Starting phenix.real_space_refine on Sat Feb 7 13:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyd_37924/02_2026/8wyd_37924.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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 130 5.16 5 C 21894 2.51 5 N 5452 2.21 5 O 6289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33765 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7964 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 7955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7955 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 5 Chain: "D" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Time building chain proxies: 7.19, per 1000 atoms: 0.21 Number of scatterers: 33765 At special positions: 0 Unit cell: (100.894, 129.012, 264.64, 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 130 16.00 O 6289 8.00 N 5452 7.00 C 21894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7734 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 14 sheets defined 68.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.616A pdb=" N MET A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.873A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.865A 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 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.527A 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 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.551A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) 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: 3.612A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.650A 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 321 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.616A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.637A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 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 495 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.562A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 removed outlier: 4.153A pdb=" N PHE A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.558A 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 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.952A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.035A 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 743 Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 768 through 787 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.783A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.155A 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 950 through 954 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 976 through 991 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: 3.941A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.726A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.595A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.154A 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 removed outlier: 3.527A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.607A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.512A pdb=" N TYR B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) 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: 3.657A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.711A 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: 3.720A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.569A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.993A 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 367 through 371 Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' 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 495 removed outlier: 3.651A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.452A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.553A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) 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: 3.605A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.754A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.793A 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 743 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.564A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.920A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.551A 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 839 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.563A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (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: 3.547A pdb=" N PHE B 933 " --> pdb=" O MET B 930 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.774A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 959 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 992 Processing helix chain 'B' and resid 993 through 1002 Processing helix chain 'E' and resid 95 through 107 removed outlier: 3.559A pdb=" N HIS E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.752A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.630A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.669A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.295A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) 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: 3.779A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.654A 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 296 removed outlier: 3.546A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.703A 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 373 removed outlier: 3.788A pdb=" N ARG C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 371 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 373' Processing helix chain 'C' and resid 374 through 392 removed outlier: 3.770A pdb=" N GLU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.571A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 445 removed outlier: 3.543A pdb=" N ASP C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 469 through 495 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'C' and resid 508 through 520 Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 546 removed outlier: 3.681A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 550 removed outlier: 4.123A pdb=" N PHE C 550 " --> pdb=" O ASP C 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 550' Processing helix chain 'C' and resid 551 through 572 Processing helix chain 'C' and resid 581 through 598 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.569A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 628 Processing helix chain 'C' and resid 648 through 659 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: 3.955A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (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 761 removed outlier: 3.544A pdb=" N LEU C 761 " --> pdb=" O TRP C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.744A pdb=" N ILE C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 812 removed outlier: 3.774A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 812 " --> pdb=" O ILE C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.524A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 878 through 897 Processing helix chain 'C' and resid 912 through 922 Processing helix chain 'C' and resid 929 through 934 removed outlier: 4.072A pdb=" N ILE C 934 " --> pdb=" O GLU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 945 removed outlier: 3.654A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 954 Processing helix chain 'C' and resid 955 through 956 No H-bonds generated for 'chain 'C' and resid 955 through 956' Processing helix chain 'C' and resid 957 through 962 removed outlier: 3.950A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 962 " --> pdb=" O TRP C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 962' Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 976 through 991 Processing helix chain 'C' and resid 994 through 1004 Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.137A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.624A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 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: 3.836A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 179 through 183 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 210 Processing helix chain 'D' and resid 222 through 234 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 298 removed outlier: 3.660A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 321 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.828A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 3.516A pdb=" N SER D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 374 through 391 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.561A 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 462 Processing helix chain 'D' and resid 468 through 495 removed outlier: 3.722A pdb=" N TYR D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 524 through 530 removed outlier: 4.582A pdb=" N PHE D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.339A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 580 through 598 Processing helix chain 'D' and resid 600 through 604 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 removed outlier: 3.600A pdb=" N GLU D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.897A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (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 761 removed outlier: 3.545A pdb=" N TYR D 755 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 785 Processing helix chain 'D' and resid 786 through 788 No H-bonds generated for 'chain 'D' and resid 786 through 788' Processing helix chain 'D' and resid 800 through 813 removed outlier: 4.037A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 805 " --> pdb=" O SER D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 840 removed outlier: 3.537A pdb=" N PHE D 837 " --> pdb=" O LYS D 833 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 855 removed outlier: 3.860A pdb=" N SER D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.501A pdb=" N LEU D 865 " --> pdb=" O ASN D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 895 removed outlier: 3.779A pdb=" N GLU D 882 " --> pdb=" O THR D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 922 removed outlier: 3.525A pdb=" N TRP D 919 " --> pdb=" O THR D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 934 removed outlier: 3.569A pdb=" N PHE D 933 " --> pdb=" O MET D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 955 through 962 removed outlier: 3.519A pdb=" N TYR D 962 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 976 through 992 Processing helix chain 'D' and resid 993 through 1004 removed outlier: 3.676A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.591A pdb=" N ARG F 105 " --> pdb=" O HIS F 101 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER F 107 " --> pdb=" O SER F 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.254A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.226A 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 'A' and resid 574 through 575 removed outlier: 5.899A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.231A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.730A pdb=" N ILE E 66 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU E 38 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU E 33 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN E 40 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE E 31 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE E 44 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL E 27 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU E 28 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA E 86 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP E 30 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.730A pdb=" N ILE E 66 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU E 115 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE E 44 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL E 117 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS E 46 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.231A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AB1, first strand: chain 'C' and resid 573 through 575 removed outlier: 3.759A pdb=" N THR F 22 " --> pdb=" O HIS F 17 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.181A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'F' and resid 71 through 72 removed outlier: 7.230A pdb=" N GLU F 38 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU F 33 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE F 44 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 27 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU F 28 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA F 86 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP F 30 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 71 through 72 removed outlier: 10.182A pdb=" N GLU F 115 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE F 44 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL F 117 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS F 46 " --> pdb=" O VAL F 117 " (cutoff:3.500A) 1846 hydrogen bonds defined for protein. 5286 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: 6.51 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10662 1.34 - 1.46: 7950 1.46 - 1.58: 15722 1.58 - 1.70: 1 1.70 - 1.81: 214 Bond restraints: 34549 Sorted by residual: bond pdb=" CG PRO C 745 " pdb=" CD PRO C 745 " ideal model delta sigma weight residual 1.503 1.325 0.178 3.40e-02 8.65e+02 2.74e+01 bond pdb=" CB PRO C 843 " pdb=" CG PRO C 843 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.24e+00 bond pdb=" C ASP B 111 " pdb=" N LYS B 112 " ideal model delta sigma weight residual 1.329 1.294 0.035 1.35e-02 5.49e+03 6.80e+00 bond pdb=" N ASN C 299 " pdb=" CA ASN C 299 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.34e+00 bond pdb=" N GLU C 298 " pdb=" CA GLU C 298 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.20e+00 ... (remaining 34544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 46380 3.42 - 6.85: 149 6.85 - 10.27: 14 10.27 - 13.70: 2 13.70 - 17.12: 2 Bond angle restraints: 46547 Sorted by residual: angle pdb=" CA PRO C 843 " pdb=" N PRO C 843 " pdb=" CD PRO C 843 " ideal model delta sigma weight residual 112.00 94.88 17.12 1.40e+00 5.10e-01 1.50e+02 angle pdb=" N PRO C 745 " pdb=" CD PRO C 745 " pdb=" CG PRO C 745 " ideal model delta sigma weight residual 103.20 88.24 14.96 1.50e+00 4.44e-01 9.95e+01 angle pdb=" CA PRO E 50 " pdb=" N PRO E 50 " pdb=" CD PRO E 50 " ideal model delta sigma weight residual 112.00 103.00 9.00 1.40e+00 5.10e-01 4.13e+01 angle pdb=" CA PRO C 745 " pdb=" CB PRO C 745 " pdb=" CG PRO C 745 " ideal model delta sigma weight residual 104.50 93.50 11.00 1.90e+00 2.77e-01 3.35e+01 angle pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" CD PRO C 745 " ideal model delta sigma weight residual 112.00 104.09 7.91 1.40e+00 5.10e-01 3.19e+01 ... (remaining 46542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 17056 17.74 - 35.48: 2572 35.48 - 53.22: 738 53.22 - 70.96: 146 70.96 - 88.70: 49 Dihedral angle restraints: 20561 sinusoidal: 8552 harmonic: 12009 Sorted by residual: dihedral pdb=" CA LYS E 19 " pdb=" C LYS E 19 " pdb=" N ILE E 20 " pdb=" CA ILE E 20 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS B 974 " pdb=" C LYS B 974 " pdb=" N HIS B 975 " pdb=" CA HIS B 975 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU B1000 " pdb=" C LEU B1000 " pdb=" N MET B1001 " pdb=" CA MET B1001 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 20558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4393 0.061 - 0.122: 537 0.122 - 0.182: 26 0.182 - 0.243: 1 0.243 - 0.304: 2 Chirality restraints: 4959 Sorted by residual: chirality pdb=" CB ILE C 302 " pdb=" CA ILE C 302 " pdb=" CG1 ILE C 302 " pdb=" CG2 ILE C 302 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA GLN C 297 " pdb=" N GLN C 297 " pdb=" C GLN C 297 " pdb=" CB GLN C 297 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE C 808 " pdb=" CA ILE C 808 " pdb=" CG1 ILE C 808 " pdb=" CG2 ILE C 808 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4956 not shown) Planarity restraints: 5915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 842 " 0.103 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO C 843 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO C 843 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 843 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 49 " -0.095 5.00e-02 4.00e+02 1.38e-01 3.07e+01 pdb=" N PRO E 50 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO E 50 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 50 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 919 " 0.025 2.00e-02 2.50e+03 2.19e-02 1.19e+01 pdb=" CG TRP B 919 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 919 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 919 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 919 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 919 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 919 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 919 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 919 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 919 " 0.001 2.00e-02 2.50e+03 ... (remaining 5912 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 433 2.63 - 3.20: 30870 3.20 - 3.76: 55395 3.76 - 4.33: 79010 4.33 - 4.90: 126142 Nonbonded interactions: 291850 Sorted by model distance: nonbonded pdb=" OH TYR C 709 " pdb=" OD2 ASP C 748 " model vdw 2.060 3.040 nonbonded pdb=" OG SER D 366 " pdb=" OE1 GLU D 369 " model vdw 2.113 3.040 nonbonded pdb=" OG SER B 366 " pdb=" OE1 GLU B 369 " model vdw 2.124 3.040 nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU A 668 " pdb=" OH TYR A 725 " model vdw 2.146 3.040 ... (remaining 291845 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 15 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005)) selection = (chain 'B' and (resid 15 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) selection = (chain 'C' and (resid 15 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005)) selection = (chain 'D' and (resid 15 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.380 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.003 0.178 34549 Z= 0.145 Angle : 0.581 17.124 46547 Z= 0.322 Chirality : 0.040 0.304 4959 Planarity : 0.004 0.140 5915 Dihedral : 18.489 88.698 12827 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.68 % Allowed : 33.07 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 3987 helix: 0.82 (0.10), residues: 2454 sheet: 0.11 (0.57), residues: 68 loop : 0.04 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 517 TYR 0.024 0.001 TYR D 962 PHE 0.028 0.001 PHE A 837 TRP 0.060 0.002 TRP B 919 HIS 0.009 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00340 (34549) covalent geometry : angle 0.58101 (46547) hydrogen bonds : bond 0.18248 ( 1829) hydrogen bonds : angle 6.50114 ( 5286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 597 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7005 (mp0) REVERT: A 396 MET cc_start: 0.7944 (mmm) cc_final: 0.7710 (mmm) REVERT: A 399 ASP cc_start: 0.7279 (m-30) cc_final: 0.6510 (t0) REVERT: A 553 ASP cc_start: 0.8119 (t0) cc_final: 0.7905 (m-30) REVERT: A 590 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: A 646 PHE cc_start: 0.8357 (p90) cc_final: 0.7844 (p90) REVERT: A 729 SER cc_start: 0.7938 (p) cc_final: 0.7399 (p) REVERT: A 731 GLU cc_start: 0.7874 (tt0) cc_final: 0.7534 (pp20) REVERT: A 738 LYS cc_start: 0.7071 (tptp) cc_final: 0.6409 (ttmm) REVERT: A 812 GLU cc_start: 0.6364 (pt0) cc_final: 0.5588 (tp30) REVERT: A 833 LYS cc_start: 0.5796 (mmmm) cc_final: 0.5244 (ttmm) REVERT: A 912 TYR cc_start: 0.6952 (m-80) cc_final: 0.6663 (m-80) REVERT: A 953 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6562 (pttp) REVERT: A 976 MET cc_start: 0.6312 (pmm) cc_final: 0.5947 (ptt) REVERT: A 1003 TYR cc_start: 0.8337 (m-80) cc_final: 0.8124 (m-80) REVERT: B 134 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8084 (p90) REVERT: B 165 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7460 (mtp85) REVERT: B 179 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7950 (mptt) REVERT: B 226 ASN cc_start: 0.7966 (m110) cc_final: 0.7606 (m-40) REVERT: B 434 ASP cc_start: 0.7912 (m-30) cc_final: 0.7377 (m-30) REVERT: B 526 ASP cc_start: 0.7293 (m-30) cc_final: 0.6863 (p0) REVERT: B 557 LYS cc_start: 0.8817 (mttm) cc_final: 0.8552 (mttp) REVERT: B 560 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 616 MET cc_start: 0.8969 (mmm) cc_final: 0.8751 (mmm) REVERT: B 629 ARG cc_start: 0.6865 (ttp80) cc_final: 0.5352 (mmm160) REVERT: B 647 MET cc_start: 0.8043 (mtp) cc_final: 0.7604 (mtp) REVERT: B 677 ARG cc_start: 0.7356 (ptt180) cc_final: 0.6905 (ptm160) REVERT: B 693 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6682 (mp0) REVERT: B 710 THR cc_start: 0.8876 (m) cc_final: 0.8628 (p) REVERT: B 746 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 774 ILE cc_start: 0.7676 (mm) cc_final: 0.7403 (mt) REVERT: B 776 ASP cc_start: 0.7882 (t70) cc_final: 0.7560 (OUTLIER) REVERT: B 857 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7191 (mptt) REVERT: B 921 PHE cc_start: 0.7884 (t80) cc_final: 0.7350 (t80) REVERT: B 957 SER cc_start: 0.7579 (m) cc_final: 0.7375 (t) REVERT: B 969 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7899 (tttp) REVERT: E 28 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6130 (mp0) REVERT: E 58 ASP cc_start: 0.6470 (m-30) cc_final: 0.6259 (m-30) REVERT: E 62 SER cc_start: 0.8312 (p) cc_final: 0.8039 (m) REVERT: C 134 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8033 (p90) REVERT: C 226 ASN cc_start: 0.7460 (m-40) cc_final: 0.6930 (m-40) REVERT: C 249 ASP cc_start: 0.7465 (m-30) cc_final: 0.7241 (m-30) REVERT: C 285 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.5696 (tpp80) REVERT: C 421 MET cc_start: -0.1919 (mtm) cc_final: -0.2163 (pmm) REVERT: C 647 MET cc_start: 0.0311 (tpt) cc_final: -0.0279 (tpp) REVERT: D 32 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7480 (mm-30) REVERT: D 175 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7820 (mtm180) REVERT: D 930 MET cc_start: 0.0737 (tpt) cc_final: 0.0379 (tmm) outliers start: 100 outliers final: 27 residues processed: 684 average time/residue: 0.6713 time to fit residues: 548.2764 Evaluate side-chains 368 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 339 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain F residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 523 ASN A 591 ASN A 666 ASN A 765 ASN A 810 HIS A 881 HIS A 979 HIS A1002 ASN B 39 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 377 GLN B 491 GLN B 493 ASN B 765 ASN B 782 GLN B 834 GLN B 939 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN C 89 GLN C 196 ASN C 523 ASN C 711 GLN C1002 ASN D 25 ASN D 521 ASN D 711 GLN D 927 ASN D 939 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.225716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139146 restraints weight = 41825.843| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.40 r_work: 0.3365 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34549 Z= 0.268 Angle : 0.652 12.190 46547 Z= 0.343 Chirality : 0.045 0.236 4959 Planarity : 0.005 0.069 5915 Dihedral : 5.108 53.884 4477 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 6.35 % Allowed : 26.94 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 3987 helix: 0.75 (0.10), residues: 2506 sheet: -0.82 (0.52), residues: 68 loop : -0.05 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 669 TYR 0.029 0.002 TYR C 482 PHE 0.022 0.002 PHE D 933 TRP 0.021 0.002 TRP D 958 HIS 0.011 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00631 (34549) covalent geometry : angle 0.65249 (46547) hydrogen bonds : bond 0.04576 ( 1829) hydrogen bonds : angle 4.95790 ( 5286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 372 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8554 (m-30) cc_final: 0.8339 (m-30) REVERT: A 281 ASP cc_start: 0.8331 (t0) cc_final: 0.8124 (t0) REVERT: A 509 ASP cc_start: 0.7990 (m-30) cc_final: 0.7771 (m-30) REVERT: A 512 LEU cc_start: 0.7777 (mm) cc_final: 0.7466 (mt) REVERT: A 516 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: A 518 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 566 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8423 (mtt-85) REVERT: A 731 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7958 (pp20) REVERT: A 763 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6598 (mmtt) REVERT: A 785 LYS cc_start: 0.8586 (mttt) cc_final: 0.8237 (mtmm) REVERT: A 812 GLU cc_start: 0.6708 (pt0) cc_final: 0.5821 (tp30) REVERT: A 818 LYS cc_start: 0.7996 (mptt) cc_final: 0.7740 (mmtt) REVERT: A 833 LYS cc_start: 0.6201 (mmmm) cc_final: 0.5906 (tttm) REVERT: B 35 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7552 (mm-30) REVERT: B 90 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8280 (mt) REVERT: B 165 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7775 (mtp85) REVERT: B 179 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8020 (mptt) REVERT: B 279 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: B 363 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 509 ASP cc_start: 0.8098 (t0) cc_final: 0.7759 (m-30) REVERT: B 526 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 549 GLN cc_start: 0.8576 (mt0) cc_final: 0.8329 (pt0) REVERT: B 587 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8172 (ttt180) REVERT: B 629 ARG cc_start: 0.8017 (ttp80) cc_final: 0.6530 (mmm160) REVERT: B 662 ASP cc_start: 0.7954 (m-30) cc_final: 0.7754 (t0) REVERT: B 675 LYS cc_start: 0.6529 (tmtt) cc_final: 0.5741 (tptp) REVERT: B 677 ARG cc_start: 0.8019 (ptt180) cc_final: 0.7361 (ptm160) REVERT: B 738 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8285 (ttmt) REVERT: B 754 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8996 (ttm110) REVERT: B 852 HIS cc_start: 0.7409 (t-90) cc_final: 0.7141 (t-170) REVERT: B 857 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7302 (mptt) REVERT: B 930 MET cc_start: 0.7937 (mtt) cc_final: 0.7654 (ptp) REVERT: B 969 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8076 (tttp) REVERT: E 28 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6379 (mp0) REVERT: E 62 SER cc_start: 0.8759 (p) cc_final: 0.8444 (m) REVERT: C 34 THR cc_start: 0.7970 (m) cc_final: 0.7670 (p) REVERT: C 87 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8657 (mp) REVERT: C 176 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8284 (mtmt) REVERT: C 516 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.4739 (pt0) REVERT: C 520 THR cc_start: 0.3813 (OUTLIER) cc_final: 0.3419 (m) REVERT: C 629 ARG cc_start: 0.1526 (OUTLIER) cc_final: 0.1125 (mtp85) REVERT: C 647 MET cc_start: -0.0808 (tpt) cc_final: -0.1066 (tpp) REVERT: C 681 GLN cc_start: 0.3286 (OUTLIER) cc_final: 0.2576 (pm20) REVERT: C 866 MET cc_start: 0.4101 (tmm) cc_final: 0.3415 (tpt) REVERT: C 912 TYR cc_start: 0.1471 (OUTLIER) cc_final: 0.0519 (t80) REVERT: D 21 MET cc_start: 0.5363 (pp-130) cc_final: 0.5089 (pp-130) REVERT: D 134 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8754 (p90) REVERT: D 296 SER cc_start: 0.7854 (t) cc_final: 0.7633 (m) REVERT: D 461 ASN cc_start: 0.6353 (m-40) cc_final: 0.5964 (p0) REVERT: D 478 ARG cc_start: 0.4110 (ttp-170) cc_final: 0.3415 (tmm160) REVERT: D 517 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5165 (tpp-160) REVERT: D 537 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5314 (mppt) REVERT: D 648 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4675 (mp0) REVERT: D 704 MET cc_start: 0.1516 (tpt) cc_final: 0.0882 (mpp) REVERT: D 747 ARG cc_start: -0.0672 (OUTLIER) cc_final: -0.1402 (mtt180) REVERT: D 882 GLU cc_start: -0.0373 (OUTLIER) cc_final: -0.1518 (tt0) REVERT: D 930 MET cc_start: 0.0320 (OUTLIER) cc_final: -0.0029 (tmm) REVERT: D 976 MET cc_start: -0.0395 (OUTLIER) cc_final: -0.1234 (mpp) outliers start: 237 outliers final: 63 residues processed: 557 average time/residue: 0.5640 time to fit residues: 385.3953 Evaluate side-chains 408 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 321 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 979 HIS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 517 ARG Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 983 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 247 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 286 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 0.0970 chunk 344 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 339 optimal weight: 6.9990 chunk 79 optimal weight: 0.0770 chunk 129 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN B 765 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 125 GLN C 224 ASN C 610 GLN D 549 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.228072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142357 restraints weight = 41828.624| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.64 r_work: 0.3404 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34549 Z= 0.122 Angle : 0.514 10.575 46547 Z= 0.272 Chirality : 0.040 0.234 4959 Planarity : 0.003 0.063 5915 Dihedral : 4.360 50.894 4447 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.42 % Allowed : 26.78 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 3987 helix: 1.10 (0.10), residues: 2489 sheet: -1.16 (0.46), residues: 80 loop : 0.05 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 669 TYR 0.023 0.001 TYR C 482 PHE 0.020 0.001 PHE B 916 TRP 0.010 0.001 TRP A 757 HIS 0.006 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00270 (34549) covalent geometry : angle 0.51426 (46547) hydrogen bonds : bond 0.03715 ( 1829) hydrogen bonds : angle 4.60833 ( 5286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 344 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: A 55 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: A 222 ASP cc_start: 0.8595 (m-30) cc_final: 0.8391 (m-30) REVERT: A 281 ASP cc_start: 0.8221 (t0) cc_final: 0.8006 (t0) REVERT: A 310 ASP cc_start: 0.8207 (m-30) cc_final: 0.7886 (m-30) REVERT: A 407 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7566 (mt) REVERT: A 512 LEU cc_start: 0.7616 (mm) cc_final: 0.7254 (mt) REVERT: A 516 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 533 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6842 (t80) REVERT: A 646 PHE cc_start: 0.8508 (p90) cc_final: 0.8276 (p90) REVERT: A 731 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7737 (pp20) REVERT: A 738 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7238 (ttmm) REVERT: A 763 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6613 (mptt) REVERT: A 785 LYS cc_start: 0.8469 (mttt) cc_final: 0.8132 (mtpt) REVERT: A 802 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6186 (ppp80) REVERT: A 812 GLU cc_start: 0.6668 (pt0) cc_final: 0.5671 (tp30) REVERT: A 833 LYS cc_start: 0.6050 (mmmm) cc_final: 0.5717 (ttmm) REVERT: A 938 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6215 (OUTLIER) REVERT: A 949 PHE cc_start: 0.6903 (t80) cc_final: 0.6275 (t80) REVERT: B 35 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7416 (mm-30) REVERT: B 165 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7460 (mtp85) REVERT: B 179 LYS cc_start: 0.8587 (mtmm) cc_final: 0.7964 (mptt) REVERT: B 181 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: B 279 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: B 310 ASP cc_start: 0.8646 (m-30) cc_final: 0.8434 (m-30) REVERT: B 328 ILE cc_start: 0.8783 (tp) cc_final: 0.8456 (pt) REVERT: B 335 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: B 363 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 377 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (mm110) REVERT: B 462 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 509 ASP cc_start: 0.8039 (t0) cc_final: 0.7706 (m-30) REVERT: B 526 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7728 (p0) REVERT: B 549 GLN cc_start: 0.8571 (mt0) cc_final: 0.8266 (pt0) REVERT: B 587 ARG cc_start: 0.8467 (ttm110) cc_final: 0.8064 (ttt180) REVERT: B 629 ARG cc_start: 0.7695 (ttp80) cc_final: 0.6306 (mmm160) REVERT: B 662 ASP cc_start: 0.7871 (m-30) cc_final: 0.7655 (t0) REVERT: B 675 LYS cc_start: 0.6345 (tmtt) cc_final: 0.5478 (tptp) REVERT: B 677 ARG cc_start: 0.7955 (ptt180) cc_final: 0.7325 (ptm160) REVERT: B 693 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 731 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: B 738 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8149 (ttmt) REVERT: B 754 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8965 (ttm110) REVERT: B 809 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6998 (mmtm) REVERT: B 852 HIS cc_start: 0.7229 (t-90) cc_final: 0.6957 (t-170) REVERT: B 969 LYS cc_start: 0.8430 (mmpt) cc_final: 0.8012 (tttp) REVERT: E 28 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6246 (mp0) REVERT: E 62 SER cc_start: 0.8732 (p) cc_final: 0.8380 (m) REVERT: C 34 THR cc_start: 0.7760 (m) cc_final: 0.7495 (p) REVERT: C 176 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8232 (mtmt) REVERT: C 511 PHE cc_start: 0.2156 (t80) cc_final: 0.1534 (t80) REVERT: C 558 LEU cc_start: 0.5696 (tp) cc_final: 0.5425 (pp) REVERT: C 629 ARG cc_start: 0.1706 (OUTLIER) cc_final: 0.1248 (mtp85) REVERT: C 647 MET cc_start: -0.0854 (tpt) cc_final: -0.1146 (tpp) REVERT: C 827 LEU cc_start: 0.0529 (OUTLIER) cc_final: -0.0261 (mp) REVERT: C 911 ASP cc_start: 0.0146 (OUTLIER) cc_final: -0.0652 (t70) REVERT: C 912 TYR cc_start: 0.1478 (OUTLIER) cc_final: 0.1256 (m-80) REVERT: C 1001 MET cc_start: -0.0078 (mmt) cc_final: -0.0411 (mpm) REVERT: D 28 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6555 (pm20) REVERT: D 32 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 82 ASP cc_start: 0.7860 (m-30) cc_final: 0.7599 (m-30) REVERT: D 105 LYS cc_start: 0.8652 (tttm) cc_final: 0.8326 (ttpm) REVERT: D 228 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8810 (mm) REVERT: D 478 ARG cc_start: 0.3969 (ttp-170) cc_final: 0.3273 (tmm160) REVERT: D 510 GLU cc_start: 0.3551 (pp20) cc_final: 0.2874 (tt0) REVERT: D 647 MET cc_start: 0.3792 (OUTLIER) cc_final: 0.3283 (mpp) REVERT: D 648 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4789 (mp0) REVERT: D 693 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2935 (mm-30) REVERT: D 704 MET cc_start: 0.1231 (tpt) cc_final: 0.0624 (mpp) REVERT: D 747 ARG cc_start: -0.0712 (OUTLIER) cc_final: -0.1501 (mtt-85) REVERT: D 976 MET cc_start: -0.0299 (OUTLIER) cc_final: -0.1356 (mtt) outliers start: 165 outliers final: 55 residues processed: 467 average time/residue: 0.5998 time to fit residues: 341.4870 Evaluate side-chains 401 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 315 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 928 SER Chi-restraints excluded: chain C residue 991 SER Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 647 MET Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 19 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 79 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 368 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 493 ASN B 711 GLN B 765 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN E 49 ASN E 125 GLN C 224 ASN C 979 HIS D 881 HIS F 88 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.227752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143756 restraints weight = 41969.978| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.40 r_work: 0.3379 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34549 Z= 0.144 Angle : 0.510 9.884 46547 Z= 0.269 Chirality : 0.040 0.224 4959 Planarity : 0.003 0.058 5915 Dihedral : 4.248 48.363 4443 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.61 % Allowed : 26.43 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.13), residues: 3987 helix: 1.19 (0.10), residues: 2491 sheet: -1.37 (0.45), residues: 80 loop : 0.05 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 669 TYR 0.025 0.001 TYR A 951 PHE 0.029 0.001 PHE C 381 TRP 0.014 0.001 TRP A 757 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00333 (34549) covalent geometry : angle 0.51046 (46547) hydrogen bonds : bond 0.03583 ( 1829) hydrogen bonds : angle 4.49054 ( 5286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 338 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: A 222 ASP cc_start: 0.8591 (m-30) cc_final: 0.8338 (m-30) REVERT: A 281 ASP cc_start: 0.8171 (t0) cc_final: 0.7624 (t70) REVERT: A 310 ASP cc_start: 0.8248 (m-30) cc_final: 0.7921 (m-30) REVERT: A 512 LEU cc_start: 0.7601 (mm) cc_final: 0.7254 (mt) REVERT: A 516 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: A 533 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 646 PHE cc_start: 0.8499 (p90) cc_final: 0.8290 (p90) REVERT: A 731 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: A 738 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7368 (ttmm) REVERT: A 763 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6528 (mmtt) REVERT: A 785 LYS cc_start: 0.8483 (mttt) cc_final: 0.7993 (ttmm) REVERT: A 802 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6393 (ppp80) REVERT: A 833 LYS cc_start: 0.6153 (mmmm) cc_final: 0.5801 (ttmm) REVERT: A 938 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: B 35 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7437 (mm-30) REVERT: B 165 ARG cc_start: 0.8017 (mtt90) cc_final: 0.7444 (mtp85) REVERT: B 179 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7933 (mptt) REVERT: B 181 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: B 267 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7299 (mtm-85) REVERT: B 279 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 328 ILE cc_start: 0.8828 (tp) cc_final: 0.8485 (pt) REVERT: B 335 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: B 363 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 509 ASP cc_start: 0.8176 (t0) cc_final: 0.7819 (m-30) REVERT: B 526 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7714 (p0) REVERT: B 549 GLN cc_start: 0.8525 (mt0) cc_final: 0.8246 (pt0) REVERT: B 587 ARG cc_start: 0.8462 (ttm110) cc_final: 0.8076 (ttt180) REVERT: B 626 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 629 ARG cc_start: 0.7748 (ttp80) cc_final: 0.6347 (mmm160) REVERT: B 662 ASP cc_start: 0.8018 (m-30) cc_final: 0.7769 (t0) REVERT: B 677 ARG cc_start: 0.7988 (ptt180) cc_final: 0.7270 (ptm160) REVERT: B 731 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: B 754 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (ttm110) REVERT: B 809 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7065 (mmtm) REVERT: B 852 HIS cc_start: 0.7402 (t-90) cc_final: 0.7142 (t-170) REVERT: B 969 LYS cc_start: 0.8492 (mmpt) cc_final: 0.8155 (tttt) REVERT: B 977 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7170 (mmmm) REVERT: B 1001 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: E 28 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6343 (mp0) REVERT: E 114 LYS cc_start: 0.8578 (tptm) cc_final: 0.8281 (tmtm) REVERT: C 34 THR cc_start: 0.7778 (m) cc_final: 0.7478 (p) REVERT: C 176 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8169 (mtmt) REVERT: C 511 PHE cc_start: 0.2274 (t80) cc_final: 0.1703 (t80) REVERT: C 629 ARG cc_start: 0.1750 (OUTLIER) cc_final: 0.1427 (tpt-90) REVERT: C 647 MET cc_start: -0.0812 (tpt) cc_final: -0.1140 (tpp) REVERT: C 681 GLN cc_start: 0.3206 (OUTLIER) cc_final: 0.2522 (pm20) REVERT: C 816 ILE cc_start: 0.2759 (OUTLIER) cc_final: 0.2402 (pp) REVERT: C 827 LEU cc_start: 0.0868 (OUTLIER) cc_final: 0.0004 (mp) REVERT: C 911 ASP cc_start: -0.0202 (OUTLIER) cc_final: -0.0978 (t70) REVERT: C 913 MET cc_start: -0.0022 (OUTLIER) cc_final: -0.1221 (mpt) REVERT: C 979 HIS cc_start: -0.1294 (OUTLIER) cc_final: -0.1547 (m170) REVERT: C 1001 MET cc_start: -0.0311 (mmt) cc_final: -0.0601 (mmt) REVERT: D 28 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7042 (pm20) REVERT: D 82 ASP cc_start: 0.7974 (m-30) cc_final: 0.7715 (m-30) REVERT: D 105 LYS cc_start: 0.8636 (tttm) cc_final: 0.8283 (ttpm) REVERT: D 228 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8735 (mm) REVERT: D 262 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8215 (mm-30) REVERT: D 511 PHE cc_start: 0.3933 (m-10) cc_final: 0.3709 (m-10) REVERT: D 517 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5236 (tpp-160) REVERT: D 648 GLU cc_start: 0.5083 (OUTLIER) cc_final: 0.4603 (mp0) REVERT: D 704 MET cc_start: 0.1035 (tpt) cc_final: 0.0536 (mpp) REVERT: D 747 ARG cc_start: -0.0956 (OUTLIER) cc_final: -0.1627 (mtt-85) REVERT: D 933 PHE cc_start: 0.2395 (OUTLIER) cc_final: 0.2083 (m-10) REVERT: D 936 MET cc_start: 0.2782 (mtm) cc_final: 0.2406 (mtm) REVERT: D 976 MET cc_start: -0.0513 (OUTLIER) cc_final: -0.1512 (mpp) outliers start: 172 outliers final: 58 residues processed: 471 average time/residue: 0.6427 time to fit residues: 365.4339 Evaluate side-chains 405 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 316 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 979 HIS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 517 ARG Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 983 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 235 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 317 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 961 ASN ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN B 493 ASN B 765 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN E 125 GLN C 786 HIS C 978 HIS D 226 ASN D 299 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.224071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139083 restraints weight = 41666.437| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.63 r_work: 0.3334 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34549 Z= 0.258 Angle : 0.601 12.217 46547 Z= 0.314 Chirality : 0.044 0.206 4959 Planarity : 0.004 0.056 5915 Dihedral : 4.584 50.068 4443 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.44 % Allowed : 25.27 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 3987 helix: 0.85 (0.10), residues: 2502 sheet: -1.46 (0.44), residues: 80 loop : -0.10 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 593 TYR 0.021 0.002 TYR A 951 PHE 0.024 0.002 PHE A 949 TRP 0.018 0.002 TRP A 757 HIS 0.038 0.002 HIS C 979 Details of bonding type rmsd covalent geometry : bond 0.00618 (34549) covalent geometry : angle 0.60128 (46547) hydrogen bonds : bond 0.04127 ( 1829) hydrogen bonds : angle 4.66247 ( 5286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 328 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: A 222 ASP cc_start: 0.8621 (m-30) cc_final: 0.8313 (m-30) REVERT: A 280 TYR cc_start: 0.8594 (m-10) cc_final: 0.8288 (m-10) REVERT: A 281 ASP cc_start: 0.8231 (t0) cc_final: 0.7758 (t70) REVERT: A 310 ASP cc_start: 0.8246 (m-30) cc_final: 0.7794 (m-30) REVERT: A 386 ASN cc_start: 0.8729 (m-40) cc_final: 0.8423 (m-40) REVERT: A 509 ASP cc_start: 0.7936 (m-30) cc_final: 0.7666 (m-30) REVERT: A 512 LEU cc_start: 0.7541 (mm) cc_final: 0.7292 (mt) REVERT: A 516 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 519 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8263 (mmp) REVERT: A 533 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 738 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7515 (ttpp) REVERT: A 763 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6607 (mptt) REVERT: A 785 LYS cc_start: 0.8532 (mttt) cc_final: 0.8234 (mtpt) REVERT: A 802 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6602 (ppp80) REVERT: A 833 LYS cc_start: 0.6285 (mmmm) cc_final: 0.5986 (mttm) REVERT: A 893 LYS cc_start: 0.8414 (tmtt) cc_final: 0.8121 (mtmt) REVERT: A 938 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: A 965 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8147 (tttp) REVERT: B 22 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 35 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7470 (mm-30) REVERT: B 165 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7477 (mtp85) REVERT: B 179 LYS cc_start: 0.8620 (mtmm) cc_final: 0.7984 (mptt) REVERT: B 181 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: B 267 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7309 (mtm-85) REVERT: B 279 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: B 328 ILE cc_start: 0.8912 (tp) cc_final: 0.8512 (pt) REVERT: B 460 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 491 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: B 509 ASP cc_start: 0.8170 (t0) cc_final: 0.7841 (m-30) REVERT: B 526 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 587 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8221 (ttt90) REVERT: B 626 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 629 ARG cc_start: 0.7915 (ttp80) cc_final: 0.6444 (mmm160) REVERT: B 662 ASP cc_start: 0.8076 (m-30) cc_final: 0.7844 (t0) REVERT: B 675 LYS cc_start: 0.6605 (tmtt) cc_final: 0.6144 (mptt) REVERT: B 677 ARG cc_start: 0.8061 (ptt180) cc_final: 0.7370 (ptm160) REVERT: B 697 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8638 (mttt) REVERT: B 738 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8255 (ttmt) REVERT: B 754 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.9027 (ttm110) REVERT: B 852 HIS cc_start: 0.7425 (t-90) cc_final: 0.7166 (t-170) REVERT: B 969 LYS cc_start: 0.8408 (mmpt) cc_final: 0.7965 (tttp) REVERT: B 977 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7190 (mmmm) REVERT: E 28 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6237 (mp0) REVERT: E 114 LYS cc_start: 0.8607 (tptm) cc_final: 0.8300 (tmtm) REVERT: C 21 MET cc_start: 0.7390 (tmm) cc_final: 0.6884 (ppp) REVERT: C 34 THR cc_start: 0.7826 (m) cc_final: 0.7591 (p) REVERT: C 173 ASP cc_start: 0.9054 (p0) cc_final: 0.8703 (p0) REVERT: C 176 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8268 (mtmt) REVERT: C 511 PHE cc_start: 0.2195 (t80) cc_final: 0.1560 (t80) REVERT: C 533 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.6040 (t80) REVERT: C 585 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5319 (pp) REVERT: C 647 MET cc_start: -0.0700 (tpt) cc_final: -0.1047 (tpp) REVERT: C 681 GLN cc_start: 0.3100 (OUTLIER) cc_final: 0.2428 (pm20) REVERT: C 816 ILE cc_start: 0.2759 (OUTLIER) cc_final: 0.2376 (pp) REVERT: C 827 LEU cc_start: 0.0510 (OUTLIER) cc_final: -0.0355 (mp) REVERT: C 911 ASP cc_start: 0.0019 (OUTLIER) cc_final: -0.0774 (t70) REVERT: C 913 MET cc_start: -0.0042 (OUTLIER) cc_final: -0.1240 (mpt) REVERT: C 1001 MET cc_start: -0.0670 (mmt) cc_final: -0.0974 (mmt) REVERT: D 28 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7118 (mt-10) REVERT: D 82 ASP cc_start: 0.8137 (m-30) cc_final: 0.7881 (m-30) REVERT: D 296 SER cc_start: 0.7901 (t) cc_final: 0.7642 (m) REVERT: D 394 ILE cc_start: 0.4159 (OUTLIER) cc_final: 0.3955 (mp) REVERT: D 648 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4837 (mp0) REVERT: D 704 MET cc_start: 0.1017 (tpt) cc_final: 0.0529 (mpp) REVERT: D 722 PHE cc_start: 0.3734 (t80) cc_final: 0.3329 (t80) REVERT: D 747 ARG cc_start: -0.0575 (OUTLIER) cc_final: -0.1469 (mtt180) REVERT: D 882 GLU cc_start: -0.0924 (OUTLIER) cc_final: -0.1849 (tt0) REVERT: D 930 MET cc_start: -0.0811 (OUTLIER) cc_final: -0.1407 (tpt) REVERT: D 977 LYS cc_start: 0.0984 (OUTLIER) cc_final: 0.0735 (mtpt) REVERT: F 120 ASP cc_start: 0.1134 (OUTLIER) cc_final: 0.0238 (m-30) outliers start: 203 outliers final: 64 residues processed: 483 average time/residue: 0.6027 time to fit residues: 353.4832 Evaluate side-chains 409 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 313 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 120 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 321 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 990 ASN E 125 GLN C 224 ASN D 226 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 HIS D 979 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.226287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142180 restraints weight = 41486.646| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.20 r_work: 0.3397 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34549 Z= 0.130 Angle : 0.518 10.197 46547 Z= 0.269 Chirality : 0.040 0.188 4959 Planarity : 0.003 0.052 5915 Dihedral : 4.284 47.658 4443 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.75 % Allowed : 27.02 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 3987 helix: 1.10 (0.10), residues: 2505 sheet: -1.52 (0.43), residues: 80 loop : -0.03 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 593 TYR 0.018 0.001 TYR A 951 PHE 0.016 0.001 PHE C 381 TRP 0.012 0.001 TRP A 757 HIS 0.010 0.001 HIS C 979 Details of bonding type rmsd covalent geometry : bond 0.00301 (34549) covalent geometry : angle 0.51800 (46547) hydrogen bonds : bond 0.03475 ( 1829) hydrogen bonds : angle 4.43981 ( 5286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 332 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 31 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7802 (mttm) REVERT: A 281 ASP cc_start: 0.7941 (t0) cc_final: 0.7519 (t70) REVERT: A 310 ASP cc_start: 0.8086 (m-30) cc_final: 0.7707 (m-30) REVERT: A 512 LEU cc_start: 0.7442 (mm) cc_final: 0.7096 (mt) REVERT: A 516 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 533 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 738 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7433 (ttpp) REVERT: A 744 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7917 (t80) REVERT: A 763 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6634 (mptt) REVERT: A 785 LYS cc_start: 0.8457 (mttt) cc_final: 0.8196 (mtpt) REVERT: A 802 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6601 (ppp80) REVERT: A 818 LYS cc_start: 0.7851 (mmpt) cc_final: 0.7621 (mmpt) REVERT: A 833 LYS cc_start: 0.6235 (mmmm) cc_final: 0.5922 (ttmm) REVERT: A 838 LEU cc_start: 0.7802 (mm) cc_final: 0.7431 (mm) REVERT: A 893 LYS cc_start: 0.8403 (tmtt) cc_final: 0.8155 (mtmt) REVERT: B 35 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7364 (mm-30) REVERT: B 165 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7505 (mtp85) REVERT: B 179 LYS cc_start: 0.8522 (mtmm) cc_final: 0.7910 (mptt) REVERT: B 181 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: B 267 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7256 (mtm-85) REVERT: B 328 ILE cc_start: 0.8699 (tp) cc_final: 0.8438 (pt) REVERT: B 335 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: B 491 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: B 509 ASP cc_start: 0.7965 (t0) cc_final: 0.7716 (m-30) REVERT: B 526 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 549 GLN cc_start: 0.8386 (mt0) cc_final: 0.8157 (pt0) REVERT: B 587 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7914 (ttt180) REVERT: B 626 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 629 ARG cc_start: 0.7557 (ttp80) cc_final: 0.6177 (mmm160) REVERT: B 675 LYS cc_start: 0.6403 (tmtt) cc_final: 0.6083 (mptt) REVERT: B 677 ARG cc_start: 0.7942 (ptt180) cc_final: 0.7386 (ptm160) REVERT: B 731 GLU cc_start: 0.7898 (tt0) cc_final: 0.7683 (tm-30) REVERT: B 738 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: B 852 HIS cc_start: 0.7579 (t-90) cc_final: 0.7337 (t-170) REVERT: B 927 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7208 (p0) REVERT: B 969 LYS cc_start: 0.8414 (mmpt) cc_final: 0.7989 (tttp) REVERT: B 1001 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7806 (mtm) REVERT: E 28 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6376 (mp0) REVERT: E 114 LYS cc_start: 0.8546 (tptm) cc_final: 0.8195 (tmtm) REVERT: C 28 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: C 34 THR cc_start: 0.7853 (m) cc_final: 0.7603 (p) REVERT: C 176 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8078 (mtmm) REVERT: C 351 ASN cc_start: 0.1442 (t0) cc_final: 0.1240 (t0) REVERT: C 533 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5891 (t80) REVERT: C 558 LEU cc_start: 0.5650 (tp) cc_final: 0.5340 (pp) REVERT: C 585 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5288 (pp) REVERT: C 629 ARG cc_start: 0.1674 (OUTLIER) cc_final: 0.1105 (mtp85) REVERT: C 647 MET cc_start: -0.0672 (tpt) cc_final: -0.0883 (tpp) REVERT: C 681 GLN cc_start: 0.2833 (OUTLIER) cc_final: 0.2297 (pm20) REVERT: C 816 ILE cc_start: 0.2711 (OUTLIER) cc_final: 0.2239 (pp) REVERT: C 827 LEU cc_start: 0.0066 (OUTLIER) cc_final: -0.0703 (mp) REVERT: C 911 ASP cc_start: 0.0199 (OUTLIER) cc_final: -0.0770 (t70) REVERT: C 913 MET cc_start: -0.0198 (OUTLIER) cc_final: -0.1439 (mpt) REVERT: C 933 PHE cc_start: 0.1306 (m-10) cc_final: 0.0324 (t80) REVERT: C 1001 MET cc_start: -0.0717 (mmt) cc_final: -0.0955 (mmt) REVERT: D 28 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7159 (mp0) REVERT: D 105 LYS cc_start: 0.8529 (tttm) cc_final: 0.8226 (ttpm) REVERT: D 228 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8785 (mm) REVERT: D 262 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8081 (mm-30) REVERT: D 551 LEU cc_start: 0.4475 (mt) cc_final: 0.4148 (pp) REVERT: D 648 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.4736 (pm20) REVERT: D 704 MET cc_start: 0.0912 (tpt) cc_final: 0.0540 (mpp) REVERT: D 747 ARG cc_start: -0.0443 (OUTLIER) cc_final: -0.1397 (mtt180) REVERT: D 882 GLU cc_start: -0.0716 (OUTLIER) cc_final: -0.1730 (tt0) REVERT: D 930 MET cc_start: -0.0893 (OUTLIER) cc_final: -0.1450 (tpt) REVERT: D 977 LYS cc_start: 0.1042 (OUTLIER) cc_final: 0.0698 (mtpt) REVERT: D 978 HIS cc_start: 0.0755 (OUTLIER) cc_final: 0.0474 (p90) REVERT: F 120 ASP cc_start: 0.1045 (OUTLIER) cc_final: 0.0124 (m-30) outliers start: 140 outliers final: 60 residues processed: 438 average time/residue: 0.6259 time to fit residues: 331.5229 Evaluate side-chains 407 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 315 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 120 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 365 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 296 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 143 optimal weight: 4.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 HIS B 377 GLN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN E 40 ASN E 54 ASN E 125 GLN C 979 HIS D 226 ASN ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN D 979 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.225554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139320 restraints weight = 41658.418| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.20 r_work: 0.3394 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34549 Z= 0.150 Angle : 0.531 12.641 46547 Z= 0.275 Chirality : 0.040 0.169 4959 Planarity : 0.003 0.052 5915 Dihedral : 4.243 43.368 4443 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.94 % Allowed : 26.83 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 3987 helix: 1.15 (0.10), residues: 2502 sheet: -1.38 (0.44), residues: 80 loop : -0.05 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 593 TYR 0.016 0.001 TYR C 539 PHE 0.020 0.001 PHE A 949 TRP 0.014 0.001 TRP A 757 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00352 (34549) covalent geometry : angle 0.53107 (46547) hydrogen bonds : bond 0.03494 ( 1829) hydrogen bonds : angle 4.40764 ( 5286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 322 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 31 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: A 279 GLU cc_start: 0.8439 (tt0) cc_final: 0.8135 (mm-30) REVERT: A 281 ASP cc_start: 0.8163 (t0) cc_final: 0.7720 (t70) REVERT: A 310 ASP cc_start: 0.8271 (m-30) cc_final: 0.7800 (m-30) REVERT: A 512 LEU cc_start: 0.7648 (mm) cc_final: 0.7333 (mt) REVERT: A 516 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 533 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 682 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7866 (pm20) REVERT: A 738 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7670 (ttpp) REVERT: A 759 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: A 763 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6604 (mmtt) REVERT: A 802 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6694 (ppp80) REVERT: A 833 LYS cc_start: 0.6248 (mmmm) cc_final: 0.5968 (ttmm) REVERT: A 838 LEU cc_start: 0.7790 (mm) cc_final: 0.7446 (mm) REVERT: A 893 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8149 (mtmt) REVERT: A 952 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7762 (pttp) REVERT: A 953 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7396 (mtpm) REVERT: A 964 ASP cc_start: 0.8085 (t0) cc_final: 0.7871 (t0) REVERT: B 35 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7522 (mm-30) REVERT: B 165 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7503 (mtp85) REVERT: B 179 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8000 (mptt) REVERT: B 181 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: B 267 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7323 (mtm-85) REVERT: B 328 ILE cc_start: 0.8815 (tp) cc_final: 0.8495 (pt) REVERT: B 335 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: B 417 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8171 (mmpt) REVERT: B 491 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: B 509 ASP cc_start: 0.8171 (t0) cc_final: 0.7883 (m-30) REVERT: B 526 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 549 GLN cc_start: 0.8489 (mt0) cc_final: 0.8226 (pt0) REVERT: B 587 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8235 (ttt90) REVERT: B 626 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8208 (mm-30) REVERT: B 629 ARG cc_start: 0.7813 (ttp80) cc_final: 0.6424 (mmm160) REVERT: B 675 LYS cc_start: 0.6498 (tmtt) cc_final: 0.6099 (mptt) REVERT: B 677 ARG cc_start: 0.8033 (ptt180) cc_final: 0.7365 (ptm160) REVERT: B 697 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8609 (mttt) REVERT: B 731 GLU cc_start: 0.8035 (tt0) cc_final: 0.7796 (tm-30) REVERT: B 839 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: B 852 HIS cc_start: 0.7520 (t-90) cc_final: 0.7280 (t-170) REVERT: B 927 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7179 (p0) REVERT: B 969 LYS cc_start: 0.8498 (mmpt) cc_final: 0.8072 (tttp) REVERT: B 1001 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7988 (mtm) REVERT: E 28 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6352 (mp0) REVERT: E 114 LYS cc_start: 0.8652 (tptm) cc_final: 0.8319 (tmtm) REVERT: E 115 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8469 (pt0) REVERT: C 21 MET cc_start: 0.7223 (tmm) cc_final: 0.6745 (ptt) REVERT: C 34 THR cc_start: 0.7944 (m) cc_final: 0.7703 (p) REVERT: C 173 ASP cc_start: 0.8985 (p0) cc_final: 0.8671 (p0) REVERT: C 176 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8072 (mtmm) REVERT: C 533 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.6035 (t80) REVERT: C 558 LEU cc_start: 0.5549 (tp) cc_final: 0.5230 (pp) REVERT: C 585 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5272 (pp) REVERT: C 647 MET cc_start: -0.0702 (tpt) cc_final: -0.0958 (tpp) REVERT: C 681 GLN cc_start: 0.2963 (OUTLIER) cc_final: 0.2383 (pm20) REVERT: C 816 ILE cc_start: 0.2661 (OUTLIER) cc_final: 0.2172 (pp) REVERT: C 827 LEU cc_start: 0.0104 (OUTLIER) cc_final: -0.0683 (mp) REVERT: C 866 MET cc_start: 0.3419 (tpp) cc_final: 0.2770 (tpt) REVERT: C 911 ASP cc_start: -0.0082 (OUTLIER) cc_final: -0.0695 (t70) REVERT: C 912 TYR cc_start: 0.0754 (OUTLIER) cc_final: -0.0229 (t80) REVERT: C 913 MET cc_start: -0.0213 (OUTLIER) cc_final: -0.1428 (mpt) REVERT: C 933 PHE cc_start: 0.1282 (m-10) cc_final: 0.0407 (t80) REVERT: C 1001 MET cc_start: -0.0739 (mmt) cc_final: -0.0958 (mmt) REVERT: D 28 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7139 (mt-10) REVERT: D 228 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8820 (mm) REVERT: D 262 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8338 (mm-30) REVERT: D 510 GLU cc_start: 0.5003 (pm20) cc_final: 0.3679 (tt0) REVERT: D 537 LYS cc_start: 0.6936 (ttpt) cc_final: 0.5970 (mppt) REVERT: D 551 LEU cc_start: 0.4601 (mt) cc_final: 0.4291 (pp) REVERT: D 647 MET cc_start: 0.4431 (mmm) cc_final: 0.4231 (tmm) REVERT: D 648 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.4225 (mp0) REVERT: D 704 MET cc_start: 0.1148 (tpt) cc_final: 0.0645 (mpp) REVERT: D 747 ARG cc_start: -0.0525 (OUTLIER) cc_final: -0.1483 (mtt180) REVERT: D 930 MET cc_start: -0.0875 (tmm) cc_final: -0.1563 (tpp) REVERT: D 977 LYS cc_start: 0.1177 (OUTLIER) cc_final: 0.0854 (mtpt) REVERT: D 978 HIS cc_start: 0.0722 (OUTLIER) cc_final: 0.0408 (p90) REVERT: F 120 ASP cc_start: 0.1040 (OUTLIER) cc_final: 0.0112 (m-30) outliers start: 147 outliers final: 71 residues processed: 433 average time/residue: 0.6629 time to fit residues: 346.7997 Evaluate side-chains 413 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 310 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER 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 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 866 MET Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 114 LYS Chi-restraints excluded: chain F residue 120 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 250 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 368 optimal weight: 0.0770 chunk 221 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 256 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 HIS B 814 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN E 40 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN C 224 ASN D 226 ASN ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.226262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141536 restraints weight = 41472.829| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.16 r_work: 0.3402 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34549 Z= 0.124 Angle : 0.521 14.082 46547 Z= 0.270 Chirality : 0.039 0.175 4959 Planarity : 0.003 0.051 5915 Dihedral : 4.133 43.697 4443 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.43 % Allowed : 27.37 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.13), residues: 3987 helix: 1.25 (0.11), residues: 2503 sheet: -1.38 (0.42), residues: 80 loop : -0.01 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 593 TYR 0.017 0.001 TYR C 539 PHE 0.024 0.001 PHE F 44 TRP 0.012 0.001 TRP A 757 HIS 0.005 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00287 (34549) covalent geometry : angle 0.52119 (46547) hydrogen bonds : bond 0.03304 ( 1829) hydrogen bonds : angle 4.33417 ( 5286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 328 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 31 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: A 115 ASN cc_start: 0.8657 (m-40) cc_final: 0.8434 (m110) REVERT: A 310 ASP cc_start: 0.8310 (m-30) cc_final: 0.7951 (m-30) REVERT: A 512 LEU cc_start: 0.7671 (mm) cc_final: 0.7383 (mt) REVERT: A 516 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: A 533 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6904 (t80) REVERT: A 738 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7694 (ttpp) REVERT: A 744 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7966 (t80) REVERT: A 763 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6629 (mmtt) REVERT: A 785 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8212 (ttmm) REVERT: A 802 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6727 (ppp80) REVERT: A 838 LEU cc_start: 0.7827 (mm) cc_final: 0.7477 (mm) REVERT: A 893 LYS cc_start: 0.8396 (tmtt) cc_final: 0.8092 (mtmt) REVERT: A 952 LYS cc_start: 0.8351 (mmtp) cc_final: 0.7832 (pttp) REVERT: B 35 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7528 (mm-30) REVERT: B 165 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7479 (mtp85) REVERT: B 179 LYS cc_start: 0.8575 (mtmm) cc_final: 0.7980 (mptt) REVERT: B 181 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: B 267 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: B 328 ILE cc_start: 0.8798 (tp) cc_final: 0.8491 (pt) REVERT: B 335 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: B 399 ASP cc_start: 0.7586 (t0) cc_final: 0.7307 (t0) REVERT: B 417 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8117 (mmpt) REVERT: B 509 ASP cc_start: 0.8141 (t0) cc_final: 0.7873 (m-30) REVERT: B 526 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7935 (p0) REVERT: B 549 GLN cc_start: 0.8479 (mt0) cc_final: 0.8195 (pt0) REVERT: B 587 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8212 (ttt90) REVERT: B 626 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 629 ARG cc_start: 0.7789 (ttp80) cc_final: 0.6485 (mmm160) REVERT: B 675 LYS cc_start: 0.6452 (tmtt) cc_final: 0.5567 (tptp) REVERT: B 677 ARG cc_start: 0.8015 (ptt180) cc_final: 0.7368 (ptm160) REVERT: B 697 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8636 (mttt) REVERT: B 731 GLU cc_start: 0.8023 (tt0) cc_final: 0.7787 (tm-30) REVERT: B 738 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8300 (ttmt) REVERT: B 839 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 852 HIS cc_start: 0.7638 (t-90) cc_final: 0.7403 (t-170) REVERT: B 927 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.6678 (m-40) REVERT: B 969 LYS cc_start: 0.8515 (mmpt) cc_final: 0.8167 (tttp) REVERT: B 1001 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: E 28 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6445 (mp0) REVERT: E 114 LYS cc_start: 0.8662 (tptm) cc_final: 0.8337 (tmtm) REVERT: C 21 MET cc_start: 0.7133 (tmm) cc_final: 0.6678 (ptt) REVERT: C 34 THR cc_start: 0.7946 (m) cc_final: 0.7711 (p) REVERT: C 176 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8072 (mtmm) REVERT: C 533 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.6090 (t80) REVERT: C 558 LEU cc_start: 0.5586 (tp) cc_final: 0.5326 (pp) REVERT: C 585 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5271 (pp) REVERT: C 629 ARG cc_start: 0.1508 (OUTLIER) cc_final: 0.1242 (tpt90) REVERT: C 647 MET cc_start: -0.0872 (tpt) cc_final: -0.1111 (tpp) REVERT: C 681 GLN cc_start: 0.3092 (OUTLIER) cc_final: 0.2452 (pm20) REVERT: C 816 ILE cc_start: 0.2592 (OUTLIER) cc_final: 0.2204 (pp) REVERT: C 827 LEU cc_start: 0.0371 (OUTLIER) cc_final: -0.0528 (mp) REVERT: C 866 MET cc_start: 0.3297 (tpp) cc_final: 0.2545 (tpt) REVERT: C 911 ASP cc_start: -0.0196 (OUTLIER) cc_final: -0.0687 (t70) REVERT: C 912 TYR cc_start: 0.0631 (OUTLIER) cc_final: -0.0313 (t80) REVERT: C 913 MET cc_start: -0.0206 (OUTLIER) cc_final: -0.1333 (mpt) REVERT: C 933 PHE cc_start: 0.1317 (m-10) cc_final: 0.0520 (t80) REVERT: D 21 MET cc_start: 0.5855 (ppp) cc_final: 0.5613 (pp-130) REVERT: D 28 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6679 (mt-10) REVERT: D 32 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: D 105 LYS cc_start: 0.8626 (tttm) cc_final: 0.8301 (ttpm) REVERT: D 228 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8791 (mm) REVERT: D 262 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8214 (mm-30) REVERT: D 537 LYS cc_start: 0.6935 (ttpt) cc_final: 0.6012 (mppt) REVERT: D 551 LEU cc_start: 0.4605 (mt) cc_final: 0.4372 (pp) REVERT: D 648 GLU cc_start: 0.4988 (OUTLIER) cc_final: 0.4741 (pm20) REVERT: D 704 MET cc_start: 0.1043 (tpt) cc_final: 0.0498 (mpp) REVERT: D 747 ARG cc_start: -0.0559 (OUTLIER) cc_final: -0.1491 (mtt180) REVERT: D 930 MET cc_start: -0.0652 (OUTLIER) cc_final: -0.1256 (tpp) REVERT: D 977 LYS cc_start: 0.1144 (OUTLIER) cc_final: 0.0885 (mtpt) REVERT: D 978 HIS cc_start: 0.0748 (OUTLIER) cc_final: 0.0466 (p90) REVERT: F 120 ASP cc_start: 0.1127 (OUTLIER) cc_final: 0.0260 (m-30) outliers start: 128 outliers final: 59 residues processed: 421 average time/residue: 0.6431 time to fit residues: 327.9232 Evaluate side-chains 409 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 866 MET Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 114 LYS Chi-restraints excluded: chain F residue 120 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 31 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 257 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 87 optimal weight: 0.0050 chunk 145 optimal weight: 0.9990 chunk 383 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 HIS A 990 ASN B 377 GLN B 814 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN E 40 ASN E 125 GLN D 226 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.226791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140376 restraints weight = 41474.596| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.87 r_work: 0.3414 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34549 Z= 0.115 Angle : 0.529 14.640 46547 Z= 0.272 Chirality : 0.039 0.171 4959 Planarity : 0.003 0.050 5915 Dihedral : 4.054 43.859 4442 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.98 % Allowed : 28.09 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.13), residues: 3987 helix: 1.31 (0.11), residues: 2505 sheet: -1.41 (0.41), residues: 116 loop : 0.04 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 593 TYR 0.018 0.001 TYR C 539 PHE 0.027 0.001 PHE A 949 TRP 0.012 0.001 TRP A 757 HIS 0.005 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00260 (34549) covalent geometry : angle 0.52896 (46547) hydrogen bonds : bond 0.03288 ( 1829) hydrogen bonds : angle 4.29219 ( 5286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 324 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7875 (mttm) REVERT: A 115 ASN cc_start: 0.8657 (m-40) cc_final: 0.8399 (m110) REVERT: A 279 GLU cc_start: 0.8308 (tt0) cc_final: 0.7987 (mm-30) REVERT: A 281 ASP cc_start: 0.8130 (t0) cc_final: 0.7909 (t0) REVERT: A 310 ASP cc_start: 0.8239 (m-30) cc_final: 0.7855 (m-30) REVERT: A 512 LEU cc_start: 0.7481 (mm) cc_final: 0.7176 (mt) REVERT: A 516 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 524 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8682 (tp) REVERT: A 738 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7591 (ttpp) REVERT: A 744 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7844 (t80) REVERT: A 785 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7979 (ttmm) REVERT: A 802 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6690 (ppp80) REVERT: A 838 LEU cc_start: 0.7745 (mm) cc_final: 0.7418 (mm) REVERT: A 893 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8182 (mtmt) REVERT: A 949 PHE cc_start: 0.6990 (t80) cc_final: 0.6647 (t80) REVERT: A 952 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7723 (pttp) REVERT: A 953 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7532 (ptmm) REVERT: B 35 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7481 (mm-30) REVERT: B 165 ARG cc_start: 0.7953 (mtt90) cc_final: 0.7472 (mtp85) REVERT: B 179 LYS cc_start: 0.8549 (mtmm) cc_final: 0.7932 (mptt) REVERT: B 181 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: B 328 ILE cc_start: 0.8773 (tp) cc_final: 0.8474 (pt) REVERT: B 335 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: B 399 ASP cc_start: 0.7549 (t0) cc_final: 0.7273 (t0) REVERT: B 417 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8134 (mmpt) REVERT: B 509 ASP cc_start: 0.8176 (t0) cc_final: 0.7906 (m-30) REVERT: B 549 GLN cc_start: 0.8467 (mt0) cc_final: 0.8190 (pt0) REVERT: B 587 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8205 (ttt90) REVERT: B 626 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 629 ARG cc_start: 0.7692 (ttp80) cc_final: 0.6398 (mmm160) REVERT: B 677 ARG cc_start: 0.7990 (ptt180) cc_final: 0.7316 (ptm160) REVERT: B 697 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (mttt) REVERT: B 731 GLU cc_start: 0.7979 (tt0) cc_final: 0.7742 (tm-30) REVERT: B 738 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8202 (ttmt) REVERT: B 747 ARG cc_start: 0.8226 (ptt-90) cc_final: 0.7857 (ptp-170) REVERT: B 809 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7434 (mmtm) REVERT: B 813 LYS cc_start: 0.7827 (tptm) cc_final: 0.7496 (tppt) REVERT: B 839 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: B 852 HIS cc_start: 0.7537 (t-90) cc_final: 0.7275 (t-170) REVERT: B 927 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.6691 (m-40) REVERT: B 969 LYS cc_start: 0.8502 (mmpt) cc_final: 0.8117 (tttp) REVERT: E 28 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6291 (mp0) REVERT: E 114 LYS cc_start: 0.8600 (tptm) cc_final: 0.8243 (tmtm) REVERT: C 21 MET cc_start: 0.7206 (tmm) cc_final: 0.6705 (ptt) REVERT: C 34 THR cc_start: 0.7826 (m) cc_final: 0.7580 (p) REVERT: C 176 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8073 (mtmm) REVERT: C 533 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.5991 (t80) REVERT: C 558 LEU cc_start: 0.5710 (tp) cc_final: 0.5397 (pp) REVERT: C 585 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5291 (pp) REVERT: C 629 ARG cc_start: 0.1477 (OUTLIER) cc_final: 0.1226 (tpt90) REVERT: C 647 MET cc_start: -0.1012 (tpt) cc_final: -0.1239 (tpp) REVERT: C 681 GLN cc_start: 0.3189 (OUTLIER) cc_final: 0.2545 (pm20) REVERT: C 816 ILE cc_start: 0.2516 (OUTLIER) cc_final: 0.2158 (pp) REVERT: C 827 LEU cc_start: 0.0558 (OUTLIER) cc_final: -0.0340 (mp) REVERT: C 866 MET cc_start: 0.3232 (tpp) cc_final: 0.2493 (tpt) REVERT: C 911 ASP cc_start: -0.0210 (OUTLIER) cc_final: -0.0530 (t70) REVERT: C 912 TYR cc_start: 0.0489 (OUTLIER) cc_final: -0.0356 (t80) REVERT: C 913 MET cc_start: -0.0206 (OUTLIER) cc_final: -0.1297 (mpt) REVERT: C 933 PHE cc_start: 0.1452 (m-10) cc_final: 0.0620 (t80) REVERT: C 1001 MET cc_start: -0.0238 (mmt) cc_final: -0.0475 (mtm) REVERT: D 21 MET cc_start: 0.5726 (ppp) cc_final: 0.5480 (pp-130) REVERT: D 28 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6638 (mt-10) REVERT: D 32 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: D 105 LYS cc_start: 0.8577 (tttm) cc_final: 0.8259 (ttpm) REVERT: D 228 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8796 (mm) REVERT: D 262 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8186 (mm-30) REVERT: D 454 LEU cc_start: 0.4511 (mp) cc_final: 0.3937 (tp) REVERT: D 510 GLU cc_start: 0.5041 (pm20) cc_final: 0.3565 (tt0) REVERT: D 537 LYS cc_start: 0.6892 (ttpt) cc_final: 0.6034 (mppt) REVERT: D 551 LEU cc_start: 0.4464 (mt) cc_final: 0.4164 (pp) REVERT: D 704 MET cc_start: 0.1050 (tpt) cc_final: 0.0483 (mpp) REVERT: D 747 ARG cc_start: -0.0621 (OUTLIER) cc_final: -0.1462 (mtt-85) REVERT: D 930 MET cc_start: -0.0793 (tmm) cc_final: -0.1348 (mmm) REVERT: D 977 LYS cc_start: 0.1231 (OUTLIER) cc_final: 0.0983 (mtpt) REVERT: D 978 HIS cc_start: 0.0707 (OUTLIER) cc_final: 0.0411 (p90) outliers start: 111 outliers final: 54 residues processed: 408 average time/residue: 0.6794 time to fit residues: 336.0825 Evaluate side-chains 391 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 310 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 114 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 331 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 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 978 HIS B 814 ASN B 863 ASN B 867 ASN B 990 ASN E 40 ASN E 125 GLN D 226 ASN D 339 HIS ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140760 restraints weight = 41737.059| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.48 r_work: 0.3388 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34549 Z= 0.133 Angle : 0.540 15.499 46547 Z= 0.278 Chirality : 0.040 0.202 4959 Planarity : 0.003 0.050 5915 Dihedral : 4.062 43.685 4440 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.52 % Allowed : 28.41 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 3987 helix: 1.27 (0.11), residues: 2511 sheet: -1.29 (0.45), residues: 80 loop : -0.02 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 593 TYR 0.019 0.001 TYR C 539 PHE 0.025 0.001 PHE A 837 TRP 0.013 0.001 TRP A 757 HIS 0.006 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00309 (34549) covalent geometry : angle 0.54050 (46547) hydrogen bonds : bond 0.03362 ( 1829) hydrogen bonds : angle 4.29107 ( 5286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 316 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8616 (m-40) cc_final: 0.8313 (m110) REVERT: A 281 ASP cc_start: 0.8168 (t0) cc_final: 0.7949 (t0) REVERT: A 310 ASP cc_start: 0.8303 (m-30) cc_final: 0.7929 (m-30) REVERT: A 512 LEU cc_start: 0.7569 (mm) cc_final: 0.7292 (mt) REVERT: A 516 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: A 524 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 682 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7858 (pm20) REVERT: A 738 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7591 (ttpp) REVERT: A 744 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7904 (t80) REVERT: A 785 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8176 (ttmm) REVERT: A 802 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6714 (ppp80) REVERT: A 838 LEU cc_start: 0.7805 (mm) cc_final: 0.7486 (mm) REVERT: A 893 LYS cc_start: 0.8393 (tmtt) cc_final: 0.8114 (mtmt) REVERT: A 952 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7787 (pttp) REVERT: B 35 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7504 (mm-30) REVERT: B 165 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7478 (mtp85) REVERT: B 179 LYS cc_start: 0.8584 (mtmm) cc_final: 0.7973 (mptt) REVERT: B 181 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: B 267 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7311 (mtm-85) REVERT: B 328 ILE cc_start: 0.8817 (tp) cc_final: 0.8506 (pt) REVERT: B 335 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: B 399 ASP cc_start: 0.7620 (t0) cc_final: 0.7287 (t0) REVERT: B 509 ASP cc_start: 0.8210 (t0) cc_final: 0.7941 (m-30) REVERT: B 549 GLN cc_start: 0.8521 (mt0) cc_final: 0.8239 (pt0) REVERT: B 587 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8230 (ttt90) REVERT: B 626 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8189 (mm-30) REVERT: B 629 ARG cc_start: 0.7762 (ttp80) cc_final: 0.6462 (mmm160) REVERT: B 675 LYS cc_start: 0.6417 (tmtt) cc_final: 0.5630 (tptp) REVERT: B 677 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7360 (ptm160) REVERT: B 697 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8674 (mttt) REVERT: B 731 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: B 747 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7868 (ptp-170) REVERT: B 813 LYS cc_start: 0.7763 (tptm) cc_final: 0.7521 (tppt) REVERT: B 839 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: B 852 HIS cc_start: 0.7642 (t-90) cc_final: 0.7382 (t-170) REVERT: B 927 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.6710 (m-40) REVERT: B 969 LYS cc_start: 0.8480 (mmpt) cc_final: 0.8123 (tttp) REVERT: E 28 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6335 (mp0) REVERT: E 71 LYS cc_start: 0.7787 (mmpt) cc_final: 0.7237 (tmtp) REVERT: E 114 LYS cc_start: 0.8624 (tptm) cc_final: 0.8333 (tmtm) REVERT: C 34 THR cc_start: 0.7863 (m) cc_final: 0.7600 (p) REVERT: C 176 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8076 (mtmm) REVERT: C 510 GLU cc_start: 0.5901 (tp30) cc_final: 0.5498 (pt0) REVERT: C 516 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.5088 (pt0) REVERT: C 533 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 558 LEU cc_start: 0.5521 (tp) cc_final: 0.5287 (pp) REVERT: C 585 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5250 (pp) REVERT: C 629 ARG cc_start: 0.1521 (OUTLIER) cc_final: 0.1245 (tpt90) REVERT: C 647 MET cc_start: -0.1068 (tpt) cc_final: -0.1316 (tpp) REVERT: C 681 GLN cc_start: 0.3290 (OUTLIER) cc_final: 0.2651 (pm20) REVERT: C 816 ILE cc_start: 0.2317 (OUTLIER) cc_final: 0.1930 (pp) REVERT: C 827 LEU cc_start: 0.0486 (OUTLIER) cc_final: -0.0463 (mp) REVERT: C 866 MET cc_start: 0.3116 (tpp) cc_final: 0.2431 (tpt) REVERT: C 911 ASP cc_start: -0.0171 (OUTLIER) cc_final: -0.0453 (t70) REVERT: C 912 TYR cc_start: 0.0438 (OUTLIER) cc_final: -0.0381 (t80) REVERT: C 913 MET cc_start: -0.0225 (OUTLIER) cc_final: -0.1349 (mpt) REVERT: C 933 PHE cc_start: 0.1435 (m-10) cc_final: 0.0604 (t80) REVERT: D 21 MET cc_start: 0.5836 (ppp) cc_final: 0.5576 (pp-130) REVERT: D 28 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6545 (mt-10) REVERT: D 32 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: D 105 LYS cc_start: 0.8600 (tttm) cc_final: 0.8271 (ttpm) REVERT: D 228 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 262 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8394 (mm-30) REVERT: D 510 GLU cc_start: 0.4997 (pm20) cc_final: 0.3578 (tt0) REVERT: D 537 LYS cc_start: 0.6926 (ttpt) cc_final: 0.6183 (tppt) REVERT: D 551 LEU cc_start: 0.4618 (mt) cc_final: 0.4247 (pp) REVERT: D 704 MET cc_start: 0.1059 (tpt) cc_final: 0.0491 (mpp) REVERT: D 747 ARG cc_start: -0.0571 (OUTLIER) cc_final: -0.1444 (mtt-85) REVERT: D 930 MET cc_start: -0.0824 (tmm) cc_final: -0.1389 (mpp) REVERT: D 977 LYS cc_start: 0.1311 (OUTLIER) cc_final: 0.1033 (mtpt) REVERT: D 978 HIS cc_start: 0.0596 (OUTLIER) cc_final: 0.0299 (p90) outliers start: 94 outliers final: 55 residues processed: 391 average time/residue: 0.6318 time to fit residues: 298.8325 Evaluate side-chains 382 residues out of total 3731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 911 ASP Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER 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 251 SER Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 978 HIS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 114 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 104 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 389 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 391 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 397 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN E 40 ASN E 125 GLN D 226 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.224518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140641 restraints weight = 41433.687| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.59 r_work: 0.3365 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34549 Z= 0.198 Angle : 0.583 17.343 46547 Z= 0.299 Chirality : 0.042 0.229 4959 Planarity : 0.005 0.234 5915 Dihedral : 4.236 43.276 4440 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 28.17 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 3987 helix: 1.11 (0.10), residues: 2504 sheet: -1.14 (0.47), residues: 80 loop : -0.05 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 478 TYR 0.034 0.002 TYR D 452 PHE 0.035 0.002 PHE A 949 TRP 0.018 0.002 TRP A 757 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00473 (34549) covalent geometry : angle 0.58328 (46547) hydrogen bonds : bond 0.03666 ( 1829) hydrogen bonds : angle 4.40622 ( 5286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21916.06 seconds wall clock time: 371 minutes 28.22 seconds (22288.22 seconds total)