 37789 Nonbonded interactions: 88548 Sorted by model distance: nonbonded pdb=" OD2 ASP C 910 " pdb=" OH TYR C 921 " model vdw 2.115 2.440 nonbonded pdb=" OG SER C 148 " pdb=" OD1 ASP C 150 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR C 590 " pdb=" OE1 GLU C 591 " model vdw 2.187 2.440 nonbonded pdb=" OD2 ASP C 961 " pdb="CA CA C1713 " model vdw 2.202 2.510 nonbonded pdb=" OE1 GLU C 958 " pdb="CA CA C1713 " model vdw 2.213 2.510 ... (remaining 88543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.000 Extract box with map and model: 2.880 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 34.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 0.161 11037 Z= 0.260 Angle : 0.761 33.705 14995 Z= 0.467 Chirality : 0.048 0.389 1632 Planarity : 0.005 0.079 1972 Dihedral : 14.794 88.905 4160 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.32 % Favored : 94.16 % Rotamer: Outliers : 0.50 % Allowed : 12.16 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -0.22 (0.24), residues: 1353 helix: 0.16 (0.33), residues: 239 sheet: -0.72 (0.32), residues: 273 loop : 0.08 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 259 HIS 0.007 0.001 HIS C 430 PHE 0.030 0.002 PHE Q1312 TYR 0.013 0.002 TYR C 252 ARG 0.005 0.001 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 187 average time/residue: 0.2731 time to fit residues: 69.9199 Evaluate side-chains 131 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0982 time to fit residues: 2.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 246 ASN C 292 ASN C 499 ASN C 619 ASN C 629 ASN C 650 ASN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 905 ASN P 49 ASN P 73 ASN ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 112 HIS P 161 HIS P 176 ASN P 199 GLN Q1358 GLN ** Q1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1487 ASN Q1519 ASN Q1565 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11037 Z= 0.385 Angle : 0.638 8.705 14995 Z= 0.331 Chirality : 0.048 0.231 1632 Planarity : 0.005 0.080 1972 Dihedral : 5.861 54.358 1625 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.01 % Rotamer: Outliers : 3.02 % Allowed : 13.67 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -0.04 (0.24), residues: 1353 helix: 1.06 (0.36), residues: 217 sheet: -0.84 (0.32), residues: 261 loop : 0.05 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 259 HIS 0.009 0.001 HIS C 430 PHE 0.014 0.002 PHE C 486 TYR 0.018 0.002 TYR C 252 ARG 0.005 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 165 average time/residue: 0.2415 time to fit residues: 57.1650 Evaluate side-chains 146 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1233 time to fit residues: 6.2977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 121 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS C 452 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 667 GLN ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN P 98 GLN P 116 HIS Q1401 GLN Q1527 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11037 Z= 0.162 Angle : 0.535 6.900 14995 Z= 0.279 Chirality : 0.044 0.214 1632 Planarity : 0.004 0.075 1972 Dihedral : 5.449 50.860 1625 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.36 % Favored : 95.20 % Rotamer: Outliers : 1.76 % Allowed : 15.60 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.12 (0.24), residues: 1353 helix: 1.38 (0.36), residues: 217 sheet: -0.85 (0.33), residues: 262 loop : 0.14 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.020 0.001 PHE P 162 TYR 0.015 0.001 TYR C 463 ARG 0.004 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 163 average time/residue: 0.2244 time to fit residues: 52.8857 Evaluate side-chains 134 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1043 time to fit residues: 2.9476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS C 452 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN P 98 GLN P 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11037 Z= 0.312 Angle : 0.580 6.877 14995 Z= 0.300 Chirality : 0.046 0.192 1632 Planarity : 0.005 0.077 1972 Dihedral : 5.430 50.970 1625 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.40 % Favored : 94.31 % Rotamer: Outliers : 2.68 % Allowed : 15.18 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.08 (0.24), residues: 1353 helix: 1.07 (0.36), residues: 223 sheet: -0.68 (0.32), residues: 265 loop : 0.12 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 259 HIS 0.006 0.001 HIS C 562 PHE 0.011 0.001 PHE C 574 TYR 0.015 0.002 TYR C 252 ARG 0.008 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 167 average time/residue: 0.2285 time to fit residues: 55.0740 Evaluate side-chains 144 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1070 time to fit residues: 5.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 0.0060 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS C 278 HIS C 430 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11037 Z= 0.164 Angle : 0.545 14.966 14995 Z= 0.278 Chirality : 0.044 0.180 1632 Planarity : 0.004 0.075 1972 Dihedral : 5.242 50.861 1625 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.07 % Favored : 95.64 % Rotamer: Outliers : 1.34 % Allowed : 17.11 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.17 (0.24), residues: 1353 helix: 1.41 (0.36), residues: 217 sheet: -0.69 (0.33), residues: 253 loop : 0.12 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.027 0.001 PHE P 162 TYR 0.013 0.001 TYR C 463 ARG 0.010 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 156 average time/residue: 0.2444 time to fit residues: 54.7021 Evaluate side-chains 135 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1215 time to fit residues: 3.0102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN C 967 ASN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11037 Z= 0.204 Angle : 0.549 14.458 14995 Z= 0.281 Chirality : 0.044 0.171 1632 Planarity : 0.004 0.074 1972 Dihedral : 5.161 50.594 1625 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.66 % Favored : 95.05 % Rotamer: Outliers : 1.59 % Allowed : 17.37 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.20 (0.24), residues: 1353 helix: 1.27 (0.36), residues: 224 sheet: -0.58 (0.32), residues: 265 loop : 0.17 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.024 0.001 PHE Q1298 TYR 0.012 0.001 TYR C 463 ARG 0.012 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 158 average time/residue: 0.2378 time to fit residues: 53.7862 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1652 time to fit residues: 4.0252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11037 Z= 0.200 Angle : 0.558 14.914 14995 Z= 0.286 Chirality : 0.044 0.168 1632 Planarity : 0.004 0.073 1972 Dihedral : 5.224 50.737 1625 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.66 % Favored : 95.05 % Rotamer: Outliers : 1.01 % Allowed : 18.12 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.24 (0.24), residues: 1353 helix: 1.27 (0.36), residues: 224 sheet: -0.59 (0.32), residues: 265 loop : 0.22 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 807 HIS 0.006 0.001 HIS C 314 PHE 0.027 0.001 PHE P 162 TYR 0.014 0.001 TYR C 203 ARG 0.011 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 0.2374 time to fit residues: 54.2461 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1104 time to fit residues: 2.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 0.0570 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 GLN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11037 Z= 0.246 Angle : 0.581 14.763 14995 Z= 0.298 Chirality : 0.044 0.205 1632 Planarity : 0.004 0.074 1972 Dihedral : 5.486 50.563 1625 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.10 % Favored : 94.60 % Rotamer: Outliers : 1.17 % Allowed : 18.46 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.19 (0.24), residues: 1353 helix: 1.18 (0.36), residues: 224 sheet: -0.63 (0.32), residues: 265 loop : 0.20 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 259 HIS 0.006 0.001 HIS C 562 PHE 0.017 0.001 PHE Q1298 TYR 0.014 0.002 TYR C 203 ARG 0.012 0.000 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 149 average time/residue: 0.2302 time to fit residues: 49.5401 Evaluate side-chains 141 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1062 time to fit residues: 3.0976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.245 > 50: distance: 44 - 48: 10.782 distance: 48 - 49: 11.070 distance: 48 - 54: 24.709 distance: 49 - 50: 5.179 distance: 49 - 52: 9.502 distance: 50 - 51: 4.476 distance: 50 - 55: 7.040 distance: 52 - 53: 15.545 distance: 53 - 54: 29.079 distance: 55 - 56: 17.045 distance: 56 - 57: 35.443 distance: 56 - 59: 28.534 distance: 57 - 58: 13.928 distance: 57 - 63: 13.677 distance: 59 - 60: 4.969 distance: 60 - 61: 27.752 distance: 60 - 62: 4.710 distance: 63 - 64: 18.487 distance: 63 - 265: 19.898 distance: 64 - 65: 10.119 distance: 64 - 67: 15.092 distance: 65 - 66: 11.679 distance: 65 - 72: 12.468 distance: 66 - 262: 17.764 distance: 67 - 68: 6.818 distance: 68 - 69: 9.623 distance: 69 - 70: 23.424 distance: 70 - 71: 13.892 distance: 72 - 73: 13.351 distance: 73 - 74: 15.933 distance: 73 - 76: 14.645 distance: 74 - 75: 17.821 distance: 74 - 84: 12.817 distance: 76 - 77: 3.581 distance: 77 - 78: 5.722 distance: 77 - 79: 8.028 distance: 78 - 80: 8.349 distance: 79 - 81: 6.676 distance: 80 - 82: 4.568 distance: 84 - 85: 4.922 distance: 84 - 251: 9.875 distance: 85 - 86: 5.066 distance: 85 - 88: 3.314 distance: 86 - 87: 6.114 distance: 86 - 93: 8.757 distance: 87 - 248: 15.008 distance: 88 - 89: 6.532 distance: 89 - 90: 7.480 distance: 90 - 91: 8.798 distance: 91 - 92: 10.011 distance: 93 - 94: 3.325 distance: 94 - 95: 13.088 distance: 94 - 97: 10.025 distance: 95 - 96: 7.726 distance: 95 - 100: 14.909 distance: 97 - 98: 18.938 distance: 97 - 99: 18.052 distance: 100 - 231: 3.867 distance: 101 - 102: 5.817 distance: 101 - 104: 6.086 distance: 102 - 103: 8.721 distance: 102 - 107: 8.249 distance: 103 - 228: 17.226 distance: 104 - 105: 4.656 distance: 104 - 106: 15.779 distance: 107 - 108: 6.317 distance: 108 - 109: 5.294 distance: 108 - 111: 7.393 distance: 109 - 110: 3.306 distance: 109 - 118: 5.743 distance: 111 - 112: 9.764 distance: 113 - 114: 5.456 distance: 114 - 115: 5.705 distance: 115 - 116: 7.069 distance: 115 - 117: 4.904 distance: 118 - 119: 13.011 distance: 118 - 211: 7.600 distance: 119 - 120: 5.186 distance: 119 - 122: 15.363 distance: 120 - 121: 3.726 distance: 121 - 208: 8.518 distance: 122 - 123: 12.793 distance: 123 - 124: 7.873 distance: 123 - 125: 15.095 distance: 126 - 127: 11.065 distance: 126 - 132: 18.358 distance: 127 - 128: 4.495 distance: 127 - 130: 14.319 distance: 128 - 129: 6.162 distance: 131 - 132: 15.294