Starting phenix.real_space_refine on Thu May 16 13:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_37924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_37924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_37924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_37924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyd_37924/05_2024/8wyd_37924.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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 Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B GLU 982": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 621": "OE1" <-> "OE2" Residue "C GLU 624": "OE1" <-> "OE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C GLU 694": "OE1" <-> "OE2" Residue "C GLU 746": "OE1" <-> "OE2" Residue "C GLU 882": "OE1" <-> "OE2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C GLU 931": "OE1" <-> "OE2" Residue "C GLU 982": "OE1" <-> "OE2" Residue "C GLU 986": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 621": "OE1" <-> "OE2" Residue "D GLU 626": "OE1" <-> "OE2" Residue "D GLU 633": "OE1" <-> "OE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 693": "OE1" <-> "OE2" Residue "D GLU 694": "OE1" <-> "OE2" Residue "D GLU 731": "OE1" <-> "OE2" Residue "D GLU 880": "OE1" <-> "OE2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D GLU 924": "OE1" <-> "OE2" Residue "D GLU 986": "OE1" <-> "OE2" Residue "F GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/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: 15.91, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.86 Conformation dependent library (CDL) restraints added in 5.7 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: 3.68 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: 14.01 Time building geometry restraints manager: 14.88 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: 88.24 - 97.47: 4 97.47 - 106.70: 548 106.70 - 115.93: 20771 115.93 - 125.16: 24867 125.16 - 134.39: 357 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 2.440 nonbonded pdb=" OG SER D 366 " pdb=" OE1 GLU D 369 " model vdw 2.113 2.440 nonbonded pdb=" OG SER B 366 " pdb=" OE1 GLU B 369 " model vdw 2.124 2.440 nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 2.143 2.440 nonbonded pdb=" OE1 GLU A 668 " pdb=" OH TYR A 725 " model vdw 2.146 2.440 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 37.250 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 87.970 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.100 ------------------------------------------------------------------------------- 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= 0.219 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (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 TRP 0.060 0.002 TRP B 919 HIS 0.009 0.001 HIS E 123 PHE 0.028 0.001 PHE A 837 TYR 0.024 0.001 TYR D 962 ARG 0.012 0.001 ARG C 517 *********************** 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 fitting. rotamer outliers: 100 poor density : 597 time to evaluate : 3.701 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: 0.7376 (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: 0.8752 (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: 1.5070 time to fit residues: 1231.3839 Evaluate side-chains 368 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 339 time to evaluate : 3.953 ------------------------------------------------------------------------------- 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 339 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 315 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 234 optimal weight: 0.0270 chunk 365 optimal weight: 9.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 523 ASN A 666 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS A 881 HIS A 979 HIS A1002 ASN B 39 ASN B 377 GLN B 491 GLN B 493 ASN B 765 ASN B 834 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN C 711 GLN C1002 ASN D 25 ASN D 711 GLN D 927 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1928 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= 0.181 Angle : 0.540 10.137 46547 Z= 0.283 Chirality : 0.040 0.266 4959 Planarity : 0.004 0.063 5915 Dihedral : 4.842 51.322 4477 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.07 % Allowed : 29.40 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.13), residues: 3987 helix: 1.19 (0.10), residues: 2490 sheet: -0.67 (0.51), residues: 68 loop : 0.15 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 958 HIS 0.010 0.001 HIS A 881 PHE 0.031 0.001 PHE B 645 TYR 0.024 0.001 TYR C 482 ARG 0.007 0.000 ARG C 175 *********************** 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 554 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 365 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (m) REVERT: A 222 ASP cc_start: 0.8060 (m-30) cc_final: 0.7653 (m-30) REVERT: A 396 MET cc_start: 0.7926 (mmm) cc_final: 0.7717 (mmm) REVERT: A 399 ASP cc_start: 0.7471 (m-30) cc_final: 0.6662 (t0) REVERT: A 407 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7451 (tp) REVERT: A 516 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: A 553 ASP cc_start: 0.8136 (t0) cc_final: 0.7915 (m-30) REVERT: A 566 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (mmt90) REVERT: A 607 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: A 731 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: A 812 GLU cc_start: 0.6512 (pt0) cc_final: 0.5511 (tp30) REVERT: A 818 LYS cc_start: 0.7585 (mptt) cc_final: 0.7321 (mmtt) REVERT: A 833 LYS cc_start: 0.5912 (mmmm) cc_final: 0.5341 (ttmm) REVERT: A 949 PHE cc_start: 0.6305 (t80) cc_final: 0.5707 (t80) REVERT: A 951 TYR cc_start: 0.6759 (m-80) cc_final: 0.5912 (m-80) REVERT: B 134 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8375 (p90) REVERT: B 165 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7544 (mtp85) REVERT: B 179 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7760 (mptt) REVERT: B 226 ASN cc_start: 0.7952 (m110) cc_final: 0.7540 (m-40) REVERT: B 279 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: B 283 LEU cc_start: 0.8653 (tp) cc_final: 0.8413 (tm) REVERT: B 335 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: B 509 ASP cc_start: 0.7816 (t0) cc_final: 0.7539 (m-30) REVERT: B 526 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7168 (p0) REVERT: B 557 LYS cc_start: 0.8829 (mttm) cc_final: 0.8511 (mttt) REVERT: B 560 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8371 (mm-30) REVERT: B 616 MET cc_start: 0.8976 (mmm) cc_final: 0.8771 (mmm) REVERT: B 629 ARG cc_start: 0.7034 (ttp80) cc_final: 0.5684 (mmm160) REVERT: B 677 ARG cc_start: 0.7356 (ptt180) cc_final: 0.6945 (ptm160) REVERT: B 693 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6696 (mp0) REVERT: B 710 THR cc_start: 0.8969 (m) cc_final: 0.8676 (p) REVERT: B 727 LYS cc_start: 0.8229 (tptt) cc_final: 0.7917 (tptt) REVERT: B 746 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 810 HIS cc_start: 0.8216 (t-90) cc_final: 0.7990 (t-90) REVERT: B 857 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7152 (mptt) REVERT: B 921 PHE cc_start: 0.7966 (t80) cc_final: 0.7426 (t80) REVERT: B 969 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7794 (tttp) REVERT: E 21 ASN cc_start: 0.7817 (p0) cc_final: 0.7410 (p0) REVERT: E 28 GLU cc_start: 0.6546 (mm-30) cc_final: 0.5949 (mp0) REVERT: E 58 ASP cc_start: 0.6622 (m-30) cc_final: 0.6403 (m-30) REVERT: E 62 SER cc_start: 0.8379 (p) cc_final: 0.8080 (m) REVERT: C 34 THR cc_start: 0.8322 (m) cc_final: 0.8076 (p) REVERT: C 134 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8145 (p90) REVERT: C 421 MET cc_start: -0.1707 (mtm) cc_final: -0.2495 (pmm) REVERT: C 588 LEU cc_start: 0.1651 (OUTLIER) cc_final: 0.1260 (tp) REVERT: C 647 MET cc_start: 0.0382 (tpt) cc_final: -0.0149 (tpp) REVERT: C 912 TYR cc_start: 0.1346 (OUTLIER) cc_final: 0.0543 (m-80) REVERT: D 134 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8511 (p90) REVERT: D 175 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7930 (mtm180) REVERT: D 519 MET cc_start: 0.5754 (mmm) cc_final: 0.5430 (mmm) REVERT: D 648 GLU cc_start: 0.4391 (OUTLIER) cc_final: 0.4148 (mp0) REVERT: D 693 GLU cc_start: 0.3640 (OUTLIER) cc_final: 0.3069 (mm-30) REVERT: D 704 MET cc_start: 0.2003 (tpt) cc_final: 0.1283 (mpp) REVERT: D 747 ARG cc_start: 0.0408 (OUTLIER) cc_final: -0.0821 (mtt-85) REVERT: D 976 MET cc_start: -0.0068 (OUTLIER) cc_final: -0.1484 (mpp) outliers start: 189 outliers final: 50 residues processed: 509 average time/residue: 1.3171 time to fit residues: 821.5470 Evaluate side-chains 395 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 327 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 374 SER 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 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 566 ARG Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 750 ASP 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 90 ILE Chi-restraints excluded: chain B residue 98 MET 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 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 615 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 912 TYR 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 134 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET 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 582 ILE Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 693 GLU Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 866 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 202 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 365 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 297 GLN A 391 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 493 ASN B 765 ASN B 782 GLN B 939 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 34549 Z= 0.430 Angle : 0.627 11.071 46547 Z= 0.330 Chirality : 0.045 0.401 4959 Planarity : 0.005 0.059 5915 Dihedral : 5.006 53.381 4457 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.16 % Allowed : 26.70 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 3987 helix: 0.74 (0.10), residues: 2499 sheet: -1.10 (0.47), residues: 82 loop : -0.00 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 757 HIS 0.010 0.002 HIS E 123 PHE 0.026 0.002 PHE C 334 TYR 0.022 0.002 TYR C 482 ARG 0.006 0.001 ARG B 669 *********************** 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 574 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 344 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 139 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8563 (m-30) REVERT: A 509 ASP cc_start: 0.7680 (m-30) cc_final: 0.7465 (m-30) REVERT: A 512 LEU cc_start: 0.7412 (mm) cc_final: 0.7050 (mt) REVERT: A 516 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 518 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 533 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6729 (t80) REVERT: A 553 ASP cc_start: 0.8368 (t0) cc_final: 0.8106 (m-30) REVERT: A 566 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7826 (mtt-85) REVERT: A 607 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: A 704 MET cc_start: 0.5673 (ttp) cc_final: 0.5437 (tmm) REVERT: A 738 LYS cc_start: 0.7424 (tptp) cc_final: 0.6699 (ttmm) REVERT: A 833 LYS cc_start: 0.6111 (mmmm) cc_final: 0.5847 (mttm) REVERT: A 838 LEU cc_start: 0.7523 (mm) cc_final: 0.7154 (mm) REVERT: A 938 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6477 (m-30) REVERT: A 949 PHE cc_start: 0.6921 (t80) cc_final: 0.6402 (t80) REVERT: A 995 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7747 (tpt170) REVERT: B 22 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7606 (mp) REVERT: B 165 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (mtp85) REVERT: B 179 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8025 (mptt) REVERT: B 279 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 363 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 509 ASP cc_start: 0.7739 (t0) cc_final: 0.7535 (m-30) REVERT: B 526 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7840 (p0) REVERT: B 587 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7792 (ttt90) REVERT: B 626 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 629 ARG cc_start: 0.7149 (ttp80) cc_final: 0.5738 (mmm160) REVERT: B 675 LYS cc_start: 0.6435 (tmtt) cc_final: 0.5979 (mptt) REVERT: B 677 ARG cc_start: 0.7644 (ptt180) cc_final: 0.7065 (ptm160) REVERT: B 693 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6832 (mp0) REVERT: B 697 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8065 (mttt) REVERT: B 738 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7235 (ttmt) REVERT: B 809 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7120 (mmtm) REVERT: B 852 HIS cc_start: 0.7246 (t-90) cc_final: 0.6940 (t-170) REVERT: B 921 PHE cc_start: 0.8140 (t80) cc_final: 0.7849 (t80) REVERT: B 927 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7075 (p0) REVERT: B 930 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7146 (ptp) REVERT: B 969 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7745 (tttp) REVERT: B 982 GLU cc_start: 0.7276 (pp20) cc_final: 0.7071 (pp20) REVERT: E 21 ASN cc_start: 0.8107 (p0) cc_final: 0.7832 (p0) REVERT: E 28 GLU cc_start: 0.6669 (mm-30) cc_final: 0.5957 (mp0) REVERT: E 58 ASP cc_start: 0.6768 (m-30) cc_final: 0.6509 (m-30) REVERT: C 34 THR cc_start: 0.8585 (m) cc_final: 0.8362 (p) REVERT: C 548 ASN cc_start: 0.2667 (OUTLIER) cc_final: 0.2314 (m110) REVERT: C 588 LEU cc_start: 0.1510 (OUTLIER) cc_final: 0.1017 (tp) REVERT: C 629 ARG cc_start: 0.1876 (OUTLIER) cc_final: 0.1520 (mtp85) REVERT: C 647 MET cc_start: 0.0577 (tpt) cc_final: 0.0162 (tpp) REVERT: C 911 ASP cc_start: 0.0431 (OUTLIER) cc_final: -0.0763 (t70) REVERT: C 912 TYR cc_start: 0.1125 (OUTLIER) cc_final: 0.0224 (m-80) REVERT: C 913 MET cc_start: -0.0248 (OUTLIER) cc_final: -0.1512 (mpt) REVERT: C 977 LYS cc_start: 0.1362 (OUTLIER) cc_final: 0.1159 (tppt) REVERT: D 111 ASP cc_start: 0.8261 (p0) cc_final: 0.8026 (p0) REVERT: D 328 ILE cc_start: 0.3544 (OUTLIER) cc_final: 0.3166 (pt) REVERT: D 510 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5101 (pm20) REVERT: D 537 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5803 (tttp) REVERT: D 704 MET cc_start: 0.1631 (tpt) cc_final: 0.1074 (mpp) REVERT: D 747 ARG cc_start: 0.0485 (OUTLIER) cc_final: -0.0998 (mtt180) REVERT: D 930 MET cc_start: -0.0540 (tmm) cc_final: -0.1297 (tpt) REVERT: D 933 PHE cc_start: 0.2456 (OUTLIER) cc_final: 0.1475 (m-10) REVERT: D 976 MET cc_start: -0.0248 (OUTLIER) cc_final: -0.1553 (mtt) outliers start: 230 outliers final: 74 residues processed: 529 average time/residue: 1.3800 time to fit residues: 891.3092 Evaluate side-chains 413 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 308 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 404 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 537 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 856 PHE 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 934 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU 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 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 674 ASP 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 794 VAL Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 930 MET 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 98 ILE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 113 VAL 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 87 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 521 ASN Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 593 ARG 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 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 C residue 928 SER Chi-restraints excluded: chain C residue 977 LYS 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 204 MET Chi-restraints excluded: chain D residue 233 ARG 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 393 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 LYS Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 747 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 chunk 189 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 174 optimal weight: 0.0870 chunk 245 optimal weight: 10.0000 chunk 367 optimal weight: 0.5980 chunk 388 optimal weight: 20.0000 chunk 191 optimal weight: 0.6980 chunk 347 optimal weight: 0.0770 chunk 104 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 391 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN B 493 ASN B 765 ASN B 834 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 224 ASN D 24 ASN D 549 GLN D 979 HIS F 88 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34549 Z= 0.151 Angle : 0.486 9.622 46547 Z= 0.255 Chirality : 0.039 0.192 4959 Planarity : 0.003 0.056 5915 Dihedral : 4.343 49.860 4450 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.13 % Allowed : 27.82 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 3987 helix: 1.23 (0.10), residues: 2489 sheet: -1.22 (0.46), residues: 82 loop : 0.07 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 60 HIS 0.007 0.001 HIS A 978 PHE 0.016 0.001 PHE B 942 TYR 0.017 0.001 TYR C 482 ARG 0.005 0.000 ARG A 677 *********************** 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 494 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 340 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8137 (m-30) cc_final: 0.7744 (m-30) REVERT: A 310 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: A 512 LEU cc_start: 0.7363 (mm) cc_final: 0.7001 (mt) REVERT: A 516 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 533 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 553 ASP cc_start: 0.8252 (t0) cc_final: 0.7977 (m-30) REVERT: A 785 LYS cc_start: 0.8290 (mttt) cc_final: 0.7871 (ttmm) REVERT: A 833 LYS cc_start: 0.6075 (mmmm) cc_final: 0.5819 (mttm) REVERT: A 838 LEU cc_start: 0.7300 (mm) cc_final: 0.6775 (mt) REVERT: A 949 PHE cc_start: 0.7175 (t80) cc_final: 0.6183 (t80) REVERT: B 165 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7618 (mtp85) REVERT: B 179 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7965 (mptt) REVERT: B 279 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: B 363 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 491 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: B 526 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 587 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7647 (ttt90) REVERT: B 626 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 629 ARG cc_start: 0.6953 (ttp80) cc_final: 0.5624 (mmm160) REVERT: B 677 ARG cc_start: 0.7595 (ptt180) cc_final: 0.6994 (ptm160) REVERT: B 731 GLU cc_start: 0.7539 (tt0) cc_final: 0.7268 (tm-30) REVERT: B 738 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7165 (ttmt) REVERT: B 852 HIS cc_start: 0.7358 (t-90) cc_final: 0.7016 (t-170) REVERT: B 921 PHE cc_start: 0.8089 (t80) cc_final: 0.7826 (t80) REVERT: B 927 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7087 (p0) REVERT: B 930 MET cc_start: 0.7554 (mtp) cc_final: 0.7018 (ptp) REVERT: B 969 LYS cc_start: 0.8263 (mmpt) cc_final: 0.7788 (tttp) REVERT: B 977 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6540 (mmmm) REVERT: E 21 ASN cc_start: 0.7889 (p0) cc_final: 0.7624 (p0) REVERT: E 28 GLU cc_start: 0.6678 (mm-30) cc_final: 0.5945 (mp0) REVERT: E 58 ASP cc_start: 0.6716 (m-30) cc_final: 0.6432 (m-30) REVERT: E 68 SER cc_start: 0.7879 (p) cc_final: 0.7643 (m) REVERT: E 115 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: C 34 THR cc_start: 0.8521 (m) cc_final: 0.8315 (p) REVERT: C 588 LEU cc_start: 0.1802 (OUTLIER) cc_final: 0.1325 (tp) REVERT: C 629 ARG cc_start: 0.1955 (OUTLIER) cc_final: 0.1508 (mtp85) REVERT: C 647 MET cc_start: 0.0418 (tpt) cc_final: 0.0087 (tpp) REVERT: C 816 ILE cc_start: 0.2816 (OUTLIER) cc_final: 0.2262 (pp) REVERT: C 911 ASP cc_start: 0.0676 (OUTLIER) cc_final: -0.0450 (t70) REVERT: C 912 TYR cc_start: 0.0717 (OUTLIER) cc_final: -0.0129 (m-80) REVERT: C 933 PHE cc_start: 0.1264 (m-10) cc_final: 0.0369 (t80) REVERT: C 979 HIS cc_start: 0.0338 (OUTLIER) cc_final: 0.0135 (t-170) REVERT: C 1001 MET cc_start: -0.0153 (mmt) cc_final: -0.0710 (mmt) REVERT: D 111 ASP cc_start: 0.8153 (p0) cc_final: 0.7926 (p0) REVERT: D 510 GLU cc_start: 0.5326 (tt0) cc_final: 0.4991 (pm20) REVERT: D 704 MET cc_start: 0.1394 (tpt) cc_final: 0.1078 (mpp) REVERT: D 747 ARG cc_start: 0.0440 (OUTLIER) cc_final: -0.0931 (mtt180) REVERT: D 930 MET cc_start: -0.0772 (OUTLIER) cc_final: -0.1259 (tpt) REVERT: D 976 MET cc_start: 0.0136 (OUTLIER) cc_final: -0.1279 (mtm) REVERT: F 20 ILE cc_start: 0.0596 (OUTLIER) cc_final: 0.0298 (mp) outliers start: 154 outliers final: 48 residues processed: 457 average time/residue: 1.3630 time to fit residues: 759.2517 Evaluate side-chains 380 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 311 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 406 SER 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 537 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 363 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 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 927 ASN 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 98 ILE 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 82 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 816 ILE 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 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 204 MET 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 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 866 MET Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 323 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 chunk 268 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 348 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN B 765 ASN B1002 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN D 299 ASN D 711 GLN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34549 Z= 0.268 Angle : 0.523 9.949 46547 Z= 0.272 Chirality : 0.040 0.166 4959 Planarity : 0.004 0.054 5915 Dihedral : 4.383 50.314 4448 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.66 % Allowed : 26.88 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 3987 helix: 1.15 (0.10), residues: 2502 sheet: -1.30 (0.44), residues: 82 loop : -0.01 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 757 HIS 0.007 0.001 HIS A 979 PHE 0.016 0.002 PHE B 943 TYR 0.015 0.001 TYR C 482 ARG 0.004 0.000 ARG D 285 *********************** 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 493 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 319 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: A 222 ASP cc_start: 0.8215 (m-30) cc_final: 0.7730 (m-30) REVERT: A 512 LEU cc_start: 0.7399 (mm) cc_final: 0.7048 (mt) REVERT: A 516 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: A 533 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6629 (t80) REVERT: A 553 ASP cc_start: 0.8303 (t0) cc_final: 0.8016 (m-30) REVERT: A 738 LYS cc_start: 0.7311 (tmtt) cc_final: 0.6809 (ttpp) REVERT: A 785 LYS cc_start: 0.8315 (mttt) cc_final: 0.7990 (mtpt) REVERT: A 833 LYS cc_start: 0.6167 (mmmm) cc_final: 0.5843 (tttm) REVERT: A 838 LEU cc_start: 0.7416 (mm) cc_final: 0.7153 (mm) REVERT: A 913 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7101 (mtm) REVERT: A 949 PHE cc_start: 0.6945 (t80) cc_final: 0.6359 (t80) REVERT: A 965 LYS cc_start: 0.8228 (mmmt) cc_final: 0.8028 (tttp) REVERT: A 995 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7785 (tpt170) REVERT: B 22 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7611 (mp) REVERT: B 165 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7672 (mtp85) REVERT: B 179 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8022 (mptt) REVERT: B 279 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 335 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: B 363 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 491 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: B 526 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7754 (p0) REVERT: B 587 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7650 (ttt180) REVERT: B 626 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7672 (mm-30) REVERT: B 629 ARG cc_start: 0.7021 (ttp80) cc_final: 0.5675 (mmm160) REVERT: B 675 LYS cc_start: 0.6249 (tmtt) cc_final: 0.5380 (tptp) REVERT: B 677 ARG cc_start: 0.7611 (ptt180) cc_final: 0.6994 (ptm160) REVERT: B 693 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 731 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 809 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7037 (mmtm) REVERT: B 852 HIS cc_start: 0.7394 (t-90) cc_final: 0.7088 (t-170) REVERT: B 921 PHE cc_start: 0.8078 (t80) cc_final: 0.7840 (t80) REVERT: B 927 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.6987 (p0) REVERT: B 930 MET cc_start: 0.7625 (mtp) cc_final: 0.7224 (mtm) REVERT: B 969 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7779 (tttp) REVERT: E 21 ASN cc_start: 0.7943 (p0) cc_final: 0.7636 (p0) REVERT: E 28 GLU cc_start: 0.6705 (mm-30) cc_final: 0.5933 (mp0) REVERT: E 58 ASP cc_start: 0.6619 (m-30) cc_final: 0.6264 (m-30) REVERT: E 68 SER cc_start: 0.7959 (p) cc_final: 0.7739 (m) REVERT: C 173 ASP cc_start: 0.9004 (p0) cc_final: 0.8720 (p0) REVERT: C 533 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5837 (t80) REVERT: C 547 ASP cc_start: 0.2275 (OUTLIER) cc_final: 0.1807 (t70) REVERT: C 588 LEU cc_start: 0.1685 (OUTLIER) cc_final: 0.1208 (tp) REVERT: C 629 ARG cc_start: 0.2126 (OUTLIER) cc_final: 0.1398 (tpt90) REVERT: C 647 MET cc_start: 0.0628 (tpt) cc_final: 0.0330 (tpp) REVERT: C 816 ILE cc_start: 0.2811 (OUTLIER) cc_final: 0.2257 (pp) REVERT: C 911 ASP cc_start: 0.0631 (OUTLIER) cc_final: -0.0486 (t70) REVERT: C 912 TYR cc_start: 0.0686 (OUTLIER) cc_final: -0.0170 (m-80) REVERT: C 979 HIS cc_start: 0.0326 (OUTLIER) cc_final: -0.0095 (OUTLIER) REVERT: C 984 LEU cc_start: 0.0193 (OUTLIER) cc_final: -0.0064 (tp) REVERT: C 1001 MET cc_start: -0.0235 (mmt) cc_final: -0.0743 (mmt) REVERT: D 510 GLU cc_start: 0.5389 (tt0) cc_final: 0.5030 (pm20) REVERT: D 656 SER cc_start: 0.4626 (OUTLIER) cc_final: 0.3692 (m) REVERT: D 704 MET cc_start: 0.1399 (tpt) cc_final: 0.1144 (mpp) REVERT: D 747 ARG cc_start: 0.0535 (OUTLIER) cc_final: -0.0980 (mtt180) REVERT: D 930 MET cc_start: -0.0435 (OUTLIER) cc_final: -0.1107 (tpp) REVERT: D 976 MET cc_start: -0.0059 (OUTLIER) cc_final: -0.1297 (mtm) REVERT: F 20 ILE cc_start: 0.0554 (OUTLIER) cc_final: 0.0335 (mp) outliers start: 174 outliers final: 73 residues processed: 456 average time/residue: 1.3123 time to fit residues: 734.8914 Evaluate side-chains 402 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 301 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 406 SER 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 533 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 995 ARG 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 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 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 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 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 927 ASN Chi-restraints excluded: chain B residue 1001 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 18 SER 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 139 ASP 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 317 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 521 ASN Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 588 LEU 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 737 VAL Chi-restraints excluded: chain C residue 816 ILE 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 979 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 54 SER 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 278 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 874 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 Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 130 optimal weight: 0.8980 chunk 349 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 322 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN B 790 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN D 226 ASN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34549 Z= 0.270 Angle : 0.533 13.837 46547 Z= 0.275 Chirality : 0.040 0.178 4959 Planarity : 0.004 0.153 5915 Dihedral : 4.408 48.592 4448 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.69 % Allowed : 27.12 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.13), residues: 3987 helix: 1.12 (0.10), residues: 2504 sheet: -1.27 (0.43), residues: 82 loop : -0.05 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 757 HIS 0.007 0.001 HIS A 979 PHE 0.020 0.002 PHE A 933 TYR 0.015 0.001 TYR C 539 ARG 0.014 0.000 ARG C 593 *********************** 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 487 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 312 time to evaluate : 4.164 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: 0.7487 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 139 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: A 512 LEU cc_start: 0.7404 (mm) cc_final: 0.7052 (mt) REVERT: A 516 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: A 533 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6645 (t80) REVERT: A 553 ASP cc_start: 0.8278 (t0) cc_final: 0.8007 (m-30) REVERT: A 738 LYS cc_start: 0.7395 (tmtt) cc_final: 0.6838 (ttpp) REVERT: A 833 LYS cc_start: 0.6215 (mmmm) cc_final: 0.5708 (tttm) REVERT: A 838 LEU cc_start: 0.7440 (mm) cc_final: 0.7154 (mm) REVERT: A 949 PHE cc_start: 0.6950 (t80) cc_final: 0.6270 (t80) REVERT: A 965 LYS cc_start: 0.8260 (mmmt) cc_final: 0.8038 (tttp) REVERT: B 179 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8024 (mptt) REVERT: B 267 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.6987 (mtm-85) REVERT: B 279 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 335 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: B 363 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 526 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7769 (p0) REVERT: B 587 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7640 (ttt180) REVERT: B 626 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 629 ARG cc_start: 0.7022 (ttp80) cc_final: 0.5683 (mmm160) REVERT: B 675 LYS cc_start: 0.6375 (tmtt) cc_final: 0.5476 (tptp) REVERT: B 677 ARG cc_start: 0.7632 (ptt180) cc_final: 0.6982 (ptm160) REVERT: B 693 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 731 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: B 738 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7239 (ttmt) REVERT: B 753 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7403 (mmmm) REVERT: B 809 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7249 (mmtt) REVERT: B 852 HIS cc_start: 0.7454 (t-90) cc_final: 0.7153 (t-170) REVERT: B 927 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.6562 (m-40) REVERT: B 969 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7750 (tttp) REVERT: E 21 ASN cc_start: 0.7903 (p0) cc_final: 0.7585 (p0) REVERT: E 28 GLU cc_start: 0.6748 (mm-30) cc_final: 0.5946 (mp0) REVERT: E 58 ASP cc_start: 0.6499 (m-30) cc_final: 0.6173 (m-30) REVERT: E 68 SER cc_start: 0.7981 (p) cc_final: 0.7734 (m) REVERT: C 82 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7618 (p0) REVERT: C 173 ASP cc_start: 0.9005 (p0) cc_final: 0.8716 (p0) REVERT: C 533 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5960 (t80) REVERT: C 547 ASP cc_start: 0.2477 (OUTLIER) cc_final: 0.2058 (t70) REVERT: C 629 ARG cc_start: 0.2256 (OUTLIER) cc_final: 0.1467 (tpt90) REVERT: C 647 MET cc_start: 0.0480 (tpt) cc_final: 0.0171 (tpp) REVERT: C 816 ILE cc_start: 0.2848 (OUTLIER) cc_final: 0.2313 (pp) REVERT: C 911 ASP cc_start: 0.0419 (OUTLIER) cc_final: -0.0536 (t70) REVERT: C 912 TYR cc_start: 0.0432 (OUTLIER) cc_final: -0.0341 (m-80) REVERT: C 979 HIS cc_start: 0.0335 (OUTLIER) cc_final: 0.0058 (t-170) REVERT: C 1001 MET cc_start: -0.0559 (mmt) cc_final: -0.0982 (mmt) REVERT: D 510 GLU cc_start: 0.5378 (tt0) cc_final: 0.5023 (pm20) REVERT: D 537 LYS cc_start: 0.6443 (ttpt) cc_final: 0.6078 (mppt) REVERT: D 656 SER cc_start: 0.4720 (OUTLIER) cc_final: 0.3800 (m) REVERT: D 704 MET cc_start: 0.1365 (tpt) cc_final: 0.1143 (mpp) REVERT: D 747 ARG cc_start: 0.0635 (OUTLIER) cc_final: -0.1012 (mtt180) REVERT: D 930 MET cc_start: -0.0446 (tmm) cc_final: -0.1147 (tpp) REVERT: F 20 ILE cc_start: 0.0396 (OUTLIER) cc_final: 0.0170 (mp) outliers start: 175 outliers final: 88 residues processed: 452 average time/residue: 1.3078 time to fit residues: 728.2790 Evaluate side-chains 414 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 300 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 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 481 ILE 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 537 LYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 875 ASP 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 981 ILE 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 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 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE 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 753 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 816 ILE 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 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 82 ASP Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 139 ASP 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 317 SER Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 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 737 VAL Chi-restraints excluded: chain C residue 816 ILE 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 979 HIS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 848 ASN Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 374 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 217 optimal weight: 0.3980 chunk 387 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS B 765 ASN B 790 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN C 457 ASN D 160 ASN D 226 ASN ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34549 Z= 0.192 Angle : 0.503 12.986 46547 Z= 0.259 Chirality : 0.039 0.174 4959 Planarity : 0.003 0.084 5915 Dihedral : 4.244 45.863 4448 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.26 % Allowed : 27.63 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 3987 helix: 1.24 (0.10), residues: 2499 sheet: -1.26 (0.42), residues: 82 loop : 0.00 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.005 0.001 HIS B 339 PHE 0.016 0.001 PHE A 837 TYR 0.015 0.001 TYR C 539 ARG 0.008 0.000 ARG C 593 *********************** 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 466 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 307 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 139 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: A 222 ASP cc_start: 0.8188 (m-30) cc_final: 0.7733 (m-30) REVERT: A 310 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: A 512 LEU cc_start: 0.7371 (mm) cc_final: 0.7042 (mt) REVERT: A 516 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 533 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6638 (t80) REVERT: A 553 ASP cc_start: 0.8256 (t0) cc_final: 0.7974 (m-30) REVERT: A 682 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7384 (pm20) REVERT: A 738 LYS cc_start: 0.7407 (tmtt) cc_final: 0.6747 (ttpp) REVERT: A 785 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7940 (ttmm) REVERT: A 833 LYS cc_start: 0.6215 (mmmm) cc_final: 0.5974 (mptm) REVERT: A 838 LEU cc_start: 0.7462 (mm) cc_final: 0.7192 (mm) REVERT: A 860 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: A 949 PHE cc_start: 0.6975 (t80) cc_final: 0.6285 (t80) REVERT: A 952 LYS cc_start: 0.8314 (mmtp) cc_final: 0.7738 (pttp) REVERT: A 953 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7324 (mtpm) REVERT: A 965 LYS cc_start: 0.8251 (mmmt) cc_final: 0.8045 (tttp) REVERT: B 165 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7681 (mtp85) REVERT: B 179 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8012 (mptt) REVERT: B 267 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.6967 (mtm-85) REVERT: B 335 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: B 363 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 399 ASP cc_start: 0.7283 (t0) cc_final: 0.7016 (t0) REVERT: B 526 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7717 (p0) REVERT: B 587 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7668 (ttt90) REVERT: B 626 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 629 ARG cc_start: 0.6979 (ttp80) cc_final: 0.5684 (mmm160) REVERT: B 677 ARG cc_start: 0.7655 (ptt180) cc_final: 0.7028 (ptm160) REVERT: B 693 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 731 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: B 753 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7351 (mmmm) REVERT: B 809 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7062 (mmtm) REVERT: B 852 HIS cc_start: 0.7496 (t-90) cc_final: 0.7188 (t-170) REVERT: B 857 LYS cc_start: 0.7988 (tppt) cc_final: 0.7524 (pmtt) REVERT: B 927 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.6529 (m-40) REVERT: B 969 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7792 (tttp) REVERT: B 1001 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7566 (mtm) REVERT: E 21 ASN cc_start: 0.7870 (p0) cc_final: 0.7566 (p0) REVERT: E 28 GLU cc_start: 0.6745 (mm-30) cc_final: 0.5935 (mp0) REVERT: E 58 ASP cc_start: 0.6404 (m-30) cc_final: 0.6124 (m-30) REVERT: E 68 SER cc_start: 0.7972 (p) cc_final: 0.7737 (m) REVERT: E 97 GLU cc_start: 0.6629 (pm20) cc_final: 0.6301 (pp20) REVERT: C 82 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7625 (p0) REVERT: C 533 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 547 ASP cc_start: 0.2551 (OUTLIER) cc_final: 0.2005 (t70) REVERT: C 629 ARG cc_start: 0.1992 (OUTLIER) cc_final: 0.1292 (tpt90) REVERT: C 647 MET cc_start: 0.0434 (tpt) cc_final: 0.0069 (tpp) REVERT: C 816 ILE cc_start: 0.2838 (OUTLIER) cc_final: 0.2302 (pp) REVERT: C 911 ASP cc_start: 0.0451 (OUTLIER) cc_final: -0.0550 (t70) REVERT: C 912 TYR cc_start: 0.0331 (OUTLIER) cc_final: -0.0388 (m-80) REVERT: C 913 MET cc_start: -0.0483 (OUTLIER) cc_final: -0.1689 (mpt) REVERT: C 933 PHE cc_start: 0.1275 (m-10) cc_final: 0.0358 (t80) REVERT: C 979 HIS cc_start: 0.0253 (OUTLIER) cc_final: 0.0014 (t-170) REVERT: C 1001 MET cc_start: -0.0590 (mmt) cc_final: -0.0881 (mmt) REVERT: D 160 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: D 285 ARG cc_start: 0.7537 (mpp80) cc_final: 0.7201 (ttm110) REVERT: D 510 GLU cc_start: 0.5374 (tt0) cc_final: 0.5043 (pm20) REVERT: D 537 LYS cc_start: 0.6462 (ttpt) cc_final: 0.6137 (mppt) REVERT: D 656 SER cc_start: 0.4475 (OUTLIER) cc_final: 0.3530 (m) REVERT: D 747 ARG cc_start: 0.0562 (OUTLIER) cc_final: -0.0930 (mtt-85) REVERT: D 930 MET cc_start: -0.0487 (tmm) cc_final: -0.1712 (mpp) REVERT: D 977 LYS cc_start: 0.0610 (OUTLIER) cc_final: -0.0205 (pttp) REVERT: F 20 ILE cc_start: 0.0434 (OUTLIER) cc_final: 0.0215 (mp) outliers start: 159 outliers final: 77 residues processed: 431 average time/residue: 1.3667 time to fit residues: 724.5488 Evaluate side-chains 410 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 302 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 310 ASP 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 525 ASP Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 875 ASP 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 981 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 165 ARG 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 363 LEU 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 663 ASP Chi-restraints excluded: chain B residue 691 ILE 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 753 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 816 ILE 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 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 119 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 131 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 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 816 ILE 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 C residue 979 HIS Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 239 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 246 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 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 115 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS B 467 ASN B 790 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN E 40 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN D 160 ASN D 226 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34549 Z= 0.185 Angle : 0.517 14.160 46547 Z= 0.263 Chirality : 0.039 0.202 4959 Planarity : 0.003 0.066 5915 Dihedral : 4.134 43.600 4444 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.18 % Allowed : 27.79 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 3987 helix: 1.30 (0.11), residues: 2499 sheet: -1.20 (0.43), residues: 82 loop : 0.02 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 757 HIS 0.006 0.001 HIS D 503 PHE 0.019 0.001 PHE A 837 TYR 0.017 0.001 TYR C 539 ARG 0.007 0.000 ARG C 593 *********************** 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 467 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 311 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8661 (m-30) REVERT: A 222 ASP cc_start: 0.8175 (m-30) cc_final: 0.7743 (m-30) REVERT: A 512 LEU cc_start: 0.7374 (mm) cc_final: 0.7052 (mt) REVERT: A 516 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: A 533 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 553 ASP cc_start: 0.8229 (t0) cc_final: 0.7951 (m-30) REVERT: A 738 LYS cc_start: 0.7458 (tmtt) cc_final: 0.6905 (ttpp) REVERT: A 785 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7766 (ttmm) REVERT: A 833 LYS cc_start: 0.6245 (mmmm) cc_final: 0.6019 (mptm) REVERT: A 838 LEU cc_start: 0.7468 (mm) cc_final: 0.7208 (mm) REVERT: A 860 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: A 949 PHE cc_start: 0.6927 (t80) cc_final: 0.6312 (t80) REVERT: A 952 LYS cc_start: 0.8376 (mmtp) cc_final: 0.7845 (pttp) REVERT: A 965 LYS cc_start: 0.8262 (mmmt) cc_final: 0.8055 (tttp) REVERT: B 23 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: B 165 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7668 (mtp85) REVERT: B 179 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8012 (mptt) REVERT: B 267 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6988 (mtm-85) REVERT: B 335 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: B 363 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 399 ASP cc_start: 0.7210 (t0) cc_final: 0.6996 (t0) REVERT: B 491 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: B 526 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7729 (p0) REVERT: B 587 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7666 (ttt180) REVERT: B 626 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 629 ARG cc_start: 0.6940 (ttp80) cc_final: 0.5699 (mmm160) REVERT: B 677 ARG cc_start: 0.7653 (ptt180) cc_final: 0.7032 (ptm160) REVERT: B 693 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 731 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: B 738 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7252 (ttmt) REVERT: B 753 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7313 (mmmm) REVERT: B 790 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 809 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7074 (mmtm) REVERT: B 852 HIS cc_start: 0.7532 (t-90) cc_final: 0.7242 (t-170) REVERT: B 857 LYS cc_start: 0.7991 (tppt) cc_final: 0.7517 (pmtt) REVERT: B 927 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.6573 (m-40) REVERT: B 969 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7801 (tttp) REVERT: B 1001 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: E 21 ASN cc_start: 0.7834 (p0) cc_final: 0.7487 (p0) REVERT: E 28 GLU cc_start: 0.6728 (mm-30) cc_final: 0.5910 (mp0) REVERT: E 58 ASP cc_start: 0.6380 (m-30) cc_final: 0.6092 (m-30) REVERT: E 68 SER cc_start: 0.7928 (p) cc_final: 0.7666 (m) REVERT: E 97 GLU cc_start: 0.6653 (pm20) cc_final: 0.6329 (pp20) REVERT: C 173 ASP cc_start: 0.9046 (p0) cc_final: 0.8753 (p0) REVERT: C 533 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5976 (t80) REVERT: C 547 ASP cc_start: 0.2398 (OUTLIER) cc_final: 0.2012 (t70) REVERT: C 629 ARG cc_start: 0.1927 (OUTLIER) cc_final: 0.1254 (tpt90) REVERT: C 647 MET cc_start: 0.0415 (tpt) cc_final: 0.0067 (tpp) REVERT: C 816 ILE cc_start: 0.2815 (OUTLIER) cc_final: 0.2279 (pp) REVERT: C 911 ASP cc_start: 0.0396 (OUTLIER) cc_final: -0.0492 (t70) REVERT: C 912 TYR cc_start: 0.0223 (OUTLIER) cc_final: -0.0506 (m-80) REVERT: C 913 MET cc_start: -0.0428 (OUTLIER) cc_final: -0.1661 (mpt) REVERT: C 933 PHE cc_start: 0.1242 (m-10) cc_final: 0.0352 (t80) REVERT: C 979 HIS cc_start: 0.0127 (OUTLIER) cc_final: -0.0097 (t-170) REVERT: C 1001 MET cc_start: -0.0744 (mmt) cc_final: -0.0964 (mmt) REVERT: D 21 MET cc_start: 0.6335 (ppp) cc_final: 0.6100 (pp-130) REVERT: D 160 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8166 (m110) REVERT: D 285 ARG cc_start: 0.7515 (mpp80) cc_final: 0.7191 (ttm110) REVERT: D 510 GLU cc_start: 0.5388 (tt0) cc_final: 0.5043 (pm20) REVERT: D 537 LYS cc_start: 0.6542 (ttpt) cc_final: 0.6189 (mppt) REVERT: D 647 MET cc_start: 0.3419 (ppp) cc_final: 0.3089 (tmm) REVERT: D 656 SER cc_start: 0.4382 (OUTLIER) cc_final: 0.3405 (m) REVERT: D 747 ARG cc_start: 0.0700 (OUTLIER) cc_final: -0.0816 (mtt-85) REVERT: D 930 MET cc_start: -0.0573 (tmm) cc_final: -0.1513 (mpp) REVERT: D 977 LYS cc_start: 0.0595 (OUTLIER) cc_final: -0.0226 (pttp) REVERT: F 20 ILE cc_start: 0.0369 (OUTLIER) cc_final: 0.0133 (mp) outliers start: 156 outliers final: 74 residues processed: 431 average time/residue: 1.3578 time to fit residues: 720.7287 Evaluate side-chains 400 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 295 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 238 ASP 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 533 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 875 ASP 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 981 ILE Chi-restraints excluded: chain B residue 23 ASP 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 191 LEU Chi-restraints excluded: chain B residue 267 ARG Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 LEU 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 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE 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 753 LYS Chi-restraints excluded: chain B residue 790 ASN 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 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 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 119 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 131 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 816 ILE 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 C residue 934 ILE Chi-restraints excluded: chain C residue 979 HIS 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 54 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 352 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 338 optimal weight: 3.9990 chunk 361 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 283 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 359 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN B 834 GLN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34549 Z= 0.256 Angle : 0.538 14.478 46547 Z= 0.276 Chirality : 0.040 0.179 4959 Planarity : 0.004 0.060 5915 Dihedral : 4.191 43.219 4441 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.89 % Allowed : 28.14 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 3987 helix: 1.19 (0.10), residues: 2492 sheet: -1.29 (0.43), residues: 82 loop : -0.01 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 757 HIS 0.007 0.001 HIS C 881 PHE 0.024 0.001 PHE A 837 TYR 0.030 0.001 TYR B 791 ARG 0.008 0.000 ARG C 593 *********************** 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 446 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 301 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: A 386 ASN cc_start: 0.8419 (m-40) cc_final: 0.8067 (m-40) REVERT: A 512 LEU cc_start: 0.7382 (mm) cc_final: 0.7054 (mt) REVERT: A 516 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 533 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6688 (t80) REVERT: A 553 ASP cc_start: 0.8241 (t0) cc_final: 0.7984 (m-30) REVERT: A 738 LYS cc_start: 0.7438 (tmtt) cc_final: 0.6793 (ttpp) REVERT: A 744 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 785 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7735 (ttmm) REVERT: A 833 LYS cc_start: 0.6341 (mmmm) cc_final: 0.5787 (ttmm) REVERT: A 838 LEU cc_start: 0.7521 (mm) cc_final: 0.7254 (mm) REVERT: A 860 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: A 949 PHE cc_start: 0.7035 (t80) cc_final: 0.6382 (t80) REVERT: A 952 LYS cc_start: 0.8346 (mmtp) cc_final: 0.7962 (pttp) REVERT: A 965 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8031 (tttp) REVERT: B 23 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: B 165 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7720 (mtp85) REVERT: B 179 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8025 (mptt) REVERT: B 267 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.6996 (mtm-85) REVERT: B 335 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: B 363 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 587 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7646 (ttt180) REVERT: B 626 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7598 (mm-30) REVERT: B 629 ARG cc_start: 0.6970 (ttp80) cc_final: 0.5687 (mmm160) REVERT: B 647 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8472 (mtt) REVERT: B 675 LYS cc_start: 0.6372 (tmtt) cc_final: 0.5510 (tptp) REVERT: B 677 ARG cc_start: 0.7632 (ptt180) cc_final: 0.7007 (ptm160) REVERT: B 693 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: B 731 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: B 738 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7295 (ttmt) REVERT: B 753 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7395 (mmmm) REVERT: B 790 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7385 (p0) REVERT: B 809 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7111 (mmtm) REVERT: B 839 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: B 852 HIS cc_start: 0.7524 (t-90) cc_final: 0.7192 (t-170) REVERT: B 857 LYS cc_start: 0.8005 (tppt) cc_final: 0.7582 (pmtt) REVERT: B 927 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.6582 (m-40) REVERT: B 969 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7830 (tttp) REVERT: B 1001 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7674 (mtm) REVERT: E 21 ASN cc_start: 0.7894 (p0) cc_final: 0.7553 (p0) REVERT: E 28 GLU cc_start: 0.6711 (mm-30) cc_final: 0.5940 (mp0) REVERT: E 58 ASP cc_start: 0.6400 (m-30) cc_final: 0.6109 (m-30) REVERT: E 68 SER cc_start: 0.7902 (p) cc_final: 0.7638 (m) REVERT: E 97 GLU cc_start: 0.6618 (pm20) cc_final: 0.6320 (pp20) REVERT: C 173 ASP cc_start: 0.9037 (p0) cc_final: 0.8743 (p0) REVERT: C 533 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.6036 (t80) REVERT: C 547 ASP cc_start: 0.2442 (OUTLIER) cc_final: 0.2017 (t70) REVERT: C 588 LEU cc_start: 0.1896 (OUTLIER) cc_final: 0.1458 (tp) REVERT: C 629 ARG cc_start: 0.1986 (OUTLIER) cc_final: 0.1294 (tpt90) REVERT: C 647 MET cc_start: 0.0406 (tpt) cc_final: 0.0056 (tpp) REVERT: C 816 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2264 (pp) REVERT: C 911 ASP cc_start: 0.0337 (OUTLIER) cc_final: -0.0559 (t70) REVERT: C 912 TYR cc_start: 0.0176 (OUTLIER) cc_final: -0.0569 (m-80) REVERT: C 913 MET cc_start: -0.0402 (OUTLIER) cc_final: -0.1734 (mpt) REVERT: C 933 PHE cc_start: 0.1304 (m-10) cc_final: 0.0358 (t80) REVERT: C 979 HIS cc_start: 0.0169 (OUTLIER) cc_final: -0.0062 (t-170) REVERT: C 1001 MET cc_start: -0.0795 (mmt) cc_final: -0.1031 (mmt) REVERT: D 21 MET cc_start: 0.6326 (ppp) cc_final: 0.6083 (pp-130) REVERT: D 510 GLU cc_start: 0.5402 (tt0) cc_final: 0.5038 (pm20) REVERT: D 537 LYS cc_start: 0.6575 (ttpt) cc_final: 0.6259 (mppt) REVERT: D 656 SER cc_start: 0.4408 (OUTLIER) cc_final: 0.3439 (m) REVERT: D 747 ARG cc_start: 0.0673 (OUTLIER) cc_final: -0.0903 (mtt-85) REVERT: D 930 MET cc_start: -0.0368 (tmm) cc_final: -0.1380 (mpp) REVERT: D 977 LYS cc_start: 0.0572 (OUTLIER) cc_final: -0.0265 (pttp) REVERT: F 20 ILE cc_start: 0.0264 (OUTLIER) cc_final: 0.0043 (mp) outliers start: 145 outliers final: 79 residues processed: 416 average time/residue: 1.3537 time to fit residues: 690.5130 Evaluate side-chains 408 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 296 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 292 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 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 537 LYS Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 860 GLU 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 B residue 22 LEU Chi-restraints excluded: chain B residue 23 ASP 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 165 ARG 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 363 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE 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 753 LYS Chi-restraints excluded: chain B residue 790 ASN 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 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 62 SER Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 119 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 139 ASP 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 317 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 ASP Chi-restraints excluded: chain C residue 588 LEU 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 816 ILE 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 C residue 934 ILE 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 54 SER 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 278 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 237 optimal weight: 5.9990 chunk 381 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 400 optimal weight: 0.4980 chunk 368 optimal weight: 20.0000 chunk 318 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 246 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 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 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS B 467 ASN B 789 GLN B 790 ASN B 814 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4494 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= 0.201 Angle : 0.536 16.154 46547 Z= 0.272 Chirality : 0.039 0.166 4959 Planarity : 0.003 0.056 5915 Dihedral : 4.111 42.268 4441 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.32 % Allowed : 28.92 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.13), residues: 3987 helix: 1.28 (0.11), residues: 2491 sheet: -1.09 (0.44), residues: 80 loop : 0.01 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.008 0.001 HIS C 881 PHE 0.027 0.001 PHE A 837 TYR 0.016 0.001 TYR C 539 ARG 0.007 0.000 ARG C 593 ********************** 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 428 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 304 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: A 222 ASP cc_start: 0.8191 (m-30) cc_final: 0.7738 (m-30) REVERT: A 386 ASN cc_start: 0.8404 (m-40) cc_final: 0.8049 (m-40) REVERT: A 512 LEU cc_start: 0.7374 (mm) cc_final: 0.7063 (mt) REVERT: A 516 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: A 533 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 553 ASP cc_start: 0.8249 (t0) cc_final: 0.7976 (m-30) REVERT: A 682 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7398 (pm20) REVERT: A 738 LYS cc_start: 0.7445 (tmtt) cc_final: 0.6794 (ttpp) REVERT: A 744 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7487 (t80) REVERT: A 759 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: A 785 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7729 (ttmm) REVERT: A 833 LYS cc_start: 0.6285 (mmmm) cc_final: 0.6023 (mptm) REVERT: A 838 LEU cc_start: 0.7512 (mm) cc_final: 0.7243 (mm) REVERT: A 866 MET cc_start: 0.7227 (mtm) cc_final: 0.6984 (mmm) REVERT: A 949 PHE cc_start: 0.6991 (t80) cc_final: 0.6393 (t80) REVERT: A 952 LYS cc_start: 0.8321 (mmtp) cc_final: 0.8032 (pttp) REVERT: A 965 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8053 (tttp) REVERT: B 23 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: B 165 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7685 (mtp85) REVERT: B 179 LYS cc_start: 0.8385 (mtmm) cc_final: 0.8017 (mptt) REVERT: B 267 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.6989 (mtm-85) REVERT: B 335 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 363 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 587 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7673 (ttt180) REVERT: B 626 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 629 ARG cc_start: 0.6946 (ttp80) cc_final: 0.5694 (mmm160) REVERT: B 675 LYS cc_start: 0.6368 (tmtt) cc_final: 0.5518 (tptp) REVERT: B 677 ARG cc_start: 0.7619 (ptt180) cc_final: 0.6995 (ptm160) REVERT: B 693 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: B 731 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: B 738 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7247 (ttmt) REVERT: B 747 ARG cc_start: 0.7809 (ptt-90) cc_final: 0.7391 (ptp-170) REVERT: B 753 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7355 (mmmm) REVERT: B 790 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7406 (p0) REVERT: B 809 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7078 (mmtm) REVERT: B 839 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: B 852 HIS cc_start: 0.7497 (t-90) cc_final: 0.7200 (t-170) REVERT: B 857 LYS cc_start: 0.8014 (tppt) cc_final: 0.7601 (pmtt) REVERT: B 927 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.6628 (m-40) REVERT: B 969 LYS cc_start: 0.8233 (mmpt) cc_final: 0.7841 (tttp) REVERT: E 21 ASN cc_start: 0.7823 (p0) cc_final: 0.7452 (p0) REVERT: E 28 GLU cc_start: 0.6754 (mm-30) cc_final: 0.5925 (mp0) REVERT: E 58 ASP cc_start: 0.6413 (m-30) cc_final: 0.6128 (m-30) REVERT: E 68 SER cc_start: 0.7908 (p) cc_final: 0.7665 (m) REVERT: E 97 GLU cc_start: 0.6592 (pm20) cc_final: 0.6280 (pp20) REVERT: C 173 ASP cc_start: 0.9027 (p0) cc_final: 0.8724 (p0) REVERT: C 533 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5914 (t80) REVERT: C 547 ASP cc_start: 0.2382 (OUTLIER) cc_final: 0.2028 (t70) REVERT: C 629 ARG cc_start: 0.1911 (OUTLIER) cc_final: 0.1200 (tpt90) REVERT: C 647 MET cc_start: 0.0380 (tpt) cc_final: 0.0034 (tpp) REVERT: C 816 ILE cc_start: 0.2784 (OUTLIER) cc_final: 0.2258 (pp) REVERT: C 911 ASP cc_start: 0.0308 (OUTLIER) cc_final: -0.0485 (t70) REVERT: C 912 TYR cc_start: 0.0169 (OUTLIER) cc_final: -0.0577 (m-80) REVERT: C 933 PHE cc_start: 0.1532 (m-10) cc_final: 0.0524 (t80) REVERT: C 979 HIS cc_start: 0.0290 (OUTLIER) cc_final: 0.0060 (t-170) REVERT: C 1001 MET cc_start: -0.0851 (mmt) cc_final: -0.1052 (mmt) REVERT: D 21 MET cc_start: 0.6383 (ppp) cc_final: 0.6127 (pp-130) REVERT: D 295 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: D 510 GLU cc_start: 0.5414 (tt0) cc_final: 0.5038 (pm20) REVERT: D 656 SER cc_start: 0.4373 (OUTLIER) cc_final: 0.3359 (m) REVERT: D 704 MET cc_start: 0.2174 (mpt) cc_final: 0.0723 (ttt) REVERT: D 747 ARG cc_start: 0.0577 (OUTLIER) cc_final: -0.0961 (mtt-85) REVERT: D 930 MET cc_start: -0.0356 (tmm) cc_final: -0.1269 (mpp) REVERT: D 936 MET cc_start: 0.0831 (mtm) cc_final: -0.1786 (tpt) REVERT: D 977 LYS cc_start: 0.0618 (OUTLIER) cc_final: -0.0200 (pttp) REVERT: F 20 ILE cc_start: 0.0210 (OUTLIER) cc_final: 0.0000 (mp) outliers start: 124 outliers final: 75 residues processed: 402 average time/residue: 1.3257 time to fit residues: 651.8875 Evaluate side-chains 397 residues out of total 3731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 292 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 302 ILE 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 533 PHE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 759 GLU 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 B residue 22 LEU Chi-restraints excluded: chain B residue 23 ASP 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 165 ARG 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 363 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE 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 753 LYS Chi-restraints excluded: chain B residue 790 ASN 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 836 ASP Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain E residue 11 THR 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 119 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 131 THR Chi-restraints excluded: chain C residue 139 ASP 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 317 SER Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 547 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 816 ILE Chi-restraints excluded: chain C residue 911 ASP 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 54 SER 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 278 ASN Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 747 ARG Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 977 LYS Chi-restraints excluded: chain D residue 983 VAL Chi-restraints excluded: chain F residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 253 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 319 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN A 978 HIS ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 814 ASN B 848 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN E 40 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.225058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138896 restraints weight = 41288.756| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.22 r_work: 0.3393 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4557 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= 0.213 Angle : 0.536 17.281 46547 Z= 0.273 Chirality : 0.040 0.276 4959 Planarity : 0.003 0.053 5915 Dihedral : 4.122 42.256 4441 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.40 % Allowed : 28.89 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.13), residues: 3987 helix: 1.28 (0.11), residues: 2488 sheet: -1.05 (0.44), residues: 80 loop : -0.01 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 757 HIS 0.007 0.001 HIS C 881 PHE 0.028 0.001 PHE A 837 TYR 0.018 0.001 TYR C 539 ARG 0.007 0.000 ARG C 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14213.85 seconds wall clock time: 257 minutes 12.01 seconds (15432.01 seconds total)