Starting phenix.real_space_refine on Thu May 29 02:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy8_37919/05_2025/8wy8_37919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy8_37919/05_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_37919/05_2025/8wy8_37919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy8_37919/05_2025/8wy8_37919.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy8_37919/05_2025/8wy8_37919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy8_37919/05_2025/8wy8_37919.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.19, per 1000 atoms: 0.64 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: 9.99 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.23 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: 12.33 Time building geometry restraints manager: 11.26 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: 8.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 74.780 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.130 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.190 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (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 TRP 0.058 0.002 TRP C 143 HIS 0.017 0.001 HIS D 349 PHE 0.025 0.001 PHE C 744 TYR 0.025 0.001 TYR D 552 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.19309 ( 1764) hydrogen bonds : angle 6.23500 ( 5091) covalent geometry : bond 0.00238 (32121) covalent geometry : angle 0.55293 (43234) *********************** 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 : 3.350 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 731 GLU cc_start: 0.8280 (tt0) cc_final: 0.7914 (tp30) REVERT: A 930 MET cc_start: 0.4432 (mmp) cc_final: 0.3393 (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: 0.6954 (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: 0.6956 (t80) REVERT: C 616 MET cc_start: -0.1945 (mtt) cc_final: -0.2285 (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: 0.3008 (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: -0.1795 (ppp) outliers start: 7 outliers final: 2 residues processed: 416 average time/residue: 0.4489 time to fit residues: 296.0802 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 : 3.636 ------------------------------------------------------------------------------- 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 316 optimal weight: 8.9990 chunk 284 optimal weight: 0.8980 chunk 157 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** B 939 GLN 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 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 = 0.4450 r_free = 0.4450 target = 0.188721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120056 restraints weight = 51679.086| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.07 r_work: 0.3293 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32121 Z= 0.134 Angle : 0.559 16.369 43234 Z= 0.295 Chirality : 0.040 0.193 4593 Planarity : 0.004 0.051 5492 Dihedral : 4.093 39.318 4127 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.71 % Allowed : 23.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3689 helix: 1.24 (0.10), residues: 2487 sheet: -2.07 (0.73), residues: 20 loop : 0.05 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 143 HIS 0.007 0.001 HIS D 339 PHE 0.022 0.001 PHE C 544 TYR 0.026 0.001 TYR C 479 ARG 0.008 0.001 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1764) hydrogen bonds : angle 4.65351 ( 5091) covalent geometry : bond 0.00294 (32121) covalent geometry : angle 0.55922 (43234) *********************** 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 426 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 332 time to evaluate : 3.458 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: 0.8770 (tpp) cc_final: 0.8532 (ttm) REVERT: A 306 ASP cc_start: 0.7804 (p0) cc_final: 0.7597 (m-30) REVERT: A 394 ILE cc_start: 0.8942 (mm) cc_final: 0.8733 (mm) REVERT: A 398 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7606 (pttm) REVERT: A 813 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7120 (mmtp) REVERT: A 930 MET cc_start: 0.4247 (mmp) cc_final: 0.2863 (mtm) REVERT: A 936 MET cc_start: 0.3844 (mtp) cc_final: 0.3393 (mmm) REVERT: A 962 TYR cc_start: 0.5741 (m-10) cc_final: 0.5533 (m-10) REVERT: B 9 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6800 (tptp) REVERT: B 191 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 341 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 624 GLU cc_start: 0.7855 (tp30) cc_final: 0.7518 (tm-30) REVERT: B 625 TYR cc_start: 0.8451 (t80) cc_final: 0.8094 (t80) REVERT: B 714 SER cc_start: 0.9215 (t) cc_final: 0.8982 (p) REVERT: B 913 MET cc_start: 0.5793 (pmm) cc_final: 0.5545 (ttt) REVERT: B 930 MET cc_start: 0.5085 (mmp) cc_final: 0.3804 (ppp) REVERT: C 101 ASP cc_start: 0.8407 (m-30) cc_final: 0.8063 (m-30) REVERT: C 284 GLU cc_start: 0.8433 (tp30) cc_final: 0.8231 (tp30) REVERT: C 426 GLU cc_start: 0.7619 (pp20) cc_final: 0.6656 (mm-30) REVERT: C 458 ILE cc_start: 0.8254 (mt) cc_final: 0.7940 (mt) REVERT: C 654 ASN cc_start: 0.5612 (OUTLIER) cc_final: 0.5376 (m-40) REVERT: C 704 MET cc_start: 0.1487 (ppp) cc_final: 0.0462 (ptt) REVERT: C 784 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7191 (pt0) REVERT: C 866 MET cc_start: 0.4487 (mtp) cc_final: 0.3506 (tpp) REVERT: C 945 ASP cc_start: -0.2975 (OUTLIER) cc_final: -0.3181 (p0) REVERT: D 173 ASP cc_start: 0.8803 (p0) cc_final: 0.8563 (p0) REVERT: D 324 TYR cc_start: 0.5764 (t80) cc_final: 0.5496 (t80) REVERT: D 327 LYS cc_start: 0.5568 (mmtp) cc_final: 0.4522 (tttm) REVERT: D 649 TYR cc_start: 0.4820 (t80) cc_final: 0.4528 (t80) REVERT: D 704 MET cc_start: -0.0350 (tpt) cc_final: -0.0655 (tpp) REVERT: D 709 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6379 (t80) REVERT: D 976 MET cc_start: 0.1666 (tmm) cc_final: -0.1146 (ppp) outliers start: 94 outliers final: 37 residues processed: 409 average time/residue: 0.4248 time to fit residues: 282.0940 Evaluate side-chains 321 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 811 PHE 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 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 476 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 654 ASN 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 62 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 114 optimal weight: 0.1980 chunk 312 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 265 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 266 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 B 939 GLN C 591 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS D 521 ASN D 863 ASN D 939 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116631 restraints weight = 51612.122| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.77 r_work: 0.3284 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32121 Z= 0.127 Angle : 0.520 15.043 43234 Z= 0.274 Chirality : 0.039 0.197 4593 Planarity : 0.003 0.055 5492 Dihedral : 4.002 46.960 4124 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.69 % Allowed : 22.52 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3689 helix: 1.26 (0.10), residues: 2482 sheet: -2.33 (0.67), residues: 32 loop : 0.09 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 143 HIS 0.012 0.001 HIS D 349 PHE 0.023 0.001 PHE D 708 TYR 0.025 0.001 TYR D 452 ARG 0.006 0.000 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1764) hydrogen bonds : angle 4.46545 ( 5091) covalent geometry : bond 0.00283 (32121) covalent geometry : angle 0.51996 (43234) *********************** 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 395 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 302 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8719 (tpp) cc_final: 0.8476 (ttm) REVERT: A 306 ASP cc_start: 0.7799 (p0) cc_final: 0.7571 (m-30) REVERT: A 365 GLU cc_start: 0.7922 (pp20) cc_final: 0.7645 (pp20) REVERT: A 386 ASN cc_start: 0.8641 (m110) cc_final: 0.8356 (m-40) REVERT: A 398 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7642 (pttm) REVERT: A 421 MET cc_start: 0.7900 (mmm) cc_final: 0.7678 (mtp) REVERT: A 677 ARG cc_start: 0.7969 (ptt90) cc_final: 0.7612 (ttt-90) REVERT: A 743 TYR cc_start: 0.7410 (m-80) cc_final: 0.7140 (m-80) REVERT: A 930 MET cc_start: 0.4054 (mmp) cc_final: 0.2460 (mtm) REVERT: A 936 MET cc_start: 0.3887 (mtp) cc_final: 0.2726 (mmm) REVERT: B 9 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6891 (mmtt) REVERT: B 134 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8321 (p90) REVERT: B 341 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7937 (mm-30) REVERT: B 624 GLU cc_start: 0.7865 (tp30) cc_final: 0.7473 (tm-30) REVERT: B 625 TYR cc_start: 0.8452 (t80) cc_final: 0.8085 (t80) REVERT: B 714 SER cc_start: 0.9211 (t) cc_final: 0.8983 (p) REVERT: B 930 MET cc_start: 0.5085 (mmp) cc_final: 0.3794 (ppp) REVERT: C 101 ASP cc_start: 0.8361 (m-30) cc_final: 0.8011 (m-30) REVERT: C 426 GLU cc_start: 0.7719 (pp20) cc_final: 0.6879 (mm-30) REVERT: C 654 ASN cc_start: 0.5513 (OUTLIER) cc_final: 0.5201 (m-40) REVERT: C 704 MET cc_start: 0.1639 (ppp) cc_final: 0.0490 (ptp) REVERT: C 784 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7145 (pt0) REVERT: C 866 MET cc_start: 0.4291 (mtp) cc_final: 0.3300 (tpp) REVERT: D 124 MET cc_start: 0.9274 (mmm) cc_final: 0.8878 (tpt) REVERT: D 173 ASP cc_start: 0.8801 (p0) cc_final: 0.8547 (p0) REVERT: D 181 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: D 324 TYR cc_start: 0.5703 (t80) cc_final: 0.5485 (t80) REVERT: D 327 LYS cc_start: 0.5502 (mmtp) cc_final: 0.4448 (tttm) REVERT: D 391 ASN cc_start: 0.6077 (m-40) cc_final: 0.5199 (m110) REVERT: D 479 TYR cc_start: 0.6483 (t80) cc_final: 0.6267 (t80) REVERT: D 649 TYR cc_start: 0.4880 (t80) cc_final: 0.4578 (t80) REVERT: D 704 MET cc_start: -0.0334 (tpt) cc_final: -0.0764 (tpp) REVERT: D 709 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6377 (t80) outliers start: 93 outliers final: 48 residues processed: 377 average time/residue: 0.4212 time to fit residues: 257.7723 Evaluate side-chains 326 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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 366 SER Chi-restraints excluded: chain A residue 491 GLN 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 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 134 TYR Chi-restraints excluded: chain B residue 204 MET 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 672 SER Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 24 ASN 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 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 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 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 654 ASN 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 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 385 PHE Chi-restraints excluded: chain D residue 425 ILE 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 173 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 354 optimal weight: 40.0000 chunk 170 optimal weight: 0.8980 chunk 280 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 ASN C 118 HIS ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 521 ASN D 598 ASN D 782 GLN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.184332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112500 restraints weight = 51888.652| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.97 r_work: 0.3208 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32121 Z= 0.190 Angle : 0.555 15.934 43234 Z= 0.291 Chirality : 0.041 0.214 4593 Planarity : 0.004 0.047 5492 Dihedral : 4.147 53.154 4124 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.55 % Allowed : 22.44 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3689 helix: 1.10 (0.10), residues: 2492 sheet: -2.87 (0.86), residues: 20 loop : -0.02 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 143 HIS 0.007 0.001 HIS D 349 PHE 0.026 0.002 PHE D 708 TYR 0.020 0.002 TYR D 552 ARG 0.007 0.001 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1764) hydrogen bonds : angle 4.47307 ( 5091) covalent geometry : bond 0.00450 (32121) covalent geometry : angle 0.55506 (43234) *********************** 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 418 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 295 time to evaluate : 3.923 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: 0.8912 (tpp) cc_final: 0.8585 (ttm) REVERT: A 306 ASP cc_start: 0.7948 (p0) cc_final: 0.7670 (m-30) REVERT: A 354 PHE cc_start: 0.8620 (t80) cc_final: 0.8315 (t80) REVERT: A 365 GLU cc_start: 0.7911 (pp20) cc_final: 0.7639 (pp20) REVERT: A 398 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7816 (pttm) REVERT: A 677 ARG cc_start: 0.8012 (ptt90) cc_final: 0.7213 (ttt-90) REVERT: A 743 TYR cc_start: 0.7696 (m-80) cc_final: 0.7375 (m-80) REVERT: A 930 MET cc_start: 0.4016 (mmp) cc_final: 0.2409 (mtt) REVERT: A 936 MET cc_start: 0.3677 (mtp) cc_final: 0.2570 (mmm) REVERT: B 9 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6427 (mmtt) REVERT: B 134 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7035 (p90) REVERT: B 331 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8407 (mtmm) REVERT: B 341 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 624 GLU cc_start: 0.7878 (tp30) cc_final: 0.7435 (tm-30) REVERT: B 714 SER cc_start: 0.9224 (t) cc_final: 0.9003 (p) REVERT: B 936 MET cc_start: 0.2927 (pmm) cc_final: 0.2669 (pmm) REVERT: C 35 GLU cc_start: 0.8389 (tp30) cc_final: 0.8111 (tt0) REVERT: C 101 ASP cc_start: 0.8552 (m-30) cc_final: 0.8246 (m-30) REVERT: C 143 TRP cc_start: 0.7063 (OUTLIER) cc_final: 0.6752 (t60) REVERT: C 426 GLU cc_start: 0.8030 (pp20) cc_final: 0.7237 (mm-30) REVERT: C 654 ASN cc_start: 0.5556 (OUTLIER) cc_final: 0.5243 (m-40) REVERT: C 704 MET cc_start: 0.1765 (ppp) cc_final: 0.0771 (ptt) REVERT: C 784 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7141 (pt0) REVERT: C 866 MET cc_start: 0.4221 (mtp) cc_final: 0.3254 (tpp) REVERT: C 924 GLU cc_start: 0.2961 (OUTLIER) cc_final: 0.2724 (mp0) REVERT: D 173 ASP cc_start: 0.8950 (p0) cc_final: 0.8700 (p0) REVERT: D 181 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: D 291 ASP cc_start: 0.8149 (p0) cc_final: 0.7555 (m-30) REVERT: D 324 TYR cc_start: 0.6045 (t80) cc_final: 0.5682 (t80) REVERT: D 327 LYS cc_start: 0.5483 (mmtp) cc_final: 0.4367 (tttt) REVERT: D 348 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7612 (tpp80) REVERT: D 362 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.5514 (tp30) REVERT: D 391 ASN cc_start: 0.6262 (m-40) cc_final: 0.5397 (m110) REVERT: D 463 ILE cc_start: 0.4823 (OUTLIER) cc_final: 0.4141 (pt) REVERT: D 521 ASN cc_start: 0.6602 (OUTLIER) cc_final: 0.6084 (t0) REVERT: D 557 LYS cc_start: -0.2369 (OUTLIER) cc_final: -0.2882 (tmtt) REVERT: D 581 ASP cc_start: 0.4752 (OUTLIER) cc_final: 0.4001 (t0) REVERT: D 647 MET cc_start: 0.3955 (mmt) cc_final: 0.3515 (mmp) REVERT: D 649 TYR cc_start: 0.4761 (t80) cc_final: 0.4324 (t80) REVERT: D 831 LYS cc_start: 0.3618 (OUTLIER) cc_final: 0.3384 (tppt) outliers start: 123 outliers final: 67 residues processed: 394 average time/residue: 0.4197 time to fit residues: 272.1932 Evaluate side-chains 349 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 269 time to evaluate : 3.329 ------------------------------------------------------------------------------- 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 366 SER Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 685 GLU 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 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 331 LYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 581 ASP 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 811 PHE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 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 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 SER 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 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 654 ASN 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 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 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 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 277 SER 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 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 463 ILE 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 709 TYR Chi-restraints excluded: chain D residue 831 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 370 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 310 optimal weight: 0.5980 chunk 346 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 227 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 312 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 609 HIS ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.186709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113967 restraints weight = 51450.536| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.39 r_work: 0.3305 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32121 Z= 0.115 Angle : 0.511 15.490 43234 Z= 0.267 Chirality : 0.039 0.204 4593 Planarity : 0.003 0.081 5492 Dihedral : 4.035 53.633 4124 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.57 % Allowed : 23.71 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3689 helix: 1.23 (0.10), residues: 2476 sheet: -3.23 (0.89), residues: 20 loop : 0.11 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 143 HIS 0.014 0.001 HIS C 979 PHE 0.026 0.001 PHE D 708 TYR 0.026 0.001 TYR D 479 ARG 0.011 0.000 ARG C 326 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 1764) hydrogen bonds : angle 4.32872 ( 5091) covalent geometry : bond 0.00254 (32121) covalent geometry : angle 0.51079 (43234) *********************** 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 387 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 298 time to evaluate : 3.873 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: 0.8997 (tpp) cc_final: 0.8671 (ttm) REVERT: A 354 PHE cc_start: 0.8592 (t80) cc_final: 0.8363 (t80) REVERT: A 398 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7799 (pttm) REVERT: A 447 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8167 (ptm160) REVERT: A 627 ARG cc_start: 0.7153 (ttp-110) cc_final: 0.6922 (ttp-110) REVERT: A 677 ARG cc_start: 0.7872 (ptt90) cc_final: 0.7271 (ttt-90) REVERT: A 743 TYR cc_start: 0.7620 (m-80) cc_final: 0.7258 (m-80) REVERT: A 813 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7203 (mmtp) REVERT: A 930 MET cc_start: 0.4070 (mmp) cc_final: 0.2406 (mtt) REVERT: A 936 MET cc_start: 0.3899 (mtp) cc_final: 0.2717 (mmm) REVERT: B 9 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6679 (mmtt) REVERT: B 134 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7126 (p90) REVERT: B 341 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 624 GLU cc_start: 0.8096 (tp30) cc_final: 0.7732 (tm-30) REVERT: B 714 SER cc_start: 0.9236 (t) cc_final: 0.9035 (p) REVERT: B 913 MET cc_start: 0.6138 (mpp) cc_final: 0.5428 (mpp) REVERT: B 976 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4480 (tmm) REVERT: C 35 GLU cc_start: 0.8573 (tp30) cc_final: 0.8310 (tt0) REVERT: C 101 ASP cc_start: 0.8474 (m-30) cc_final: 0.8152 (m-30) REVERT: C 143 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.6861 (t60) REVERT: C 426 GLU cc_start: 0.8024 (pp20) cc_final: 0.7261 (mm-30) REVERT: C 475 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7093 (mm-40) REVERT: C 519 MET cc_start: 0.4491 (mmm) cc_final: 0.3747 (mmm) REVERT: C 654 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.5124 (m-40) REVERT: C 704 MET cc_start: 0.1827 (ppp) cc_final: 0.0816 (ptp) REVERT: C 784 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7162 (pt0) REVERT: C 866 MET cc_start: 0.4261 (mtp) cc_final: 0.3315 (tpp) REVERT: D 173 ASP cc_start: 0.8996 (p0) cc_final: 0.8756 (p0) REVERT: D 324 TYR cc_start: 0.6034 (t80) cc_final: 0.5758 (t80) REVERT: D 327 LYS cc_start: 0.5421 (mmtp) cc_final: 0.4370 (tttt) REVERT: D 348 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7386 (mtp180) REVERT: D 391 ASN cc_start: 0.6388 (m-40) cc_final: 0.5608 (m110) REVERT: D 477 ASN cc_start: 0.8017 (m110) cc_final: 0.7295 (m-40) REVERT: D 551 LEU cc_start: 0.5234 (tp) cc_final: 0.5031 (tp) REVERT: D 649 TYR cc_start: 0.4574 (t80) cc_final: 0.4058 (t80) REVERT: D 976 MET cc_start: 0.1557 (tmm) cc_final: -0.1418 (ptt) outliers start: 89 outliers final: 63 residues processed: 368 average time/residue: 0.4175 time to fit residues: 249.8303 Evaluate side-chains 341 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 3.487 ------------------------------------------------------------------------------- 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 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 656 SER 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 B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR 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 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 673 ILE 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 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 SER 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 460 LEU Chi-restraints excluded: chain C residue 475 GLN 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 611 TYR Chi-restraints excluded: chain C residue 654 ASN 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 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 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 277 SER 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 709 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3236 > 50: distance: 12 - 17: 9.649 distance: 17 - 18: 6.746 distance: 18 - 19: 16.163 distance: 18 - 21: 13.447 distance: 19 - 20: 15.247 distance: 19 - 28: 18.829 distance: 21 - 22: 13.799 distance: 22 - 23: 16.382 distance: 23 - 24: 17.305 distance: 25 - 26: 11.631 distance: 25 - 27: 11.781 distance: 28 - 29: 3.411 distance: 29 - 30: 17.315 distance: 29 - 32: 21.815 distance: 30 - 31: 18.510 distance: 30 - 35: 22.342 distance: 32 - 33: 26.050 distance: 32 - 34: 7.397 distance: 35 - 36: 20.338 distance: 36 - 37: 21.413 distance: 36 - 39: 12.379 distance: 37 - 38: 12.080 distance: 37 - 43: 30.228 distance: 39 - 40: 19.989 distance: 40 - 41: 24.983 distance: 40 - 42: 43.382 distance: 43 - 44: 17.712 distance: 43 - 49: 27.545 distance: 44 - 45: 27.265 distance: 44 - 47: 11.913 distance: 45 - 46: 33.502 distance: 45 - 50: 21.118 distance: 47 - 48: 19.281 distance: 48 - 49: 13.464 distance: 50 - 51: 6.879 distance: 51 - 52: 14.406 distance: 51 - 54: 13.565 distance: 52 - 53: 46.782 distance: 52 - 56: 28.437 distance: 54 - 55: 29.051 distance: 56 - 57: 10.642 distance: 56 - 62: 7.776 distance: 57 - 58: 12.806 distance: 57 - 60: 9.773 distance: 58 - 59: 23.272 distance: 58 - 63: 22.816 distance: 60 - 61: 3.994 distance: 61 - 62: 15.215 distance: 63 - 64: 21.714 distance: 64 - 65: 33.198 distance: 64 - 67: 24.448 distance: 65 - 66: 26.388 distance: 65 - 71: 27.729 distance: 67 - 68: 18.308 distance: 67 - 69: 5.719 distance: 71 - 72: 15.772 distance: 72 - 73: 14.680 distance: 72 - 75: 18.273 distance: 73 - 74: 24.347 distance: 73 - 80: 6.045 distance: 74 - 104: 16.275 distance: 75 - 76: 17.979 distance: 76 - 77: 11.233 distance: 77 - 78: 5.446 distance: 77 - 79: 7.644 distance: 80 - 81: 11.196 distance: 81 - 82: 14.666 distance: 81 - 84: 8.739 distance: 82 - 83: 19.899 distance: 82 - 88: 17.567 distance: 83 - 112: 13.200 distance: 84 - 85: 20.477 distance: 85 - 86: 9.206 distance: 85 - 87: 12.384 distance: 88 - 89: 7.968 distance: 89 - 90: 23.105 distance: 89 - 92: 17.853 distance: 90 - 91: 19.914 distance: 90 - 97: 15.252 distance: 91 - 119: 5.868 distance: 92 - 93: 11.966 distance: 93 - 94: 5.964 distance: 94 - 95: 12.049 distance: 94 - 96: 4.154