Starting phenix.real_space_refine on Fri Jun 27 06:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy8_37919/06_2025/8wy8_37919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy8_37919/06_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_37919/06_2025/8wy8_37919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy8_37919/06_2025/8wy8_37919.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy8_37919/06_2025/8wy8_37919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy8_37919/06_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-5710/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: 20.39, per 1000 atoms: 0.65 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: 7.25 Conformation dependent library (CDL) restraints added in 3.5 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: 3.71 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: 11.71 Time building geometry restraints manager: 8.70 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: 64.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.410 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 71.070 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.590 ------------------------------------------------------------------------------- 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 : 4.470 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: 0.4573 time to fit residues: 303.9666 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 : 3.652 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120311 restraints weight = 51679.128| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.09 r_work: 0.3294 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 4.65352 ( 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 : 3.633 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: 0.8811 (tpp) cc_final: 0.8551 (ttm) REVERT: A 306 ASP cc_start: 0.7799 (p0) cc_final: 0.7589 (m-30) REVERT: A 394 ILE cc_start: 0.8952 (mm) cc_final: 0.8741 (mm) REVERT: A 398 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7609 (pttm) REVERT: A 813 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7120 (mmtp) REVERT: A 930 MET cc_start: 0.4269 (mmp) cc_final: 0.2839 (mtm) REVERT: A 936 MET cc_start: 0.3830 (mtp) cc_final: 0.3366 (mmm) REVERT: A 962 TYR cc_start: 0.5771 (m-10) cc_final: 0.5564 (m-10) REVERT: B 9 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6774 (tptp) REVERT: B 191 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 341 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 624 GLU cc_start: 0.7844 (tp30) cc_final: 0.7502 (tm-30) REVERT: B 625 TYR cc_start: 0.8444 (t80) cc_final: 0.8084 (t80) REVERT: B 714 SER cc_start: 0.9220 (t) cc_final: 0.8985 (p) REVERT: B 930 MET cc_start: 0.4982 (mmp) cc_final: 0.3738 (ppp) REVERT: C 101 ASP cc_start: 0.8421 (m-30) cc_final: 0.8076 (m-30) REVERT: C 284 GLU cc_start: 0.8457 (tp30) cc_final: 0.8239 (tp30) REVERT: C 426 GLU cc_start: 0.7624 (pp20) cc_final: 0.6654 (mm-30) REVERT: C 458 ILE cc_start: 0.8253 (mt) cc_final: 0.7943 (mt) REVERT: C 654 ASN cc_start: 0.5512 (OUTLIER) cc_final: 0.5277 (m-40) REVERT: C 704 MET cc_start: 0.1505 (ppp) cc_final: 0.0472 (ptt) REVERT: C 784 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7179 (pt0) REVERT: C 866 MET cc_start: 0.4501 (mtp) cc_final: 0.3527 (tpp) REVERT: C 945 ASP cc_start: -0.2835 (OUTLIER) cc_final: -0.3101 (p0) REVERT: D 173 ASP cc_start: 0.8820 (p0) cc_final: 0.8577 (p0) REVERT: D 324 TYR cc_start: 0.5758 (t80) cc_final: 0.5515 (t80) REVERT: D 327 LYS cc_start: 0.5563 (mmtp) cc_final: 0.4518 (tttm) REVERT: D 649 TYR cc_start: 0.4791 (t80) cc_final: 0.4536 (t80) REVERT: D 704 MET cc_start: -0.0318 (tpt) cc_final: -0.0646 (tpp) REVERT: D 709 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6283 (t80) REVERT: D 976 MET cc_start: 0.1613 (tmm) cc_final: -0.1336 (ppp) outliers start: 94 outliers final: 37 residues processed: 409 average time/residue: 0.4458 time to fit residues: 294.9147 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 : 3.503 ------------------------------------------------------------------------------- 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: 0.0980 chunk 312 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 265 optimal weight: 9.9990 chunk 291 optimal weight: 0.2980 chunk 266 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN D 415 HIS D 521 ASN D 863 ASN D 939 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.188523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116575 restraints weight = 51885.121| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.81 r_work: 0.3290 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32121 Z= 0.122 Angle : 0.516 15.134 43234 Z= 0.272 Chirality : 0.039 0.196 4593 Planarity : 0.003 0.055 5492 Dihedral : 3.998 46.437 4124 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 22.55 % Favored : 74.85 % 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: 1.23 (0.14), residues: 3689 helix: 1.27 (0.10), residues: 2488 sheet: -2.31 (0.66), residues: 32 loop : 0.10 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 143 HIS 0.013 0.001 HIS D 349 PHE 0.023 0.001 PHE D 708 TYR 0.023 0.001 TYR D 452 ARG 0.006 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 1764) hydrogen bonds : angle 4.46674 ( 5091) covalent geometry : bond 0.00267 (32121) covalent geometry : angle 0.51567 (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 393 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 303 time to evaluate : 3.646 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: 0.8784 (tpp) cc_final: 0.8514 (ttm) REVERT: A 306 ASP cc_start: 0.7818 (p0) cc_final: 0.7541 (m-30) REVERT: A 365 GLU cc_start: 0.7906 (pp20) cc_final: 0.7673 (pp20) REVERT: A 386 ASN cc_start: 0.8646 (m110) cc_final: 0.8364 (m-40) REVERT: A 398 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7663 (pttm) REVERT: A 421 MET cc_start: 0.7843 (mmm) cc_final: 0.7620 (mtp) REVERT: A 677 ARG cc_start: 0.7935 (ptt90) cc_final: 0.7498 (ttt-90) REVERT: A 743 TYR cc_start: 0.7393 (m-80) cc_final: 0.7114 (m-80) REVERT: A 930 MET cc_start: 0.4117 (mmp) cc_final: 0.2562 (mtm) REVERT: A 936 MET cc_start: 0.3904 (mtp) cc_final: 0.2713 (mmm) REVERT: A 976 MET cc_start: 0.4193 (pmm) cc_final: 0.3982 (pmm) REVERT: B 9 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6925 (mmtt) REVERT: B 134 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8377 (p90) REVERT: B 341 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 624 GLU cc_start: 0.7780 (tp30) cc_final: 0.7360 (tm-30) REVERT: B 625 TYR cc_start: 0.8305 (t80) cc_final: 0.7928 (t80) REVERT: B 714 SER cc_start: 0.9218 (t) cc_final: 0.8982 (p) REVERT: C 101 ASP cc_start: 0.8390 (m-30) cc_final: 0.7993 (m-30) REVERT: C 426 GLU cc_start: 0.7726 (pp20) cc_final: 0.6867 (mm-30) REVERT: C 654 ASN cc_start: 0.5579 (OUTLIER) cc_final: 0.5257 (m-40) REVERT: C 704 MET cc_start: 0.1621 (ppp) cc_final: 0.0583 (ptm) REVERT: C 784 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7177 (pt0) REVERT: C 866 MET cc_start: 0.4314 (mtp) cc_final: 0.3310 (tpp) REVERT: D 124 MET cc_start: 0.9309 (mmm) cc_final: 0.8890 (tpt) REVERT: D 173 ASP cc_start: 0.8840 (p0) cc_final: 0.8575 (p0) REVERT: D 181 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: D 324 TYR cc_start: 0.5696 (t80) cc_final: 0.5483 (t80) REVERT: D 327 LYS cc_start: 0.5461 (mmtp) cc_final: 0.4410 (tttm) REVERT: D 391 ASN cc_start: 0.6039 (m-40) cc_final: 0.5151 (m110) REVERT: D 479 TYR cc_start: 0.6415 (t80) cc_final: 0.6127 (t80) REVERT: D 649 TYR cc_start: 0.4872 (t80) cc_final: 0.4557 (t80) REVERT: D 704 MET cc_start: -0.0319 (tpt) cc_final: -0.0767 (tpp) REVERT: D 709 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6415 (t80) outliers start: 90 outliers final: 48 residues processed: 376 average time/residue: 0.4252 time to fit residues: 260.1050 Evaluate side-chains 328 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 3.685 ------------------------------------------------------------------------------- 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 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 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 859 VAL 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: 8.9990 chunk 283 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 179 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 591 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4410 r_free = 0.4410 target = 0.185440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114755 restraints weight = 51741.897| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.78 r_work: 0.3235 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32121 Z= 0.176 Angle : 0.533 15.274 43234 Z= 0.280 Chirality : 0.040 0.204 4593 Planarity : 0.003 0.050 5492 Dihedral : 4.069 51.574 4124 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.97 % Allowed : 22.81 % Favored : 74.21 % 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: 1.13 (0.14), residues: 3689 helix: 1.19 (0.10), residues: 2490 sheet: -2.78 (0.85), residues: 20 loop : 0.05 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 143 HIS 0.007 0.001 HIS D 349 PHE 0.029 0.002 PHE D 708 TYR 0.018 0.001 TYR D 338 ARG 0.008 0.001 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1764) hydrogen bonds : angle 4.43400 ( 5091) covalent geometry : bond 0.00414 (32121) covalent geometry : angle 0.53316 (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 397 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 294 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8843 (tpp) cc_final: 0.8548 (ttm) REVERT: A 306 ASP cc_start: 0.7863 (p0) cc_final: 0.7619 (m-30) REVERT: A 354 PHE cc_start: 0.8642 (t80) cc_final: 0.8339 (t80) REVERT: A 365 GLU cc_start: 0.7925 (pp20) cc_final: 0.7676 (pp20) REVERT: A 386 ASN cc_start: 0.8692 (m110) cc_final: 0.8365 (m110) REVERT: A 398 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7758 (pttm) REVERT: A 569 MET cc_start: 0.6963 (mmp) cc_final: 0.6727 (mmm) REVERT: A 677 ARG cc_start: 0.8010 (ptt90) cc_final: 0.7347 (ttt-90) REVERT: A 743 TYR cc_start: 0.7673 (m-80) cc_final: 0.7352 (m-80) REVERT: A 804 TYR cc_start: 0.6392 (m-80) cc_final: 0.6161 (m-80) REVERT: A 930 MET cc_start: 0.4076 (mmp) cc_final: 0.2424 (mtt) REVERT: A 936 MET cc_start: 0.3796 (mtp) cc_final: 0.2611 (mmm) REVERT: B 9 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6709 (mmtp) REVERT: B 134 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7026 (p90) REVERT: B 331 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8404 (mtmm) REVERT: B 341 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8023 (mm-30) REVERT: B 624 GLU cc_start: 0.7871 (tp30) cc_final: 0.7442 (tm-30) REVERT: B 714 SER cc_start: 0.9221 (t) cc_final: 0.8987 (p) REVERT: B 976 MET cc_start: 0.4561 (OUTLIER) cc_final: 0.4243 (tmm) REVERT: C 101 ASP cc_start: 0.8476 (m-30) cc_final: 0.8170 (m-30) REVERT: C 143 TRP cc_start: 0.6923 (OUTLIER) cc_final: 0.6613 (t60) REVERT: C 426 GLU cc_start: 0.7901 (pp20) cc_final: 0.7117 (mm-30) REVERT: C 654 ASN cc_start: 0.5398 (OUTLIER) cc_final: 0.5138 (m-40) REVERT: C 704 MET cc_start: 0.1674 (ppp) cc_final: 0.0647 (ptp) REVERT: C 784 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7108 (pt0) REVERT: C 866 MET cc_start: 0.4322 (mtp) cc_final: 0.3328 (tpp) REVERT: D 173 ASP cc_start: 0.8931 (p0) cc_final: 0.8682 (p0) REVERT: D 181 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: D 284 GLU cc_start: 0.8523 (tp30) cc_final: 0.8190 (tp30) REVERT: D 291 ASP cc_start: 0.8106 (p0) cc_final: 0.7485 (m-30) REVERT: D 324 TYR cc_start: 0.5912 (t80) cc_final: 0.5576 (t80) REVERT: D 327 LYS cc_start: 0.5418 (mmtp) cc_final: 0.4319 (tptt) REVERT: D 348 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7434 (tpp80) REVERT: D 362 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: D 391 ASN cc_start: 0.6178 (m-40) cc_final: 0.5311 (m110) REVERT: D 557 LYS cc_start: -0.2428 (OUTLIER) cc_final: -0.2960 (tmtt) REVERT: D 581 ASP cc_start: 0.4841 (OUTLIER) cc_final: 0.4119 (t0) REVERT: D 649 TYR cc_start: 0.4800 (t80) cc_final: 0.4479 (t80) REVERT: D 709 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6337 (t80) outliers start: 103 outliers final: 58 residues processed: 375 average time/residue: 0.4281 time to fit residues: 265.0308 Evaluate side-chains 342 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 3.552 ------------------------------------------------------------------------------- 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 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 733 LEU 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 13 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 LYS 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 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 328 ILE 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 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 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 557 LYS Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 370 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 63 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 227 optimal weight: 0.0010 chunk 21 optimal weight: 0.7980 chunk 312 optimal weight: 0.0270 overall best weight: 0.3082 ------------------------------------------------------------------------------- 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** B 224 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.188029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.120790 restraints weight = 51668.170| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.10 r_work: 0.3313 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32121 Z= 0.105 Angle : 0.501 16.487 43234 Z= 0.261 Chirality : 0.038 0.293 4593 Planarity : 0.003 0.067 5492 Dihedral : 3.977 52.987 4124 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.48 % Allowed : 23.48 % Favored : 74.04 % 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: 1.25 (0.14), residues: 3689 helix: 1.30 (0.10), residues: 2485 sheet: -2.69 (0.72), residues: 32 loop : 0.10 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 143 HIS 0.010 0.001 HIS C 979 PHE 0.027 0.001 PHE C 544 TYR 0.026 0.001 TYR D 479 ARG 0.011 0.000 ARG D 370 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1764) hydrogen bonds : angle 4.27937 ( 5091) covalent geometry : bond 0.00222 (32121) covalent geometry : angle 0.50091 (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 392 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 306 time to evaluate : 3.697 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: 0.8876 (tpp) cc_final: 0.8556 (ttm) REVERT: A 354 PHE cc_start: 0.8559 (t80) cc_final: 0.8339 (t80) REVERT: A 582 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 677 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7340 (ttt-90) REVERT: A 743 TYR cc_start: 0.7482 (m-80) cc_final: 0.7165 (m-80) REVERT: A 813 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7182 (mmtp) REVERT: A 930 MET cc_start: 0.4096 (mmp) cc_final: 0.2346 (mtt) REVERT: A 936 MET cc_start: 0.3990 (mtp) cc_final: 0.2601 (mmm) REVERT: B 9 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6886 (mmtt) REVERT: B 134 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8193 (p90) REVERT: B 341 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 624 GLU cc_start: 0.7873 (tp30) cc_final: 0.7502 (tm-30) REVERT: B 714 SER cc_start: 0.9211 (t) cc_final: 0.8998 (p) REVERT: B 753 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7598 (mtpt) REVERT: B 930 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.3750 (ppp) REVERT: B 976 MET cc_start: 0.4243 (OUTLIER) cc_final: 0.4003 (tmm) REVERT: C 101 ASP cc_start: 0.8298 (m-30) cc_final: 0.7935 (m-30) REVERT: C 143 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.6629 (t60) REVERT: C 426 GLU cc_start: 0.7913 (pp20) cc_final: 0.7170 (mm-30) REVERT: C 505 LYS cc_start: 0.6118 (mmtt) cc_final: 0.5650 (tppt) REVERT: C 654 ASN cc_start: 0.5108 (OUTLIER) cc_final: 0.4738 (m-40) REVERT: C 704 MET cc_start: 0.1851 (ppp) cc_final: 0.0836 (ptp) REVERT: C 784 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7109 (pt0) REVERT: C 866 MET cc_start: 0.4316 (mtp) cc_final: 0.3498 (tpp) REVERT: C 924 GLU cc_start: 0.3527 (OUTLIER) cc_final: 0.3015 (mp0) REVERT: D 173 ASP cc_start: 0.8751 (p0) cc_final: 0.8497 (p0) REVERT: D 181 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: D 327 LYS cc_start: 0.5402 (mmtp) cc_final: 0.4375 (tptt) REVERT: D 391 ASN cc_start: 0.6311 (m-40) cc_final: 0.5556 (m110) REVERT: D 463 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.3774 (pt) REVERT: D 477 ASN cc_start: 0.7832 (m110) cc_final: 0.7067 (m-40) REVERT: D 557 LYS cc_start: -0.2387 (OUTLIER) cc_final: -0.2953 (tmtt) REVERT: D 649 TYR cc_start: 0.4688 (t80) cc_final: 0.4417 (t80) REVERT: D 709 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5955 (t80) REVERT: D 976 MET cc_start: 0.1018 (tmm) cc_final: -0.1982 (ptt) outliers start: 86 outliers final: 51 residues processed: 373 average time/residue: 0.4285 time to fit residues: 258.9018 Evaluate side-chains 335 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU 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 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 ILE 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 13 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 ASN 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 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 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 204 MET 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 557 LYS Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 5 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 355 optimal weight: 20.0000 chunk 273 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 GLN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 ASN ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111323 restraints weight = 51658.155| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.32 r_work: 0.3259 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32121 Z= 0.201 Angle : 0.556 15.295 43234 Z= 0.291 Chirality : 0.041 0.200 4593 Planarity : 0.004 0.065 5492 Dihedral : 4.097 54.820 4124 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.21 % Allowed : 23.33 % Favored : 73.46 % 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: 1.06 (0.14), residues: 3689 helix: 1.14 (0.10), residues: 2478 sheet: -3.33 (0.90), residues: 20 loop : 0.01 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 143 HIS 0.009 0.001 HIS C 979 PHE 0.027 0.002 PHE C 744 TYR 0.021 0.002 TYR D 552 ARG 0.018 0.001 ARG C 760 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1764) hydrogen bonds : angle 4.37702 ( 5091) covalent geometry : bond 0.00476 (32121) covalent geometry : angle 0.55566 (43234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 275 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 98 MET cc_start: 0.9020 (tpp) cc_final: 0.8687 (ttm) REVERT: A 447 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8170 (ptm160) REVERT: A 677 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7222 (ttt-90) REVERT: A 813 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7220 (mmtp) REVERT: A 930 MET cc_start: 0.4118 (mmp) cc_final: 0.2435 (mtt) REVERT: A 936 MET cc_start: 0.3937 (mtp) cc_final: 0.2617 (mmm) REVERT: B 9 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6465 (mmtt) REVERT: B 134 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.7246 (p90) REVERT: B 341 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 624 GLU cc_start: 0.8144 (tp30) cc_final: 0.7798 (tm-30) REVERT: B 913 MET cc_start: 0.4455 (mpp) cc_final: 0.3970 (mmm) REVERT: C 78 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7421 (t0) REVERT: C 101 ASP cc_start: 0.8558 (m-30) cc_final: 0.8286 (m-30) REVERT: C 143 TRP cc_start: 0.7242 (OUTLIER) cc_final: 0.6912 (t60) REVERT: C 281 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 426 GLU cc_start: 0.8011 (pp20) cc_final: 0.7297 (mm-30) REVERT: C 475 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6965 (mm-40) REVERT: C 704 MET cc_start: 0.1861 (ppp) cc_final: 0.0838 (ptp) REVERT: C 784 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7130 (pt0) REVERT: C 866 MET cc_start: 0.4242 (mtp) cc_final: 0.3320 (tpp) REVERT: C 924 GLU cc_start: 0.3098 (OUTLIER) cc_final: 0.2759 (mp0) REVERT: D 181 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: D 291 ASP cc_start: 0.8201 (p0) cc_final: 0.7777 (m-30) REVERT: D 327 LYS cc_start: 0.5553 (mmtp) cc_final: 0.4400 (tttt) REVERT: D 391 ASN cc_start: 0.6382 (m-40) cc_final: 0.5765 (m110) REVERT: D 463 ILE cc_start: 0.4728 (OUTLIER) cc_final: 0.3178 (tp) REVERT: D 521 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.6403 (t0) REVERT: D 557 LYS cc_start: -0.2519 (OUTLIER) cc_final: -0.3271 (ttpp) REVERT: D 649 TYR cc_start: 0.4401 (t80) cc_final: 0.3834 (t80) REVERT: D 709 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6328 (t80) outliers start: 111 outliers final: 65 residues processed: 364 average time/residue: 0.4324 time to fit residues: 259.6674 Evaluate side-chains 340 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 260 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 ASP 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 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 81 SER 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 704 MET Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 281 ASP 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 709 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 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 459 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 709 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 329 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 210 optimal weight: 0.6980 chunk 171 optimal weight: 0.4980 chunk 347 optimal weight: 9.9990 chunk 276 optimal weight: 0.6980 chunk 349 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 224 ASN D 477 ASN ** D 609 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.186528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118725 restraints weight = 51527.140| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.17 r_work: 0.3277 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32121 Z= 0.111 Angle : 0.512 15.285 43234 Z= 0.268 Chirality : 0.039 0.227 4593 Planarity : 0.003 0.066 5492 Dihedral : 4.005 54.908 4124 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.25 % Allowed : 24.52 % Favored : 73.23 % 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: 2478 sheet: -3.50 (0.91), residues: 20 loop : 0.08 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 143 HIS 0.009 0.001 HIS C 979 PHE 0.026 0.001 PHE D 652 TYR 0.030 0.001 TYR D 552 ARG 0.008 0.000 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1764) hydrogen bonds : angle 4.24201 ( 5091) covalent geometry : bond 0.00247 (32121) covalent geometry : angle 0.51237 (43234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 277 time to evaluate : 5.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8876 (tpp) cc_final: 0.8532 (ttm) REVERT: A 421 MET cc_start: 0.7729 (mtp) cc_final: 0.7502 (mtp) REVERT: A 447 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8134 (ptm160) REVERT: A 677 ARG cc_start: 0.7681 (ptt90) cc_final: 0.7033 (ttt-90) REVERT: A 743 TYR cc_start: 0.7350 (m-80) cc_final: 0.7143 (m-80) REVERT: A 778 PHE cc_start: 0.8398 (t80) cc_final: 0.7953 (t80) REVERT: A 813 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: A 930 MET cc_start: 0.4078 (mmp) cc_final: 0.2418 (mtt) REVERT: A 936 MET cc_start: 0.4011 (mtp) cc_final: 0.2651 (mmm) REVERT: B 9 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6673 (mmtt) REVERT: B 134 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7038 (p90) REVERT: B 341 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 624 GLU cc_start: 0.7857 (tp30) cc_final: 0.7488 (tm-30) REVERT: B 930 MET cc_start: 0.4925 (mmp) cc_final: 0.3870 (ppp) REVERT: B 976 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.4166 (tmm) REVERT: C 101 ASP cc_start: 0.8310 (m-30) cc_final: 0.7978 (m-30) REVERT: C 143 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.6598 (t60) REVERT: C 281 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7327 (t0) REVERT: C 357 MET cc_start: 0.7477 (mtp) cc_final: 0.7221 (mmm) REVERT: C 396 MET cc_start: 0.5614 (mmm) cc_final: 0.5385 (mmm) REVERT: C 426 GLU cc_start: 0.8068 (pp20) cc_final: 0.7343 (mm-30) REVERT: C 441 PHE cc_start: 0.8258 (m-10) cc_final: 0.7617 (m-80) REVERT: C 654 ASN cc_start: 0.5185 (OUTLIER) cc_final: 0.4925 (m-40) REVERT: C 704 MET cc_start: 0.1897 (ppp) cc_final: 0.0995 (ptp) REVERT: C 784 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7125 (pt0) REVERT: C 866 MET cc_start: 0.4224 (mtp) cc_final: 0.3350 (tpp) REVERT: C 924 GLU cc_start: 0.3233 (OUTLIER) cc_final: 0.2806 (mp0) REVERT: D 327 LYS cc_start: 0.5399 (mmtp) cc_final: 0.4216 (tptt) REVERT: D 391 ASN cc_start: 0.6187 (m-40) cc_final: 0.5559 (m110) REVERT: D 463 ILE cc_start: 0.4555 (OUTLIER) cc_final: 0.3153 (tp) REVERT: D 709 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.6208 (t80) outliers start: 78 outliers final: 47 residues processed: 341 average time/residue: 0.5145 time to fit residues: 291.7150 Evaluate side-chains 319 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP 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 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 281 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN 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 277 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 341 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 356 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 325 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.182116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110528 restraints weight = 51694.918| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.70 r_work: 0.3189 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 32121 Z= 0.249 Angle : 0.596 14.696 43234 Z= 0.311 Chirality : 0.043 0.294 4593 Planarity : 0.004 0.067 5492 Dihedral : 4.167 22.117 4122 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.69 % Allowed : 24.37 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3689 helix: 0.96 (0.10), residues: 2487 sheet: -3.58 (0.93), residues: 20 loop : -0.06 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 143 HIS 0.009 0.001 HIS C 979 PHE 0.025 0.002 PHE D 708 TYR 0.039 0.002 TYR D 649 ARG 0.006 0.001 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1764) hydrogen bonds : angle 4.46614 ( 5091) covalent geometry : bond 0.00596 (32121) covalent geometry : angle 0.59614 (43234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 271 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: A 98 MET cc_start: 0.9144 (tpp) cc_final: 0.8782 (ttm) REVERT: A 354 PHE cc_start: 0.8475 (t80) cc_final: 0.8267 (t80) REVERT: A 447 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8102 (ptm160) REVERT: A 569 MET cc_start: 0.6093 (mmm) cc_final: 0.5892 (mmm) REVERT: A 677 ARG cc_start: 0.7974 (ptt90) cc_final: 0.7334 (ttt-90) REVERT: A 743 TYR cc_start: 0.7738 (m-80) cc_final: 0.7410 (m-80) REVERT: A 813 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7292 (mmtp) REVERT: A 930 MET cc_start: 0.4230 (mmp) cc_final: 0.2560 (mtt) REVERT: A 936 MET cc_start: 0.3866 (mtp) cc_final: 0.3022 (mmm) REVERT: A 979 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7330 (p90) REVERT: B 134 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.7239 (p90) REVERT: B 339 HIS cc_start: 0.8624 (m-70) cc_final: 0.8412 (m-70) REVERT: B 341 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8187 (mm-30) REVERT: B 580 SER cc_start: 0.8531 (m) cc_final: 0.8145 (t) REVERT: B 624 GLU cc_start: 0.8095 (tp30) cc_final: 0.7698 (tm-30) REVERT: C 143 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6702 (t60) REVERT: C 281 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7517 (t0) REVERT: C 396 MET cc_start: 0.5705 (mmm) cc_final: 0.5292 (mmm) REVERT: C 426 GLU cc_start: 0.8132 (pp20) cc_final: 0.7399 (mm-30) REVERT: C 704 MET cc_start: 0.1610 (ppp) cc_final: 0.0728 (ptp) REVERT: C 784 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7202 (pt0) REVERT: C 866 MET cc_start: 0.4177 (mtp) cc_final: 0.3299 (tpp) REVERT: C 924 GLU cc_start: 0.3022 (OUTLIER) cc_final: 0.2736 (mp0) REVERT: D 291 ASP cc_start: 0.8273 (p0) cc_final: 0.7766 (m-30) REVERT: D 327 LYS cc_start: 0.5647 (mmtp) cc_final: 0.4483 (tttt) REVERT: D 463 ILE cc_start: 0.4554 (OUTLIER) cc_final: 0.3281 (tp) REVERT: D 477 ASN cc_start: 0.8095 (m110) cc_final: 0.7417 (m-40) REVERT: D 649 TYR cc_start: 0.4388 (t80) cc_final: 0.4074 (t80) REVERT: D 709 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6467 (t80) outliers start: 93 outliers final: 64 residues processed: 348 average time/residue: 0.4452 time to fit residues: 254.0621 Evaluate side-chains 323 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 562 THR 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 691 ILE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 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 328 ILE 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 897 ILE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 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 281 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 625 TYR Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 95 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 154 optimal weight: 0.0070 chunk 251 optimal weight: 20.0000 chunk 249 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 313 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.184577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112641 restraints weight = 51622.865| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.54 r_work: 0.3279 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32121 Z= 0.121 Angle : 0.533 14.988 43234 Z= 0.278 Chirality : 0.039 0.255 4593 Planarity : 0.003 0.066 5492 Dihedral : 4.026 21.708 4122 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 25.06 % Favored : 72.83 % 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: 1.03 (0.14), residues: 3689 helix: 1.11 (0.10), residues: 2485 sheet: -3.76 (0.91), residues: 20 loop : 0.04 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 143 HIS 0.009 0.001 HIS C 979 PHE 0.029 0.001 PHE C 708 TYR 0.035 0.001 TYR D 552 ARG 0.006 0.000 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 1764) hydrogen bonds : angle 4.31704 ( 5091) covalent geometry : bond 0.00277 (32121) covalent geometry : angle 0.53315 (43234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: A 98 MET cc_start: 0.9050 (tpp) cc_final: 0.8709 (ttm) REVERT: A 447 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (mtp180) REVERT: A 677 ARG cc_start: 0.7897 (ptt90) cc_final: 0.7238 (ttt-90) REVERT: A 743 TYR cc_start: 0.7471 (m-80) cc_final: 0.7216 (m-80) REVERT: A 813 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7229 (mmtp) REVERT: A 930 MET cc_start: 0.4292 (mmp) cc_final: 0.2560 (mtt) REVERT: A 936 MET cc_start: 0.3955 (mtp) cc_final: 0.3148 (mmm) REVERT: B 9 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6531 (mmtt) REVERT: B 134 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.7313 (p90) REVERT: B 341 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 624 GLU cc_start: 0.8120 (tp30) cc_final: 0.7778 (tm-30) REVERT: B 1004 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.4896 (m-80) REVERT: C 101 ASP cc_start: 0.8417 (m-30) cc_final: 0.8069 (m-30) REVERT: C 143 TRP cc_start: 0.7172 (OUTLIER) cc_final: 0.6637 (t60) REVERT: C 281 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7592 (t0) REVERT: C 396 MET cc_start: 0.5862 (mmm) cc_final: 0.5593 (mmm) REVERT: C 426 GLU cc_start: 0.8100 (pp20) cc_final: 0.7365 (mm-30) REVERT: C 704 MET cc_start: 0.1561 (ppp) cc_final: 0.0766 (ptt) REVERT: C 866 MET cc_start: 0.4247 (mtp) cc_final: 0.3391 (tpp) REVERT: C 924 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2776 (mp0) REVERT: D 350 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6717 (mmtt) REVERT: D 396 MET cc_start: 0.4692 (tpt) cc_final: 0.4390 (tpt) REVERT: D 463 ILE cc_start: 0.4356 (OUTLIER) cc_final: 0.3168 (tp) REVERT: D 709 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6329 (t80) outliers start: 73 outliers final: 51 residues processed: 330 average time/residue: 0.4241 time to fit residues: 229.2834 Evaluate side-chains 323 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 260 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS 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 691 ILE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN 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 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 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 281 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 625 TYR Chi-restraints excluded: chain C residue 709 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 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 211 optimal weight: 0.3980 chunk 238 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 391 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.184520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114193 restraints weight = 51569.934| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.82 r_work: 0.3242 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32121 Z= 0.126 Angle : 0.538 13.961 43234 Z= 0.281 Chirality : 0.039 0.293 4593 Planarity : 0.003 0.066 5492 Dihedral : 3.991 23.091 4122 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.96 % Allowed : 25.35 % Favored : 72.68 % 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: 1.09 (0.14), residues: 3689 helix: 1.16 (0.10), residues: 2483 sheet: -3.82 (0.92), residues: 20 loop : 0.05 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 143 HIS 0.024 0.001 HIS D 349 PHE 0.028 0.001 PHE C 712 TYR 0.046 0.001 TYR D 649 ARG 0.006 0.000 ARG D 348 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 1764) hydrogen bonds : angle 4.27107 ( 5091) covalent geometry : bond 0.00290 (32121) covalent geometry : angle 0.53833 (43234) ********************** REFINEMENT MACRO_CYCLE 10 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 330 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8892 (tpp) cc_final: 0.8550 (ttm) REVERT: A 447 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8171 (ptm160) REVERT: A 569 MET cc_start: 0.5896 (mmm) cc_final: 0.5671 (mmm) REVERT: A 677 ARG cc_start: 0.7863 (ptt90) cc_final: 0.7181 (ttt-90) REVERT: A 743 TYR cc_start: 0.7440 (m-80) cc_final: 0.7129 (m-80) REVERT: A 813 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7265 (mmtp) REVERT: A 930 MET cc_start: 0.4271 (mmp) cc_final: 0.2565 (mtt) REVERT: A 936 MET cc_start: 0.3920 (mtp) cc_final: 0.3153 (mmm) REVERT: A 979 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7222 (p90) REVERT: B 9 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6518 (mmtt) REVERT: B 134 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7096 (p90) REVERT: B 341 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7902 (mm-30) REVERT: B 624 GLU cc_start: 0.7882 (tp30) cc_final: 0.7505 (tm-30) REVERT: B 1004 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: C 101 ASP cc_start: 0.8196 (m-30) cc_final: 0.7836 (m-30) REVERT: C 143 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.6275 (t60) REVERT: C 281 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7332 (t0) REVERT: C 304 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6645 (pttt) REVERT: C 396 MET cc_start: 0.5680 (mmm) cc_final: 0.5324 (mmm) REVERT: C 426 GLU cc_start: 0.8111 (pp20) cc_final: 0.7378 (mm-30) REVERT: C 704 MET cc_start: 0.1576 (ppp) cc_final: 0.0778 (ptt) REVERT: C 866 MET cc_start: 0.4227 (mtp) cc_final: 0.3377 (tpp) REVERT: C 924 GLU cc_start: 0.3127 (OUTLIER) cc_final: 0.2796 (mp0) REVERT: D 389 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6985 (mm-30) REVERT: D 463 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3176 (tp) REVERT: D 709 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6380 (t80) REVERT: D 976 MET cc_start: 0.0654 (tmm) cc_final: -0.2569 (ppp) outliers start: 68 outliers final: 48 residues processed: 317 average time/residue: 0.4356 time to fit residues: 226.7798 Evaluate side-chains 315 residues out of total 3463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 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 281 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 625 TYR Chi-restraints excluded: chain C residue 709 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 C residue 1001 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 64 optimal weight: 0.7980 chunk 316 optimal weight: 0.9980 chunk 321 optimal weight: 10.0000 chunk 302 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 191 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 372 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.184867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114944 restraints weight = 51354.797| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.68 r_work: 0.3254 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32121 Z= 0.121 Angle : 0.535 14.530 43234 Z= 0.278 Chirality : 0.039 0.297 4593 Planarity : 0.003 0.065 5492 Dihedral : 3.966 22.745 4122 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.11 % Allowed : 25.24 % Favored : 72.65 % 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: 1.09 (0.14), residues: 3689 helix: 1.18 (0.10), residues: 2485 sheet: -3.08 (0.78), residues: 32 loop : 0.04 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 143 HIS 0.014 0.001 HIS D 339 PHE 0.033 0.001 PHE C 708 TYR 0.046 0.001 TYR D 452 ARG 0.008 0.000 ARG C 587 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 1764) hydrogen bonds : angle 4.24815 ( 5091) covalent geometry : bond 0.00274 (32121) covalent geometry : angle 0.53540 (43234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23413.26 seconds wall clock time: 409 minutes 25.82 seconds (24565.82 seconds total)