Starting phenix.real_space_refine on Mon Oct 14 08:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykf_39369/10_2024/8ykf_39369.cif" } resolution = 3.35 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 134 5.16 5 C 22662 2.51 5 N 5658 2.21 5 O 6562 1.98 5 H 34366 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 69382 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "B" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "C" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "D" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "E" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 24.33, per 1000 atoms: 0.35 Number of scatterers: 69382 At special positions: 0 Unit cell: (102.72, 132.48, 278.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 O 6562 8.00 N 5658 7.00 C 22662 6.00 H 34366 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.28 Conformation dependent library (CDL) restraints added in 4.3 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 14 sheets defined 68.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.969A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.789A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.621A pdb=" N TYR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 4.224A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.673A 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 154 through 158 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.507A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (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 291 removed outlier: 3.678A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 4.296A pdb=" N ASN A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.503A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.674A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 448 through 462 Processing helix chain 'A' and resid 468 through 493 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.814A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.550A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.732A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.664A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 removed outlier: 4.382A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.696A 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: 4.185A 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 removed outlier: 3.737A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 4.106A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 911 through 922 removed outlier: 3.640A pdb=" N THR A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.692A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.613A 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 removed outlier: 3.575A pdb=" N PHE A 954 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.059A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.553A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.795A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.929A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.733A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.717A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.121A 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: 3.532A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.629A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.958A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.704A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 210 removed outlier: 3.594A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.583A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.579A pdb=" N LYS B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.736A pdb=" N ILE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.553A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.543A pdb=" N LEU B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.703A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 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 465 removed outlier: 3.621A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 495 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.536A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.911A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.552A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 564 through 569 removed outlier: 4.207A pdb=" N GLU B 568 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.597A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.631A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 604 " --> pdb=" O TRP B 601 " (cutoff:3.500A) No H-bonds generated for '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 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.580A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 4.419A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 726 removed outlier: 3.885A pdb=" N VAL B 726 " --> pdb=" O ALA B 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 723 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.622A 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 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.867A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 841 removed outlier: 3.579A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 903 Processing helix chain 'B' and resid 911 through 922 removed outlier: 4.263A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 932 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 961 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 991 removed outlier: 3.561A pdb=" N LYS B 977 " --> pdb=" O ASN B 973 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.595A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 23 through 39 removed outlier: 3.554A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 4.106A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 removed outlier: 3.831A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.643A pdb=" N TYR C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.609A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.771A 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 156 through 161 removed outlier: 3.756A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.508A pdb=" N TYR C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.855A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.030A 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 281 through 298 removed outlier: 3.610A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.518A pdb=" N GLY C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 326 through 334 removed outlier: 3.699A pdb=" N LEU C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.588A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 466 removed outlier: 3.735A pdb=" N ILE C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 495 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 508 through 519 removed outlier: 3.816A pdb=" N LEU C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.687A pdb=" N ASP C 526 " --> pdb=" O ASN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 547 removed outlier: 4.299A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.819A pdb=" N GLU C 568 " --> pdb=" O LYS C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.757A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.504A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 removed outlier: 3.544A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 701 removed outlier: 3.564A pdb=" N ILE C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 723 removed outlier: 4.165A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 4.385A 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 744 removed outlier: 3.789A pdb=" N PHE C 744 " --> pdb=" O LEU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.600A pdb=" N TRP C 757 " --> pdb=" O LYS C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 785 Processing helix chain 'C' and resid 786 through 788 No H-bonds generated for 'chain 'C' and resid 786 through 788' Processing helix chain 'C' and resid 800 through 812 removed outlier: 3.676A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 831 through 841 Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 855 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 878 through 903 Processing helix chain 'C' and resid 911 through 922 removed outlier: 3.960A pdb=" N THR C 915 " --> pdb=" O ASP C 911 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 916 " --> pdb=" O TYR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 950 through 954 Processing helix chain 'C' and resid 955 through 962 Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'C' and resid 973 through 992 removed outlier: 4.550A pdb=" N HIS C 978 " --> pdb=" O LYS C 974 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1003 Processing helix chain 'D' and resid 15 through 21 Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 48 through 54 removed outlier: 4.095A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.974A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.651A pdb=" N TYR D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) 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: 3.726A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 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 236 removed outlier: 3.810A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 236 " --> pdb=" O VAL D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 289 removed outlier: 3.544A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.504A pdb=" N ILE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.755A pdb=" N LEU D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 removed outlier: 3.556A pdb=" N ARG D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.785A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 removed outlier: 3.944A pdb=" N GLU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.515A pdb=" N ALA D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.624A pdb=" N ASP D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 494 Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 532 through 538 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.537A pdb=" N GLU D 543 " --> pdb=" O LYS D 540 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 550 removed outlier: 3.966A pdb=" N PHE D 550 " --> pdb=" O ASP D 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 547 through 550' Processing helix chain 'D' and resid 551 through 571 removed outlier: 3.610A pdb=" N THR D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.700A pdb=" N LEU D 585 " --> pdb=" O ASP D 581 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.799A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 637 removed outlier: 3.647A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 631 " --> pdb=" O ARG D 627 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 658 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 680 through 701 removed outlier: 4.227A pdb=" N ALA D 701 " --> pdb=" O LYS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 4.112A pdb=" N THR D 710 " --> pdb=" O VAL D 706 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 3.512A 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 743 Processing helix chain 'D' and resid 750 through 761 Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 812 removed outlier: 4.060A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 805 " --> pdb=" O SER D 801 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 827 Processing helix chain 'D' and resid 832 through 841 removed outlier: 3.628A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 857 Processing helix chain 'D' and resid 861 through 872 Processing helix chain 'D' and resid 878 through 903 Processing helix chain 'D' and resid 911 through 923 Processing helix chain 'D' and resid 927 through 933 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 955 removed outlier: 6.196A pdb=" N ILE D 955 " --> pdb=" O LYS D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 962 removed outlier: 4.074A pdb=" N LYS D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 971 Processing helix chain 'D' and resid 973 through 991 removed outlier: 3.617A pdb=" N LYS D 977 " --> pdb=" O ASN D 973 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS D 978 " --> pdb=" O LYS D 974 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.803A pdb=" N GLU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 14 removed outlier: 3.767A pdb=" N HIS F 12 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 106 removed outlier: 4.233A pdb=" N ILE F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.142A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 129 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (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 573 through 575 removed outlier: 6.362A 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: 6.579A pdb=" N VAL B 129 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (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 'C' and resid 150 through 152 removed outlier: 6.959A pdb=" N LEU C 42 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE C 130 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.564A pdb=" N VAL C 346 " --> pdb=" O CYS C 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.333A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB1, first strand: chain 'E' and resid 71 through 72 removed outlier: 5.364A pdb=" N GLU E 38 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU E 33 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN E 40 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE E 31 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE E 44 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL E 27 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 85 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL E 32 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 83 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 72 removed outlier: 4.032A pdb=" N GLU E 115 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 15 through 17 removed outlier: 6.581A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 62 through 68 removed outlier: 5.371A pdb=" N GLU F 38 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU F 33 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE F 44 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N VAL F 27 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 85 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 32 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE F 83 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 62 through 68 removed outlier: 4.330A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) 1854 hydrogen bonds defined for protein. 5307 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: 25.44 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 34320 1.03 - 1.23: 445 1.23 - 1.43: 15332 1.43 - 1.62: 19879 1.62 - 1.82: 222 Bond restraints: 70198 Sorted by residual: bond pdb=" NE ARG B 987 " pdb=" HE ARG B 987 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" NE ARG A 587 " pdb=" HE ARG A 587 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG A 669 " pdb=" HE ARG A 669 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG C 754 " pdb=" HE ARG C 754 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG B 669 " pdb=" HE ARG B 669 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 70193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.86: 126436 5.86 - 11.73: 54 11.73 - 17.59: 6 17.59 - 23.46: 2 23.46 - 29.32: 4 Bond angle restraints: 126502 Sorted by residual: angle pdb=" CB THR A 499 " pdb=" CG2 THR A 499 " pdb="HG22 THR A 499 " ideal model delta sigma weight residual 110.00 80.68 29.32 3.00e+00 1.11e-01 9.55e+01 angle pdb="HG21 THR A 499 " pdb=" CG2 THR A 499 " pdb="HG22 THR A 499 " ideal model delta sigma weight residual 109.00 79.77 29.23 3.00e+00 1.11e-01 9.50e+01 angle pdb="HG21 THR A 499 " pdb=" CG2 THR A 499 " pdb="HG23 THR A 499 " ideal model delta sigma weight residual 109.00 79.96 29.04 3.00e+00 1.11e-01 9.37e+01 angle pdb=" CB THR A 499 " pdb=" CG2 THR A 499 " pdb="HG23 THR A 499 " ideal model delta sigma weight residual 110.00 81.05 28.95 3.00e+00 1.11e-01 9.31e+01 angle pdb=" N ARG D 629 " pdb=" CA ARG D 629 " pdb=" C ARG D 629 " ideal model delta sigma weight residual 112.90 103.05 9.85 1.31e+00 5.83e-01 5.66e+01 ... (remaining 126497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 29292 17.79 - 35.58: 2754 35.58 - 53.37: 719 53.37 - 71.16: 189 71.16 - 88.95: 44 Dihedral angle restraints: 32998 sinusoidal: 17416 harmonic: 15582 Sorted by residual: dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N SER A 54 " pdb=" CA SER A 54 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU D 53 " pdb=" C LEU D 53 " pdb=" N SER D 54 " pdb=" CA SER D 54 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU B 53 " pdb=" C LEU B 53 " pdb=" N SER B 54 " pdb=" CA SER B 54 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 32995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3858 0.047 - 0.094: 831 0.094 - 0.141: 365 0.141 - 0.189: 59 0.189 - 0.236: 13 Chirality restraints: 5126 Sorted by residual: chirality pdb=" CA ILE C 269 " pdb=" N ILE C 269 " pdb=" C ILE C 269 " pdb=" CB ILE C 269 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE C 691 " pdb=" N ILE C 691 " pdb=" C ILE C 691 " pdb=" CB ILE C 691 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5123 not shown) Planarity restraints: 10282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 613 " -0.260 9.50e-02 1.11e+02 4.82e-01 5.06e+03 pdb=" NE ARG A 613 " -0.176 2.00e-02 2.50e+03 pdb=" CZ ARG A 613 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 613 " 0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG A 613 " -0.013 2.00e-02 2.50e+03 pdb="HH11 ARG A 613 " 0.855 2.00e-02 2.50e+03 pdb="HH12 ARG A 613 " -0.666 2.00e-02 2.50e+03 pdb="HH21 ARG A 613 " 0.630 2.00e-02 2.50e+03 pdb="HH22 ARG A 613 " -0.641 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 566 " -0.287 9.50e-02 1.11e+02 3.75e-01 2.96e+03 pdb=" NE ARG A 566 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 566 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 566 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A 566 " 0.016 2.00e-02 2.50e+03 pdb="HH11 ARG A 566 " -0.787 2.00e-02 2.50e+03 pdb="HH12 ARG A 566 " 0.725 2.00e-02 2.50e+03 pdb="HH21 ARG A 566 " -0.113 2.00e-02 2.50e+03 pdb="HH22 ARG A 566 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 536 " -0.171 2.00e-02 2.50e+03 4.23e-01 2.69e+03 pdb=" CD GLN A 536 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 536 " 0.166 2.00e-02 2.50e+03 pdb=" NE2 GLN A 536 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 536 " 0.710 2.00e-02 2.50e+03 pdb="HE22 GLN A 536 " -0.717 2.00e-02 2.50e+03 ... (remaining 10279 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 631 2.06 - 2.69: 108568 2.69 - 3.33: 202587 3.33 - 3.96: 252249 3.96 - 4.60: 397794 Nonbonded interactions: 961829 Sorted by model distance: nonbonded pdb="HH21 ARG A 627 " pdb="HG22 THR A 628 " model vdw 1.424 2.270 nonbonded pdb=" OE1 GLU B 510 " pdb=" H GLU B 510 " model vdw 1.438 2.450 nonbonded pdb=" OE1 GLU C 449 " pdb=" H GLU C 449 " model vdw 1.443 2.450 nonbonded pdb=" OE1 GLU B 731 " pdb=" H GLU B 731 " model vdw 1.447 2.450 nonbonded pdb=" OE1 GLU B 449 " pdb=" H GLU B 449 " model vdw 1.545 2.450 ... (remaining 961824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1005) selection = (chain 'C' and resid 14 through 1005) selection = chain 'D' } 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: 7.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.900 Extract box with map and model: 2.160 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 112.770 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 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 : 0.005 0.050 35832 Z= 0.330 Angle : 0.784 9.854 48274 Z= 0.548 Chirality : 0.049 0.236 5126 Planarity : 0.005 0.128 6162 Dihedral : 16.248 88.950 13340 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 1.27 % Allowed : 16.37 % Favored : 82.37 % 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: -0.06 (0.13), residues: 4196 helix: 0.72 (0.11), residues: 2476 sheet: -1.81 (0.32), residues: 232 loop : -0.92 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.010 0.001 HIS E 12 PHE 0.027 0.001 PHE A 440 TYR 0.026 0.001 TYR D 471 ARG 0.012 0.001 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 601 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.7051 (mmp) cc_final: 0.6187 (mmt) REVERT: A 828 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6859 (m) REVERT: A 1000 LEU cc_start: 0.7825 (tt) cc_final: 0.7547 (tp) REVERT: B 440 PHE cc_start: 0.5632 (t80) cc_final: 0.4553 (t80) REVERT: B 630 ASP cc_start: 0.6755 (m-30) cc_final: 0.6549 (m-30) REVERT: D 625 TYR cc_start: 0.5624 (t80) cc_final: 0.5281 (t80) outliers start: 49 outliers final: 21 residues processed: 634 average time/residue: 0.9893 time to fit residues: 973.0220 Evaluate side-chains 471 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 449 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 886 ILE Chi-restraints excluded: chain D residue 985 LYS Chi-restraints excluded: chain F residue 21 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 327 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 549 GLN A 666 ASN B 591 ASN B 867 ASN B 979 HIS C 115 ASN D 457 ASN ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35832 Z= 0.260 Angle : 0.557 6.715 48274 Z= 0.308 Chirality : 0.039 0.187 5126 Planarity : 0.004 0.066 6162 Dihedral : 5.434 58.184 4680 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 1.68 % Allowed : 16.86 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 4196 helix: 1.15 (0.10), residues: 2544 sheet: -2.08 (0.31), residues: 218 loop : -0.86 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.006 0.001 HIS D 128 PHE 0.020 0.001 PHE B 594 TYR 0.029 0.002 TYR D 471 ARG 0.013 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 464 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.7896 (mm) cc_final: 0.7645 (mm) REVERT: A 760 ARG cc_start: 0.6268 (mmm160) cc_final: 0.5880 (mmm160) REVERT: A 828 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7069 (m) REVERT: D 134 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6811 (p90) REVERT: D 143 TRP cc_start: 0.7209 (t60) cc_final: 0.6688 (t60) REVERT: D 289 VAL cc_start: 0.8058 (m) cc_final: 0.7617 (m) REVERT: F 44 PHE cc_start: 0.2019 (OUTLIER) cc_final: 0.1485 (m-10) outliers start: 65 outliers final: 36 residues processed: 514 average time/residue: 0.9332 time to fit residues: 754.7470 Evaluate side-chains 458 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 419 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 861 ASN Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 985 LYS Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 380 optimal weight: 20.0000 chunk 410 optimal weight: 20.0000 chunk 338 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 305 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 297 GLN D 297 GLN D 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35832 Z= 0.259 Angle : 0.515 6.082 48274 Z= 0.286 Chirality : 0.038 0.152 5126 Planarity : 0.004 0.064 6162 Dihedral : 5.096 59.933 4667 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.42 % Allowed : 17.27 % Favored : 81.31 % 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: 0.54 (0.13), residues: 4196 helix: 1.33 (0.11), residues: 2536 sheet: -2.09 (0.32), residues: 218 loop : -0.94 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.006 0.001 HIS B 128 PHE 0.021 0.001 PHE A 440 TYR 0.029 0.001 TYR D 471 ARG 0.009 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 444 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.8059 (mmm) cc_final: 0.7605 (mmp) REVERT: D 134 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6926 (p90) REVERT: D 289 VAL cc_start: 0.8113 (m) cc_final: 0.7789 (m) REVERT: D 482 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6950 (t80) REVERT: D 578 MET cc_start: 0.5994 (pmm) cc_final: 0.5579 (pmm) REVERT: E 26 ASP cc_start: 0.5596 (t0) cc_final: 0.5389 (t0) REVERT: F 44 PHE cc_start: 0.2045 (OUTLIER) cc_final: 0.1473 (m-10) REVERT: F 116 VAL cc_start: 0.3572 (OUTLIER) cc_final: 0.3013 (p) outliers start: 55 outliers final: 42 residues processed: 486 average time/residue: 0.9373 time to fit residues: 722.8005 Evaluate side-chains 454 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 408 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 861 ASN Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 985 LYS Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 381 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 199 optimal weight: 0.1980 chunk 361 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35832 Z= 0.247 Angle : 0.503 6.316 48274 Z= 0.277 Chirality : 0.038 0.162 5126 Planarity : 0.003 0.063 6162 Dihedral : 5.034 59.000 4665 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 17.74 % Favored : 80.69 % 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: 0.60 (0.13), residues: 4196 helix: 1.40 (0.10), residues: 2534 sheet: -1.84 (0.31), residues: 232 loop : -0.98 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 958 HIS 0.007 0.001 HIS B 979 PHE 0.016 0.001 PHE B 594 TYR 0.029 0.001 TYR D 471 ARG 0.004 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 424 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.8116 (mmm) cc_final: 0.7627 (mmp) REVERT: C 781 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7220 (mt) REVERT: D 134 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.6971 (p90) REVERT: D 341 GLU cc_start: 0.6209 (mp0) cc_final: 0.5931 (mp0) REVERT: D 482 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6917 (t80) REVERT: F 44 PHE cc_start: 0.2259 (OUTLIER) cc_final: 0.1527 (m-10) outliers start: 61 outliers final: 44 residues processed: 470 average time/residue: 0.9138 time to fit residues: 684.1249 Evaluate side-chains 451 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 403 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 985 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35832 Z= 0.265 Angle : 0.505 5.960 48274 Z= 0.279 Chirality : 0.038 0.178 5126 Planarity : 0.003 0.063 6162 Dihedral : 5.016 57.627 4664 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 1.78 % Allowed : 18.20 % Favored : 80.02 % 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: 0.59 (0.13), residues: 4196 helix: 1.40 (0.10), residues: 2548 sheet: -1.88 (0.31), residues: 228 loop : -1.05 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 60 HIS 0.007 0.001 HIS B 979 PHE 0.017 0.001 PHE B 100 TYR 0.029 0.001 TYR D 471 ARG 0.005 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 413 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 866 MET cc_start: 0.5860 (ppp) cc_final: 0.5399 (ppp) REVERT: D 134 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6995 (p90) REVERT: D 482 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6843 (t80) REVERT: F 44 PHE cc_start: 0.2202 (OUTLIER) cc_final: 0.1435 (m-10) REVERT: F 80 ASN cc_start: 0.3218 (t0) cc_final: 0.2910 (m-40) REVERT: F 116 VAL cc_start: 0.3519 (OUTLIER) cc_final: 0.2974 (p) outliers start: 69 outliers final: 56 residues processed: 466 average time/residue: 0.9115 time to fit residues: 683.6803 Evaluate side-chains 464 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 404 time to evaluate : 4.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain D residue 985 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 0.9990 chunk 363 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 224 ASN A 297 GLN A 483 GLN B 332 HIS B 786 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 35832 Z= 0.435 Angle : 0.583 7.226 48274 Z= 0.327 Chirality : 0.041 0.171 5126 Planarity : 0.004 0.064 6162 Dihedral : 5.202 58.130 4662 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 2.46 % Allowed : 18.38 % Favored : 79.16 % 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: 0.08 (0.13), residues: 4196 helix: 1.01 (0.10), residues: 2564 sheet: -1.93 (0.30), residues: 250 loop : -1.30 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 143 HIS 0.008 0.001 HIS D 128 PHE 0.025 0.002 PHE B 528 TYR 0.036 0.002 TYR D 471 ARG 0.005 0.001 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 421 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: B 165 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (mpp80) REVERT: B 866 MET cc_start: 0.5931 (ppp) cc_final: 0.5660 (ppp) REVERT: C 264 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7883 (mtpp) REVERT: C 284 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 709 TYR cc_start: 0.6657 (t80) cc_final: 0.6428 (t80) REVERT: D 134 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7071 (p90) REVERT: D 482 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7542 (t80) REVERT: F 44 PHE cc_start: 0.1959 (OUTLIER) cc_final: 0.1271 (m-10) REVERT: F 116 VAL cc_start: 0.3633 (OUTLIER) cc_final: 0.3066 (p) outliers start: 95 outliers final: 75 residues processed: 494 average time/residue: 0.9000 time to fit residues: 711.6147 Evaluate side-chains 480 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 397 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 367 CYS Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain C residue 861 ASN Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 599 CYS Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 40.0000 chunk 45 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS B 428 GLN ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35832 Z= 0.286 Angle : 0.523 8.028 48274 Z= 0.289 Chirality : 0.039 0.179 5126 Planarity : 0.003 0.062 6162 Dihedral : 5.052 56.610 4658 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.28 % Allowed : 19.08 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4196 helix: 1.21 (0.10), residues: 2552 sheet: -1.70 (0.34), residues: 202 loop : -1.27 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.006 0.001 HIS D 128 PHE 0.027 0.001 PHE D 708 TYR 0.034 0.001 TYR D 471 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 409 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: B 165 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7518 (mpp80) REVERT: B 866 MET cc_start: 0.5880 (ppp) cc_final: 0.5621 (ppp) REVERT: C 264 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7844 (mmmm) REVERT: C 284 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: C 709 TYR cc_start: 0.6505 (t80) cc_final: 0.6233 (t80) REVERT: D 134 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7136 (p90) REVERT: D 482 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7392 (t80) REVERT: F 44 PHE cc_start: 0.2078 (OUTLIER) cc_final: 0.1392 (m-10) REVERT: F 116 VAL cc_start: 0.3584 (OUTLIER) cc_final: 0.3031 (p) outliers start: 88 outliers final: 65 residues processed: 477 average time/residue: 0.8927 time to fit residues: 686.7842 Evaluate side-chains 473 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 400 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain C residue 861 ASN Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 620 ILE Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 240 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 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 133 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35832 Z= 0.173 Angle : 0.481 8.607 48274 Z= 0.261 Chirality : 0.037 0.154 5126 Planarity : 0.003 0.061 6162 Dihedral : 4.815 54.648 4656 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 1.47 % Allowed : 19.67 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 4196 helix: 1.53 (0.10), residues: 2560 sheet: -1.63 (0.34), residues: 202 loop : -1.16 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.007 0.001 HIS A 978 PHE 0.023 0.001 PHE D 708 TYR 0.028 0.001 TYR D 471 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 413 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7501 (mpp80) REVERT: B 866 MET cc_start: 0.5831 (ppp) cc_final: 0.5609 (ppp) REVERT: C 264 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7669 (mmmm) REVERT: D 134 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7121 (p90) REVERT: D 143 TRP cc_start: 0.7181 (t60) cc_final: 0.6754 (t60) REVERT: D 482 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7120 (t80) REVERT: F 44 PHE cc_start: 0.1995 (OUTLIER) cc_final: 0.1306 (m-10) outliers start: 57 outliers final: 49 residues processed: 455 average time/residue: 0.9098 time to fit residues: 666.2345 Evaluate side-chains 448 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 394 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 507 PHE Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 352 optimal weight: 3.9990 chunk 375 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 294 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 374 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 35832 Z= 0.309 Angle : 0.531 8.562 48274 Z= 0.292 Chirality : 0.039 0.161 5126 Planarity : 0.003 0.062 6162 Dihedral : 4.898 56.678 4656 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 1.86 % Allowed : 19.54 % Favored : 78.59 % 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: 0.51 (0.13), residues: 4196 helix: 1.39 (0.10), residues: 2552 sheet: -2.08 (0.34), residues: 188 loop : -1.19 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 60 HIS 0.007 0.001 HIS D 128 PHE 0.020 0.002 PHE D 708 TYR 0.029 0.002 TYR D 471 ARG 0.009 0.000 ARG C 747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 405 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.6374 (ptp) cc_final: 0.6137 (ptp) REVERT: A 526 ASP cc_start: 0.7826 (t70) cc_final: 0.7520 (t0) REVERT: B 165 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7530 (mpp80) REVERT: B 866 MET cc_start: 0.5991 (ppp) cc_final: 0.5780 (ppp) REVERT: C 264 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7832 (mmmm) REVERT: C 284 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: D 134 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7152 (p90) REVERT: D 143 TRP cc_start: 0.7209 (t60) cc_final: 0.6786 (t60) REVERT: D 482 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7446 (t80) REVERT: F 44 PHE cc_start: 0.2150 (OUTLIER) cc_final: 0.1307 (m-10) outliers start: 72 outliers final: 59 residues processed: 460 average time/residue: 0.9073 time to fit residues: 674.7653 Evaluate side-chains 465 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 400 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 5.9990 chunk 397 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 416 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 35832 Z= 0.401 Angle : 0.581 10.084 48274 Z= 0.322 Chirality : 0.041 0.168 5126 Planarity : 0.004 0.063 6162 Dihedral : 5.021 57.545 4654 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 1.94 % Allowed : 19.75 % Favored : 78.31 % 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: 0.15 (0.13), residues: 4196 helix: 1.09 (0.10), residues: 2564 sheet: -2.12 (0.34), residues: 188 loop : -1.35 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 143 HIS 0.008 0.001 HIS D 128 PHE 0.021 0.002 PHE B 100 TYR 0.030 0.002 TYR D 471 ARG 0.006 0.000 ARG A 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 405 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5718 (tmm) cc_final: 0.5461 (tmm) REVERT: A 341 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: A 421 MET cc_start: 0.6462 (ptp) cc_final: 0.6208 (ptp) REVERT: A 526 ASP cc_start: 0.7888 (t70) cc_final: 0.7513 (t0) REVERT: B 165 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7496 (mpp80) REVERT: B 866 MET cc_start: 0.6035 (ppp) cc_final: 0.5819 (ppp) REVERT: C 264 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7814 (mmmm) REVERT: C 284 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: D 134 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7139 (p90) REVERT: D 482 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7539 (t80) REVERT: F 44 PHE cc_start: 0.2184 (OUTLIER) cc_final: 0.1362 (m-10) outliers start: 75 outliers final: 64 residues processed: 463 average time/residue: 0.9084 time to fit residues: 672.9502 Evaluate side-chains 463 residues out of total 3868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 392 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 638 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 943 PHE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 887 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 828 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 492 PHE Chi-restraints excluded: chain D residue 892 ARG Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 CYS Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 4.9990 chunk 353 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 chunk 139 optimal weight: 0.0050 chunk 341 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.197675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131356 restraints weight = 156639.692| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.26 r_work: 0.3368 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35832 Z= 0.202 Angle : 0.508 9.629 48274 Z= 0.276 Chirality : 0.038 0.156 5126 Planarity : 0.003 0.080 6162 Dihedral : 4.749 54.384 4650 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 1.50 % Allowed : 20.27 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4196 helix: 1.44 (0.10), residues: 2568 sheet: -1.90 (0.37), residues: 164 loop : -1.22 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.018 0.001 HIS A 979 PHE 0.025 0.001 PHE A 744 TYR 0.030 0.001 TYR A 888 ARG 0.012 0.000 ARG A 747 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13447.07 seconds wall clock time: 233 minutes 22.41 seconds (14002.41 seconds total)