Starting phenix.real_space_refine on Mon Aug 25 23:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy8_37919/08_2025/8wy8_37919.cif" } resolution = 3.1 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= 0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 20363 2.51 5 N 5069 2.21 5 O 5856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s 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: 31412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7880 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 19, 'TRANS': 923} Chain breaks: 7 Chain: "B" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7869 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 19, 'TRANS': 920} Chain breaks: 7 Chain: "C" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7869 Classifications: {'peptide': 942} Link IDs: {'PTRANS': 19, 'TRANS': 922} Chain breaks: 8 Chain: "D" Number of atoms: 7794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7794 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 19, 'TRANS': 912} Chain breaks: 8 Time building chain proxies: 5.96, per 1000 atoms: 0.19 Number of scatterers: 31412 At special positions: 0 Unit cell: (100.894, 127.358, 265.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5856 8.00 N 5069 7.00 C 20363 6.00 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: 2.08 Conformation dependent library (CDL) restraints added in 980.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 9 sheets defined 73.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.176A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.738A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.621A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.802A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.331A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.561A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.598A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.092A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.762A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.506A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.699A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 571 removed outlier: 3.617A pdb=" N THR A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.928A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.711A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 744 removed outlier: 3.772A pdb=" N PHE A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.249A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.993A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.583A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.522A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 4.053A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 removed outlier: 3.508A pdb=" N ILE A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.660A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 4.138A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.892A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 976 through 991 removed outlier: 3.612A pdb=" N VAL A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.152A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.716A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.527A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.752A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.979A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.595A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.514A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.582A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.654A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.507A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.525A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 493 Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.476A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.551A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.856A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.678A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.852A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.534A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 878 through 895 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.639A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 955 removed outlier: 6.324A pdb=" N ILE B 955 " --> pdb=" O LYS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 962 removed outlier: 3.760A pdb=" N LYS B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 991 Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.633A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.923A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.704A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 Proline residue: C 88 - end of helix removed outlier: 6.938A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.899A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.505A pdb=" N ALA C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.763A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.504A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.514A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.694A pdb=" N VAL C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.931A pdb=" N ARG C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 469 through 494 removed outlier: 3.645A pdb=" N GLN C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.729A pdb=" N MET C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.833A pdb=" N LEU C 545 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 551 through 572 removed outlier: 3.516A pdb=" N SER C 570 " --> pdb=" O ARG C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.507A pdb=" N LEU C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 659 removed outlier: 3.554A pdb=" N ILE C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 699 Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.560A pdb=" N THR C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 765 removed outlier: 4.452A pdb=" N CYS C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.704A pdb=" N GLU C 784 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 785 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS C 786 " --> pdb=" O GLN C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 811 removed outlier: 3.533A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 removed outlier: 3.565A pdb=" N CYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.742A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 857 removed outlier: 3.819A pdb=" N HIS C 852 " --> pdb=" O ASN C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 872 removed outlier: 3.560A pdb=" N LEU C 865 " --> pdb=" O ASN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 897 removed outlier: 3.558A pdb=" N ASN C 895 " --> pdb=" O THR C 891 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 897 " --> pdb=" O LYS C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 922 removed outlier: 3.877A pdb=" N GLY C 917 " --> pdb=" O MET C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 934 removed outlier: 4.070A pdb=" N GLU C 931 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 934 " --> pdb=" O GLU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.898A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.502A pdb=" N LYS C 969 " --> pdb=" O LYS C 965 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS C 974 " --> pdb=" O ILE C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 991 removed outlier: 3.758A pdb=" N LYS C 989 " --> pdb=" O LYS C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1004 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 23 through 39 removed outlier: 3.578A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.029A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.719A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.834A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.517A pdb=" N VAL D 183 " --> pdb=" O GLY D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.724A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 297 removed outlier: 3.778A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 Processing helix chain 'D' and resid 318 through 321 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.531A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 3.551A pdb=" N PHE D 361 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.545A pdb=" N LYS D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.575A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 461 Processing helix chain 'D' and resid 468 through 493 Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 524 through 531 removed outlier: 4.312A pdb=" N PHE D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 removed outlier: 3.550A pdb=" N LYS D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 559 through 563 Processing helix chain 'D' and resid 580 through 598 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.789A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 635 Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 680 through 700 Processing helix chain 'D' and resid 705 through 723 removed outlier: 4.129A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 750 through 762 removed outlier: 3.592A pdb=" N THR D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.521A pdb=" N HIS D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.839A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.954A pdb=" N LYS D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 856 removed outlier: 3.557A pdb=" N SER D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 872 Processing helix chain 'D' and resid 878 through 895 Processing helix chain 'D' and resid 912 through 922 Processing helix chain 'D' and resid 929 through 934 removed outlier: 3.803A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.882A pdb=" N ASP D 945 " --> pdb=" O ASP D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 956 No H-bonds generated for 'chain 'D' and resid 955 through 956' Processing helix chain 'D' and resid 957 through 962 removed outlier: 3.980A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 962 " --> pdb=" O TRP D 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 962' Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.915A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 981 " --> pdb=" O LYS D 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 983 " --> pdb=" O HIS D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1004 removed outlier: 3.845A pdb=" N ASN D1002 " --> pdb=" O GLU D 998 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.761A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.038A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 152 removed outlier: 5.992A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 43 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE C 216 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 45 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.141A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AA9, first strand: chain 'D' and resid 646 through 647 1764 hydrogen bonds defined for protein. 5091 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: 5.00 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9916 1.34 - 1.46: 8066 1.46 - 1.58: 13931 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 32121 Sorted by residual: bond pdb=" CG LYS D 350 " pdb=" CD LYS D 350 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CA GLU D 335 " pdb=" CB GLU D 335 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.48e-02 4.57e+03 1.71e+00 bond pdb=" N LYS D 350 " pdb=" CA LYS D 350 " ideal model delta sigma weight residual 1.454 1.471 -0.017 1.40e-02 5.10e+03 1.45e+00 bond pdb=" CB ASP B 306 " pdb=" CG ASP B 306 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CA ASP B 306 " pdb=" CB ASP B 306 " ideal model delta sigma weight residual 1.530 1.550 -0.019 1.69e-02 3.50e+03 1.33e+00 ... (remaining 32116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 42995 2.95 - 5.89: 204 5.89 - 8.84: 28 8.84 - 11.78: 6 11.78 - 14.73: 1 Bond angle restraints: 43234 Sorted by residual: angle pdb=" CA GLU D 335 " pdb=" CB GLU D 335 " pdb=" CG GLU D 335 " ideal model delta sigma weight residual 114.10 124.12 -10.02 2.00e+00 2.50e-01 2.51e+01 angle pdb=" CA LEU D 551 " pdb=" CB LEU D 551 " pdb=" CG LEU D 551 " ideal model delta sigma weight residual 116.30 131.03 -14.73 3.50e+00 8.16e-02 1.77e+01 angle pdb=" CB MET A 531 " pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 112.70 123.25 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA LYS D 350 " pdb=" CB LYS D 350 " pdb=" CG LYS D 350 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB LYS D 423 " pdb=" CG LYS D 423 " pdb=" CD LYS D 423 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 ... (remaining 43229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 16160 17.88 - 35.76: 2331 35.76 - 53.64: 542 53.64 - 71.52: 87 71.52 - 89.40: 38 Dihedral angle restraints: 19158 sinusoidal: 8006 harmonic: 11152 Sorted by residual: dihedral pdb=" CA PHE C 744 " pdb=" C PHE C 744 " pdb=" N PRO C 745 " pdb=" CA PRO C 745 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE D 550 " pdb=" C PHE D 550 " pdb=" N LEU D 551 " pdb=" CA LEU D 551 " ideal model delta harmonic sigma weight residual 180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASN B 705 " pdb=" C ASN B 705 " pdb=" N VAL B 706 " pdb=" CA VAL B 706 " ideal model delta harmonic sigma weight residual -180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 19155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3414 0.039 - 0.078: 920 0.078 - 0.117: 231 0.117 - 0.156: 27 0.156 - 0.195: 1 Chirality restraints: 4593 Sorted by residual: chirality pdb=" CB ILE A 981 " pdb=" CA ILE A 981 " pdb=" CG1 ILE A 981 " pdb=" CG2 ILE A 981 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CB ILE D 934 " pdb=" CA ILE D 934 " pdb=" CG1 ILE D 934 " pdb=" CG2 ILE D 934 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA LEU B 842 " pdb=" N LEU B 842 " pdb=" C LEU B 842 " pdb=" CB LEU B 842 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 4590 not shown) Planarity restraints: 5492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 143 " -0.027 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP C 143 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP C 143 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 143 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 143 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 143 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 143 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 143 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 945 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 946 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 946 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 946 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 722 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PHE C 722 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE C 722 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA C 723 " 0.012 2.00e-02 2.50e+03 ... (remaining 5489 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 393 2.60 - 3.18: 27846 3.18 - 3.75: 52710 3.75 - 4.33: 71788 4.33 - 4.90: 115654 Nonbonded interactions: 268391 Sorted by model distance: nonbonded pdb=" OH TYR C 482 " pdb=" OE1 GLU C 516 " model vdw 2.028 3.040 nonbonded pdb=" OH TYR B 709 " pdb=" OD1 ASP B 748 " model vdw 2.129 3.040 nonbonded pdb=" O TYR C 611 " pdb=" OG SER C 615 " model vdw 2.173 3.040 nonbonded pdb=" OG SER D 37 " pdb=" O MET D 124 " model vdw 2.180 3.040 nonbonded pdb=" OE2 GLU A 668 " pdb=" NH1 ARG A 760 " model vdw 2.190 3.120 ... (remaining 268386 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 12 through 297 or resid 302 through 399 or resid 406 throu \ gh 493 or resid 504 through 565 or resid 579 through 786 or resid 793 through 10 \ 05)) selection = (chain 'B' and (resid 12 through 297 or resid 302 through 462 or resid 468 throu \ gh 629 or resid 645 through 700 or resid 703 through 1005)) selection = (chain 'C' and (resid 12 through 399 or resid 406 through 493 or resid 504 throu \ gh 565 or resid 579 through 786 or resid 793 through 1005)) selection = (chain 'D' and (resid 12 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.002 0.041 32121 Z= 0.111 Angle : 0.553 14.730 43234 Z= 0.290 Chirality : 0.038 0.195 4593 Planarity : 0.003 0.054 5492 Dihedral : 17.355 89.403 11976 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.20 % Allowed : 26.25 % Favored : 73.55 % 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: 1.01 (0.14), residues: 3689 helix: 1.16 (0.11), residues: 2421 sheet: -0.85 (0.55), residues: 30 loop : -0.11 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.025 0.001 TYR D 552 PHE 0.025 0.001 PHE C 744 TRP 0.058 0.002 TRP C 143 HIS 0.017 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00238 (32121) covalent geometry : angle 0.55293 (43234) hydrogen bonds : bond 0.19309 ( 1764) hydrogen bonds : angle 6.23500 ( 5091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 411 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8722 (tpp) cc_final: 0.8481 (ttm) REVERT: A 323 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8476 (mm110) REVERT: A 354 PHE cc_start: 0.8412 (t80) cc_final: 0.8009 (t80) REVERT: A 389 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8342 (tt0) REVERT: A 394 ILE cc_start: 0.8741 (mm) cc_final: 0.8491 (mm) REVERT: A 398 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7730 (pttm) REVERT: A 665 LYS cc_start: 0.8492 (mttm) cc_final: 0.7939 (mtpt) REVERT: A 731 GLU cc_start: 0.8280 (tt0) cc_final: 0.7914 (tp30) REVERT: A 930 MET cc_start: 0.4432 (mmp) cc_final: 0.3392 (mtm) REVERT: B 339 HIS cc_start: 0.7958 (m170) cc_final: 0.7639 (m170) REVERT: B 341 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8145 (mm-30) REVERT: B 376 LYS cc_start: 0.8614 (tttt) cc_final: 0.8357 (ttpt) REVERT: B 518 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 624 GLU cc_start: 0.7206 (tp30) cc_final: 0.6953 (tm-30) REVERT: B 625 TYR cc_start: 0.7849 (t80) cc_final: 0.7556 (t80) REVERT: B 672 SER cc_start: 0.8735 (m) cc_final: 0.8443 (p) REVERT: B 677 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7533 (ptm-80) REVERT: B 714 SER cc_start: 0.9075 (t) cc_final: 0.8779 (p) REVERT: B 730 GLU cc_start: 0.7900 (mp0) cc_final: 0.7654 (tt0) REVERT: C 101 ASP cc_start: 0.8585 (m-30) cc_final: 0.8270 (m-30) REVERT: C 173 ASP cc_start: 0.9192 (p0) cc_final: 0.8986 (p0) REVERT: C 284 GLU cc_start: 0.8412 (tp30) cc_final: 0.8108 (tp30) REVERT: C 331 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6223 (mtpp) REVERT: C 424 PHE cc_start: 0.7440 (t80) cc_final: 0.6957 (t80) REVERT: C 616 MET cc_start: -0.1945 (mtt) cc_final: -0.2288 (mtt) REVERT: C 704 MET cc_start: 0.1236 (ppp) cc_final: 0.0986 (ppp) REVERT: C 784 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7178 (pt0) REVERT: C 866 MET cc_start: 0.4078 (mtp) cc_final: 0.3009 (tpp) REVERT: D 173 ASP cc_start: 0.9153 (p0) cc_final: 0.8943 (p0) REVERT: D 316 ILE cc_start: 0.8580 (mm) cc_final: 0.8315 (mm) REVERT: D 324 TYR cc_start: 0.5634 (t80) cc_final: 0.5384 (t80) REVERT: D 327 LYS cc_start: 0.5757 (mmtp) cc_final: 0.4797 (tptt) REVERT: D 396 MET cc_start: 0.4640 (tpt) cc_final: 0.4376 (tpt) REVERT: D 454 LEU cc_start: 0.6759 (tp) cc_final: 0.6415 (mt) REVERT: D 594 PHE cc_start: 0.8530 (t80) cc_final: 0.8307 (t80) REVERT: D 596 TYR cc_start: 0.7051 (m-80) cc_final: 0.6652 (m-80) REVERT: D 704 MET cc_start: -0.0406 (tpt) cc_final: -0.0807 (tpp) REVERT: D 709 TYR cc_start: 0.7196 (t80) cc_final: 0.6356 (t80) REVERT: D 976 MET cc_start: 0.1023 (tmm) cc_final: -0.1796 (ppp) outliers start: 7 outliers final: 2 residues processed: 416 average time/residue: 0.1828 time to fit residues: 122.1729 Evaluate side-chains 296 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain C residue 912 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 351 ASN A 666 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN C 349 HIS C 386 ASN C 391 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 ASN C 786 HIS C 834 GLN C 852 HIS D 339 HIS ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 606 HIS D 782 GLN D 786 HIS ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN D1002 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.187777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116242 restraints weight = 51843.628| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.83 r_work: 0.3309 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32121 Z= 0.150 Angle : 0.568 16.253 43234 Z= 0.300 Chirality : 0.040 0.194 4593 Planarity : 0.004 0.058 5492 Dihedral : 4.111 39.713 4127 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.83 % Allowed : 22.90 % Favored : 74.27 % 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: 1.15 (0.14), residues: 3689 helix: 1.21 (0.10), residues: 2488 sheet: -1.99 (0.74), residues: 20 loop : 0.03 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 587 TYR 0.030 0.001 TYR C 479 PHE 0.023 0.001 PHE C 544 TRP 0.039 0.002 TRP C 143 HIS 0.009 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00337 (32121) covalent geometry : angle 0.56776 (43234) hydrogen bonds : bond 0.04284 ( 1764) hydrogen bonds : angle 4.67330 ( 5091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 323 time to evaluate : 1.080 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: A 98 MET cc_start: 0.8731 (tpp) cc_final: 0.8502 (ttm) REVERT: A 398 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7671 (pttm) REVERT: A 421 MET cc_start: 0.7812 (mmm) cc_final: 0.7472 (mtp) REVERT: A 665 LYS cc_start: 0.8444 (mttm) cc_final: 0.8009 (mtpt) REVERT: A 813 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7119 (mmtp) REVERT: A 930 MET cc_start: 0.4251 (mmp) cc_final: 0.2817 (mtm) REVERT: A 936 MET cc_start: 0.3907 (mtp) cc_final: 0.3402 (mmm) REVERT: A 962 TYR cc_start: 0.5761 (m-10) cc_final: 0.5514 (m-10) REVERT: B 9 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6761 (tptp) REVERT: B 191 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 341 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 624 GLU cc_start: 0.7819 (tp30) cc_final: 0.7456 (tm-30) REVERT: B 625 TYR cc_start: 0.8408 (t80) cc_final: 0.8085 (t80) REVERT: B 714 SER cc_start: 0.9215 (t) cc_final: 0.8978 (p) REVERT: B 930 MET cc_start: 0.4844 (mmp) cc_final: 0.3654 (ppp) REVERT: C 101 ASP cc_start: 0.8433 (m-30) cc_final: 0.8084 (m-30) REVERT: C 284 GLU cc_start: 0.8388 (tp30) cc_final: 0.8155 (tp30) REVERT: C 426 GLU cc_start: 0.7663 (pp20) cc_final: 0.6681 (mm-30) REVERT: C 458 ILE cc_start: 0.8289 (mt) cc_final: 0.7994 (mt) REVERT: C 704 MET cc_start: 0.1573 (ppp) cc_final: 0.0539 (ptt) REVERT: C 784 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7129 (pt0) REVERT: C 866 MET cc_start: 0.4531 (mtp) cc_final: 0.3577 (tpp) REVERT: C 945 ASP cc_start: -0.2543 (OUTLIER) cc_final: -0.2889 (p0) REVERT: D 173 ASP cc_start: 0.8798 (p0) cc_final: 0.8541 (p0) REVERT: D 181 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: D 306 ASP cc_start: 0.3972 (OUTLIER) cc_final: 0.3720 (p0) REVERT: D 324 TYR cc_start: 0.5830 (t80) cc_final: 0.5586 (t80) REVERT: D 327 LYS cc_start: 0.5595 (mmtp) cc_final: 0.4540 (tttm) REVERT: D 369 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5317 (pt0) REVERT: D 596 TYR cc_start: 0.6880 (m-80) cc_final: 0.6648 (m-80) REVERT: D 704 MET cc_start: -0.0325 (tpt) cc_final: -0.1057 (tpp) REVERT: D 863 ASN cc_start: 0.5456 (OUTLIER) cc_final: 0.5228 (p0) outliers start: 98 outliers final: 39 residues processed: 404 average time/residue: 0.1694 time to fit residues: 111.7178 Evaluate side-chains 326 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 279 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 945 ASP Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 863 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 60 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 354 optimal weight: 40.0000 chunk 198 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.184674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111774 restraints weight = 51751.284| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.78 r_work: 0.3235 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32121 Z= 0.214 Angle : 0.570 14.840 43234 Z= 0.301 Chirality : 0.041 0.196 4593 Planarity : 0.004 0.051 5492 Dihedral : 4.187 49.509 4124 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.35 % Allowed : 22.41 % Favored : 74.24 % 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: 0.89 (0.13), residues: 3689 helix: 1.02 (0.10), residues: 2491 sheet: -2.50 (0.84), residues: 20 loop : -0.08 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 348 TYR 0.027 0.002 TYR D 452 PHE 0.028 0.002 PHE C 544 TRP 0.041 0.002 TRP C 143 HIS 0.014 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00505 (32121) covalent geometry : angle 0.57034 (43234) hydrogen bonds : bond 0.04165 ( 1764) hydrogen bonds : angle 4.60297 ( 5091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 295 time to evaluate : 0.890 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: A 98 MET cc_start: 0.8898 (tpp) cc_final: 0.8625 (ttm) REVERT: A 386 ASN cc_start: 0.8637 (m110) cc_final: 0.8339 (m-40) REVERT: A 398 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7769 (pttm) REVERT: A 677 ARG cc_start: 0.8041 (ptt90) cc_final: 0.7429 (ttt-90) REVERT: A 743 TYR cc_start: 0.7563 (m-80) cc_final: 0.7314 (m-80) REVERT: A 930 MET cc_start: 0.4328 (mmp) cc_final: 0.2818 (mtt) REVERT: A 936 MET cc_start: 0.3765 (mtp) cc_final: 0.2557 (mmm) REVERT: A 970 ILE cc_start: 0.7531 (mt) cc_final: 0.7226 (tp) REVERT: B 9 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6721 (mmtp) REVERT: B 134 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7039 (p90) REVERT: B 191 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8980 (mm) REVERT: B 341 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8023 (mm-30) REVERT: B 580 SER cc_start: 0.8450 (m) cc_final: 0.8049 (t) REVERT: B 624 GLU cc_start: 0.7873 (tp30) cc_final: 0.7437 (tm-30) REVERT: B 714 SER cc_start: 0.9206 (t) cc_final: 0.8977 (p) REVERT: B 976 MET cc_start: 0.4496 (OUTLIER) cc_final: 0.4144 (tmm) REVERT: C 35 GLU cc_start: 0.8286 (tp30) cc_final: 0.8074 (tt0) REVERT: C 101 ASP cc_start: 0.8536 (m-30) cc_final: 0.8253 (m-30) REVERT: C 143 TRP cc_start: 0.6943 (t60) cc_final: 0.6634 (t60) REVERT: C 330 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (mm) REVERT: C 426 GLU cc_start: 0.7856 (pp20) cc_final: 0.6994 (mm-30) REVERT: C 527 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2662 (tp) REVERT: C 590 ASP cc_start: 0.8165 (m-30) cc_final: 0.7960 (t0) REVERT: C 704 MET cc_start: 0.1732 (ppp) cc_final: 0.0602 (ptp) REVERT: C 784 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7095 (pt0) REVERT: C 866 MET cc_start: 0.4363 (mtp) cc_final: 0.3422 (tpp) REVERT: D 107 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8523 (t80) REVERT: D 173 ASP cc_start: 0.8877 (p0) cc_final: 0.8631 (p0) REVERT: D 181 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8631 (pm20) REVERT: D 284 GLU cc_start: 0.8477 (tp30) cc_final: 0.8217 (tp30) REVERT: D 327 LYS cc_start: 0.5468 (mmtp) cc_final: 0.4361 (tptt) REVERT: D 581 ASP cc_start: 0.5093 (OUTLIER) cc_final: 0.4315 (t0) REVERT: D 596 TYR cc_start: 0.6870 (m-80) cc_final: 0.6634 (m-80) REVERT: D 704 MET cc_start: -0.0174 (tpt) cc_final: -0.0650 (tpp) REVERT: D 709 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6191 (t80) outliers start: 116 outliers final: 61 residues processed: 392 average time/residue: 0.1722 time to fit residues: 110.7014 Evaluate side-chains 345 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 240 optimal weight: 6.9990 chunk 352 optimal weight: 30.0000 chunk 286 optimal weight: 0.0050 chunk 336 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 HIS B 832 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN D 598 ASN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.184449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112299 restraints weight = 51734.166| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.81 r_work: 0.3224 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32121 Z= 0.173 Angle : 0.532 16.490 43234 Z= 0.280 Chirality : 0.040 0.185 4593 Planarity : 0.004 0.066 5492 Dihedral : 4.172 53.390 4124 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.09 % Allowed : 23.65 % Favored : 73.26 % 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: 0.95 (0.14), residues: 3689 helix: 1.06 (0.10), residues: 2481 sheet: -2.78 (0.87), residues: 20 loop : -0.03 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 587 TYR 0.019 0.001 TYR A 755 PHE 0.026 0.001 PHE D 708 TRP 0.040 0.002 TRP C 143 HIS 0.008 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00405 (32121) covalent geometry : angle 0.53241 (43234) hydrogen bonds : bond 0.03730 ( 1764) hydrogen bonds : angle 4.47889 ( 5091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 293 time to evaluate : 1.022 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: A 98 MET cc_start: 0.8889 (tpp) cc_final: 0.8611 (ttm) REVERT: A 354 PHE cc_start: 0.8660 (t80) cc_final: 0.8408 (t80) REVERT: A 677 ARG cc_start: 0.8000 (ptt90) cc_final: 0.7209 (ttt-90) REVERT: A 743 TYR cc_start: 0.7746 (m-80) cc_final: 0.7415 (m-80) REVERT: A 755 TYR cc_start: 0.7563 (t80) cc_final: 0.7284 (t80) REVERT: A 778 PHE cc_start: 0.8306 (t80) cc_final: 0.7874 (t80) REVERT: A 813 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7198 (mmtp) REVERT: A 930 MET cc_start: 0.4171 (mmp) cc_final: 0.2603 (mtt) REVERT: A 936 MET cc_start: 0.3760 (mtp) cc_final: 0.2674 (mmm) REVERT: B 9 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6687 (mmtp) REVERT: B 134 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7097 (p90) REVERT: B 341 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 624 GLU cc_start: 0.7921 (tp30) cc_final: 0.7566 (tm-30) REVERT: B 714 SER cc_start: 0.9198 (t) cc_final: 0.8969 (p) REVERT: B 913 MET cc_start: 0.6185 (mpp) cc_final: 0.5509 (mpp) REVERT: C 35 GLU cc_start: 0.8430 (tp30) cc_final: 0.8215 (tt0) REVERT: C 143 TRP cc_start: 0.6934 (OUTLIER) cc_final: 0.6705 (t60) REVERT: C 426 GLU cc_start: 0.8001 (pp20) cc_final: 0.7210 (mm-30) REVERT: C 704 MET cc_start: 0.1737 (ppp) cc_final: 0.0632 (ptp) REVERT: C 784 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7120 (pt0) REVERT: C 866 MET cc_start: 0.4201 (mtp) cc_final: 0.3240 (tpp) REVERT: C 924 GLU cc_start: 0.3044 (OUTLIER) cc_final: 0.2683 (mp0) REVERT: C 976 MET cc_start: 0.0432 (pmm) cc_final: 0.0091 (pmm) REVERT: D 107 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8530 (t80) REVERT: D 181 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: D 327 LYS cc_start: 0.5467 (mmtp) cc_final: 0.4441 (tttt) REVERT: D 463 ILE cc_start: 0.4806 (OUTLIER) cc_final: 0.4259 (pt) REVERT: D 521 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6527 (t0) REVERT: D 557 LYS cc_start: -0.2569 (OUTLIER) cc_final: -0.3059 (tmtt) REVERT: D 581 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4188 (t0) REVERT: D 709 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6323 (t80) outliers start: 107 outliers final: 64 residues processed: 384 average time/residue: 0.1720 time to fit residues: 108.5177 Evaluate side-chains 348 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 521 ASN Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 740 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 348 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 241 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 834 GLN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114803 restraints weight = 51841.645| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.92 r_work: 0.3247 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32121 Z= 0.128 Angle : 0.511 16.291 43234 Z= 0.268 Chirality : 0.039 0.200 4593 Planarity : 0.003 0.064 5492 Dihedral : 4.089 54.000 4124 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.26 % Allowed : 23.56 % Favored : 73.17 % 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 (0.14), residues: 3689 helix: 1.16 (0.10), residues: 2475 sheet: -3.09 (0.89), residues: 20 loop : 0.05 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 370 TYR 0.025 0.001 TYR D 552 PHE 0.027 0.001 PHE D 708 TRP 0.038 0.002 TRP C 143 HIS 0.013 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00292 (32121) covalent geometry : angle 0.51061 (43234) hydrogen bonds : bond 0.03520 ( 1764) hydrogen bonds : angle 4.36327 ( 5091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 298 time to evaluate : 1.236 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: A 98 MET cc_start: 0.8916 (tpp) cc_final: 0.8595 (ttm) REVERT: A 354 PHE cc_start: 0.8549 (t80) cc_final: 0.8341 (t80) REVERT: A 365 GLU cc_start: 0.7818 (pp20) cc_final: 0.7598 (pp20) REVERT: A 447 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8146 (ptm160) REVERT: A 627 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6940 (ttp-110) REVERT: A 677 ARG cc_start: 0.7767 (ptt90) cc_final: 0.7127 (ttt-90) REVERT: A 778 PHE cc_start: 0.8271 (t80) cc_final: 0.7803 (t80) REVERT: A 813 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7247 (mmtp) REVERT: A 874 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5119 (mm) REVERT: A 930 MET cc_start: 0.4096 (mmp) cc_final: 0.2536 (mtt) REVERT: A 936 MET cc_start: 0.3994 (mtp) cc_final: 0.2738 (mmm) REVERT: B 9 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6717 (mmtt) REVERT: B 134 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7077 (p90) REVERT: B 341 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 624 GLU cc_start: 0.7910 (tp30) cc_final: 0.7527 (tm-30) REVERT: B 714 SER cc_start: 0.9209 (t) cc_final: 0.8989 (p) REVERT: B 784 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8008 (tm-30) REVERT: B 913 MET cc_start: 0.6056 (mpp) cc_final: 0.5338 (mpp) REVERT: B 976 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4443 (tmm) REVERT: C 101 ASP cc_start: 0.8208 (m-30) cc_final: 0.7880 (m-30) REVERT: C 143 TRP cc_start: 0.6992 (OUTLIER) cc_final: 0.6736 (t60) REVERT: C 330 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (mm) REVERT: C 382 ASN cc_start: 0.8132 (m110) cc_final: 0.7839 (p0) REVERT: C 426 GLU cc_start: 0.8043 (pp20) cc_final: 0.7277 (mm-30) REVERT: C 441 PHE cc_start: 0.8302 (m-10) cc_final: 0.7571 (m-80) REVERT: C 519 MET cc_start: 0.4419 (mmm) cc_final: 0.3725 (mmm) REVERT: C 704 MET cc_start: 0.1847 (ppp) cc_final: 0.0859 (ptp) REVERT: C 784 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7083 (pt0) REVERT: C 866 MET cc_start: 0.4288 (mtp) cc_final: 0.3390 (tpp) REVERT: C 924 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2794 (mp0) REVERT: D 107 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8474 (t80) REVERT: D 311 TYR cc_start: 0.6626 (t80) cc_final: 0.6392 (t80) REVERT: D 327 LYS cc_start: 0.5405 (mmtp) cc_final: 0.4362 (tptt) REVERT: D 362 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.3905 (tp30) REVERT: D 369 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5641 (pt0) REVERT: D 391 ASN cc_start: 0.6246 (m-40) cc_final: 0.5627 (m110) REVERT: D 463 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4205 (pt) REVERT: D 581 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4345 (t0) REVERT: D 709 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6235 (t80) outliers start: 113 outliers final: 66 residues processed: 391 average time/residue: 0.1821 time to fit residues: 117.2360 Evaluate side-chains 349 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 740 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 281 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 HIS ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.184666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112626 restraints weight = 51342.870| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.63 r_work: 0.3259 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32121 Z= 0.134 Angle : 0.511 15.589 43234 Z= 0.268 Chirality : 0.039 0.206 4593 Planarity : 0.003 0.057 5492 Dihedral : 4.061 54.475 4124 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.03 % Allowed : 23.85 % Favored : 73.12 % 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: 1.13 (0.14), residues: 3689 helix: 1.19 (0.10), residues: 2472 sheet: -3.30 (0.90), residues: 20 loop : 0.06 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 370 TYR 0.026 0.001 TYR D 452 PHE 0.027 0.001 PHE D 652 TRP 0.039 0.002 TRP C 143 HIS 0.014 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00312 (32121) covalent geometry : angle 0.51064 (43234) hydrogen bonds : bond 0.03431 ( 1764) hydrogen bonds : angle 4.30708 ( 5091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 286 time to evaluate : 1.116 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: A 98 MET cc_start: 0.8846 (tpp) cc_final: 0.8549 (ttm) REVERT: A 447 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: A 677 ARG cc_start: 0.7816 (ptt90) cc_final: 0.7156 (ttt-90) REVERT: A 743 TYR cc_start: 0.7472 (m-80) cc_final: 0.7244 (m-80) REVERT: A 778 PHE cc_start: 0.8307 (t80) cc_final: 0.7882 (t80) REVERT: A 813 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7208 (mmtp) REVERT: A 874 ILE cc_start: 0.5559 (OUTLIER) cc_final: 0.4999 (mm) REVERT: A 930 MET cc_start: 0.4106 (mmp) cc_final: 0.2528 (mtt) REVERT: A 936 MET cc_start: 0.3829 (mtp) cc_final: 0.2599 (mmm) REVERT: B 9 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6649 (mmtt) REVERT: B 134 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.7111 (p90) REVERT: B 341 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 624 GLU cc_start: 0.7906 (tp30) cc_final: 0.7533 (tm-30) REVERT: B 714 SER cc_start: 0.9190 (t) cc_final: 0.8973 (p) REVERT: B 784 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8030 (tm-30) REVERT: B 913 MET cc_start: 0.5851 (mpp) cc_final: 0.5272 (mpp) REVERT: B 976 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.4422 (tmm) REVERT: B 1004 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.4826 (m-80) REVERT: C 101 ASP cc_start: 0.8194 (m-30) cc_final: 0.7862 (m-30) REVERT: C 143 TRP cc_start: 0.6916 (OUTLIER) cc_final: 0.6622 (t60) REVERT: C 330 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7975 (mm) REVERT: C 357 MET cc_start: 0.7512 (mtp) cc_final: 0.7266 (mmm) REVERT: C 396 MET cc_start: 0.5806 (mmm) cc_final: 0.5505 (mmm) REVERT: C 426 GLU cc_start: 0.8026 (pp20) cc_final: 0.7309 (mm-30) REVERT: C 441 PHE cc_start: 0.8292 (m-10) cc_final: 0.7593 (m-80) REVERT: C 704 MET cc_start: 0.1717 (ppp) cc_final: 0.0867 (ptp) REVERT: C 784 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7224 (pt0) REVERT: C 866 MET cc_start: 0.4208 (mtp) cc_final: 0.3307 (tpp) REVERT: C 924 GLU cc_start: 0.2988 (OUTLIER) cc_final: 0.2721 (mp0) REVERT: D 107 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8456 (t80) REVERT: D 311 TYR cc_start: 0.6789 (t80) cc_final: 0.6547 (t80) REVERT: D 327 LYS cc_start: 0.5437 (mmtp) cc_final: 0.4340 (tttt) REVERT: D 391 ASN cc_start: 0.6272 (m-40) cc_final: 0.5640 (m110) REVERT: D 463 ILE cc_start: 0.4766 (OUTLIER) cc_final: 0.3481 (tp) REVERT: D 709 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6289 (t80) outliers start: 105 outliers final: 70 residues processed: 373 average time/residue: 0.1968 time to fit residues: 119.9276 Evaluate side-chains 341 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 258 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 173 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 324 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 666 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.184997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113261 restraints weight = 51995.453| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.59 r_work: 0.3270 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32121 Z= 0.125 Angle : 0.509 15.560 43234 Z= 0.267 Chirality : 0.039 0.200 4593 Planarity : 0.003 0.052 5492 Dihedral : 4.021 55.083 4124 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.95 % Allowed : 24.17 % Favored : 72.88 % 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: 1.18 (0.14), residues: 3689 helix: 1.24 (0.10), residues: 2470 sheet: -3.42 (0.90), residues: 20 loop : 0.08 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 587 TYR 0.026 0.001 TYR D 452 PHE 0.026 0.001 PHE C 544 TRP 0.040 0.002 TRP C 143 HIS 0.011 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00288 (32121) covalent geometry : angle 0.50893 (43234) hydrogen bonds : bond 0.03342 ( 1764) hydrogen bonds : angle 4.24963 ( 5091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 285 time to evaluate : 1.091 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 98 MET cc_start: 0.9079 (tpp) cc_final: 0.8718 (ttm) REVERT: A 447 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8261 (ptm160) REVERT: A 677 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7255 (ttt-90) REVERT: A 743 TYR cc_start: 0.7409 (m-80) cc_final: 0.7142 (m-80) REVERT: A 778 PHE cc_start: 0.8354 (t80) cc_final: 0.7880 (t80) REVERT: A 813 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7225 (mmtp) REVERT: A 930 MET cc_start: 0.4224 (mmp) cc_final: 0.2562 (mtt) REVERT: A 936 MET cc_start: 0.3847 (mtp) cc_final: 0.2628 (mmm) REVERT: B 9 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6728 (mmtt) REVERT: B 134 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.7223 (p90) REVERT: B 279 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: B 341 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 624 GLU cc_start: 0.8153 (tp30) cc_final: 0.7799 (tm-30) REVERT: B 913 MET cc_start: 0.5794 (mpp) cc_final: 0.5207 (mpp) REVERT: B 976 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.4283 (tmm) REVERT: B 1004 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: C 69 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: C 101 ASP cc_start: 0.8432 (m-30) cc_final: 0.8107 (m-30) REVERT: C 143 TRP cc_start: 0.7246 (OUTLIER) cc_final: 0.6809 (t60) REVERT: C 426 GLU cc_start: 0.8106 (pp20) cc_final: 0.7396 (mm-30) REVERT: C 441 PHE cc_start: 0.8238 (m-10) cc_final: 0.7669 (m-80) REVERT: C 704 MET cc_start: 0.1584 (ppp) cc_final: 0.0731 (ptp) REVERT: C 784 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7186 (pt0) REVERT: C 866 MET cc_start: 0.4225 (mtp) cc_final: 0.3340 (tpp) REVERT: C 924 GLU cc_start: 0.3061 (OUTLIER) cc_final: 0.2751 (mp0) REVERT: D 107 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8541 (t80) REVERT: D 311 TYR cc_start: 0.6924 (t80) cc_final: 0.6661 (t80) REVERT: D 327 LYS cc_start: 0.5453 (mmtp) cc_final: 0.4456 (tttt) REVERT: D 362 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.4358 (tp30) REVERT: D 391 ASN cc_start: 0.6335 (m-40) cc_final: 0.5691 (m110) REVERT: D 463 ILE cc_start: 0.4698 (OUTLIER) cc_final: 0.3471 (tp) REVERT: D 709 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6304 (t80) outliers start: 102 outliers final: 70 residues processed: 370 average time/residue: 0.2103 time to fit residues: 126.7389 Evaluate side-chains 344 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 260 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 11 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 346 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 302 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 363 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114681 restraints weight = 51604.116| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.98 r_work: 0.3220 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32121 Z= 0.134 Angle : 0.522 14.014 43234 Z= 0.273 Chirality : 0.039 0.208 4593 Planarity : 0.003 0.050 5492 Dihedral : 4.034 55.228 4124 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.86 % Allowed : 24.52 % Favored : 72.62 % 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: 1.12 (0.14), residues: 3689 helix: 1.22 (0.10), residues: 2472 sheet: -2.92 (0.75), residues: 32 loop : 0.01 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 587 TYR 0.027 0.001 TYR D 552 PHE 0.028 0.001 PHE C 744 TRP 0.040 0.002 TRP C 143 HIS 0.023 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00310 (32121) covalent geometry : angle 0.52189 (43234) hydrogen bonds : bond 0.03333 ( 1764) hydrogen bonds : angle 4.26197 ( 5091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 267 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 98 MET cc_start: 0.8958 (tpp) cc_final: 0.8606 (ttm) REVERT: A 354 PHE cc_start: 0.8572 (t80) cc_final: 0.8366 (t80) REVERT: A 447 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8166 (ptm160) REVERT: A 677 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7203 (ttt-90) REVERT: A 743 TYR cc_start: 0.7479 (m-80) cc_final: 0.7186 (m-80) REVERT: A 778 PHE cc_start: 0.8405 (t80) cc_final: 0.8031 (t80) REVERT: A 813 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7286 (mmtp) REVERT: A 930 MET cc_start: 0.4200 (mmp) cc_final: 0.2525 (mtt) REVERT: A 936 MET cc_start: 0.3827 (mtp) cc_final: 0.2680 (mmm) REVERT: A 979 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7313 (p90) REVERT: B 9 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6662 (mmtt) REVERT: B 134 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.7084 (p90) REVERT: B 279 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: B 341 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 624 GLU cc_start: 0.7940 (tp30) cc_final: 0.7568 (tm-30) REVERT: B 913 MET cc_start: 0.5778 (mpp) cc_final: 0.5137 (ttt) REVERT: B 976 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.4252 (tmm) REVERT: B 1004 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4884 (m-80) REVERT: C 69 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 101 ASP cc_start: 0.8309 (m-30) cc_final: 0.7970 (m-30) REVERT: C 143 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6494 (t60) REVERT: C 304 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6666 (pttp) REVERT: C 396 MET cc_start: 0.5075 (mmm) cc_final: 0.4801 (mmm) REVERT: C 426 GLU cc_start: 0.8119 (pp20) cc_final: 0.7400 (mm-30) REVERT: C 441 PHE cc_start: 0.8287 (m-10) cc_final: 0.7655 (m-80) REVERT: C 704 MET cc_start: 0.1597 (ppp) cc_final: 0.0807 (ptp) REVERT: C 866 MET cc_start: 0.4240 (mtp) cc_final: 0.3375 (tpp) REVERT: C 924 GLU cc_start: 0.3099 (OUTLIER) cc_final: 0.2783 (mp0) REVERT: D 107 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8484 (t80) REVERT: D 311 TYR cc_start: 0.6837 (t80) cc_final: 0.6578 (t80) REVERT: D 327 LYS cc_start: 0.5470 (mmtp) cc_final: 0.4433 (tttt) REVERT: D 362 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.4776 (tp30) REVERT: D 391 ASN cc_start: 0.6225 (m-40) cc_final: 0.5534 (m110) REVERT: D 463 ILE cc_start: 0.4550 (OUTLIER) cc_final: 0.3283 (tp) REVERT: D 709 TYR cc_start: 0.6926 (OUTLIER) cc_final: 0.6299 (t80) outliers start: 99 outliers final: 69 residues processed: 349 average time/residue: 0.1822 time to fit residues: 104.8666 Evaluate side-chains 344 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 258 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 179 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 368 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113217 restraints weight = 51256.814| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.72 r_work: 0.3237 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32121 Z= 0.154 Angle : 0.536 14.226 43234 Z= 0.279 Chirality : 0.040 0.232 4593 Planarity : 0.003 0.048 5492 Dihedral : 4.066 55.702 4124 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.89 % Allowed : 24.49 % Favored : 72.62 % 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 (0.14), residues: 3689 helix: 1.18 (0.10), residues: 2478 sheet: -3.55 (0.92), residues: 20 loop : -0.02 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 587 TYR 0.028 0.001 TYR D 452 PHE 0.034 0.001 PHE D 528 TRP 0.041 0.002 TRP C 143 HIS 0.021 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00364 (32121) covalent geometry : angle 0.53644 (43234) hydrogen bonds : bond 0.03381 ( 1764) hydrogen bonds : angle 4.26802 ( 5091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 266 time to evaluate : 1.304 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: A 32 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: A 98 MET cc_start: 0.8903 (tpp) cc_final: 0.8559 (ttm) REVERT: A 354 PHE cc_start: 0.8540 (t80) cc_final: 0.8328 (t80) REVERT: A 447 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8160 (ptm160) REVERT: A 677 ARG cc_start: 0.7838 (ptt90) cc_final: 0.7180 (ttt-90) REVERT: A 743 TYR cc_start: 0.7423 (m-80) cc_final: 0.7147 (m-80) REVERT: A 813 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7267 (mmtp) REVERT: A 930 MET cc_start: 0.4212 (mmp) cc_final: 0.2574 (mtt) REVERT: A 936 MET cc_start: 0.3819 (mtp) cc_final: 0.3089 (mmm) REVERT: B 9 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6538 (mmtt) REVERT: B 134 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7083 (p90) REVERT: B 279 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: B 331 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8369 (mtpt) REVERT: B 341 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 428 GLN cc_start: 0.8166 (tp40) cc_final: 0.7857 (tm-30) REVERT: B 624 GLU cc_start: 0.7900 (tp30) cc_final: 0.7502 (tm-30) REVERT: B 784 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7882 (tm-30) REVERT: B 913 MET cc_start: 0.5760 (mpp) cc_final: 0.5122 (ttt) REVERT: B 1004 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4888 (m-80) REVERT: C 69 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: C 101 ASP cc_start: 0.8289 (m-30) cc_final: 0.7943 (m-30) REVERT: C 143 TRP cc_start: 0.7050 (OUTLIER) cc_final: 0.6492 (t60) REVERT: C 304 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6666 (pttp) REVERT: C 396 MET cc_start: 0.5206 (mmm) cc_final: 0.4790 (mmm) REVERT: C 426 GLU cc_start: 0.8119 (pp20) cc_final: 0.7395 (mm-30) REVERT: C 441 PHE cc_start: 0.8303 (m-10) cc_final: 0.7629 (m-80) REVERT: C 704 MET cc_start: 0.1592 (ppp) cc_final: 0.0793 (ptp) REVERT: C 784 GLU cc_start: 0.7852 (tp30) cc_final: 0.7487 (pt0) REVERT: C 866 MET cc_start: 0.4235 (mtp) cc_final: 0.3335 (tpp) REVERT: C 924 GLU cc_start: 0.3092 (OUTLIER) cc_final: 0.2808 (mp0) REVERT: D 107 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8489 (t80) REVERT: D 311 TYR cc_start: 0.6868 (t80) cc_final: 0.6608 (t80) REVERT: D 327 LYS cc_start: 0.5519 (mmtp) cc_final: 0.4390 (tttt) REVERT: D 362 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.4869 (tp30) REVERT: D 391 ASN cc_start: 0.6239 (m-40) cc_final: 0.5518 (m110) REVERT: D 463 ILE cc_start: 0.4518 (OUTLIER) cc_final: 0.3278 (tp) REVERT: D 646 PHE cc_start: 0.4956 (t80) cc_final: 0.4726 (t80) REVERT: D 709 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6406 (t80) outliers start: 100 outliers final: 75 residues processed: 349 average time/residue: 0.1970 time to fit residues: 111.9590 Evaluate side-chains 348 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 257 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 64.3415 > 50: distance: 80 - 102: 3.523 distance: 89 - 107: 10.220 distance: 93 - 116: 15.842 distance: 98 - 102: 5.539 distance: 99 - 121: 17.180 distance: 102 - 103: 6.882 distance: 103 - 104: 3.275 distance: 103 - 106: 12.765 distance: 104 - 105: 23.923 distance: 104 - 107: 10.216 distance: 105 - 126: 23.848 distance: 107 - 108: 13.792 distance: 108 - 109: 12.381 distance: 108 - 111: 13.275 distance: 109 - 110: 12.025 distance: 110 - 134: 17.599 distance: 111 - 112: 20.587 distance: 112 - 113: 21.199 distance: 113 - 114: 19.413 distance: 114 - 115: 9.332 distance: 116 - 117: 4.024 distance: 117 - 118: 10.634 distance: 117 - 120: 16.128 distance: 118 - 119: 8.236 distance: 118 - 121: 6.288 distance: 119 - 146: 27.334 distance: 121 - 122: 15.503 distance: 122 - 123: 7.928 distance: 122 - 125: 8.299 distance: 123 - 126: 13.355 distance: 124 - 157: 19.672 distance: 127 - 128: 18.922 distance: 127 - 130: 14.046 distance: 128 - 129: 11.780 distance: 128 - 134: 13.018 distance: 130 - 131: 5.785 distance: 131 - 132: 6.471 distance: 131 - 133: 34.956 distance: 134 - 135: 15.423 distance: 135 - 136: 7.783 distance: 135 - 138: 20.352 distance: 136 - 137: 24.251 distance: 136 - 146: 17.853 distance: 138 - 139: 6.643 distance: 139 - 140: 19.801 distance: 139 - 141: 5.325 distance: 140 - 142: 18.951 distance: 141 - 143: 3.677 distance: 142 - 144: 8.549 distance: 143 - 144: 19.387 distance: 144 - 145: 8.592 distance: 146 - 147: 7.685 distance: 147 - 150: 9.994 distance: 148 - 149: 31.117 distance: 148 - 157: 20.776 distance: 151 - 152: 18.850 distance: 151 - 153: 11.464 distance: 152 - 154: 29.450 distance: 153 - 155: 15.913 distance: 154 - 156: 27.674 distance: 155 - 156: 16.549 distance: 157 - 158: 27.741 distance: 158 - 159: 32.317 distance: 158 - 161: 35.945 distance: 159 - 160: 40.314 distance: 159 - 162: 32.025 distance: 162 - 163: 28.215 distance: 163 - 164: 23.148 distance: 163 - 166: 7.989 distance: 164 - 165: 8.937 distance: 164 - 171: 21.443 distance: 166 - 167: 46.887 distance: 167 - 168: 23.506 distance: 168 - 169: 37.220 distance: 169 - 170: 32.569 distance: 171 - 172: 39.027 distance: 172 - 173: 23.997 distance: 172 - 175: 27.351 distance: 173 - 174: 13.554 distance: 173 - 183: 22.103 distance: 175 - 176: 20.294 distance: 176 - 177: 6.223 distance: 176 - 178: 15.019 distance: 177 - 179: 16.144 distance: 178 - 180: 16.309 distance: 179 - 181: 17.106 distance: 180 - 181: 21.157 distance: 181 - 182: 11.459