Starting phenix.real_space_refine on Wed Jan 22 14:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_39369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_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/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_39369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_39369.map" model { file = "/net/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_39369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ykf_39369/01_2025/8ykf_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-5571/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: 23.58, per 1000 atoms: 0.34 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: 13.18 Conformation dependent library (CDL) restraints added in 4.0 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: 4.10 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: 26.39 Time building geometry restraints manager: 16.06 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: 0.01 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: 6.420 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: 0.830 Extract box with map and model: 2.000 Check model and map are aligned: 0.380 Set scattering table: 0.480 Process input model: 110.350 Find NCS groups from input model: 1.670 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: 124.620 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 49 poor density : 601 time to evaluate : 4.006 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: 0.9862 time to fit residues: 972.2468 Evaluate side-chains 471 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 449 time to evaluate : 4.001 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.201560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133450 restraints weight = 158075.606| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.39 r_work: 0.3435 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 to be fit. rotamer outliers: 65 poor density : 464 time to evaluate : 4.135 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: 0.7894 (mm) cc_final: 0.7597 (mm) REVERT: A 441 PHE cc_start: 0.8157 (m-10) cc_final: 0.7820 (m-10) REVERT: A 487 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 760 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7135 (mmm160) REVERT: A 950 ASP cc_start: 0.8363 (t0) cc_final: 0.8092 (t0) REVERT: B 976 MET cc_start: 0.7419 (mmm) cc_final: 0.7214 (mmm) REVERT: B 993 ASP cc_start: 0.8362 (t0) cc_final: 0.8031 (t0) REVERT: B 996 TYR cc_start: 0.7864 (m-80) cc_final: 0.7445 (m-80) REVERT: D 134 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7137 (p90) REVERT: D 143 TRP cc_start: 0.8059 (t60) cc_final: 0.7524 (t60) REVERT: D 289 VAL cc_start: 0.8437 (m) cc_final: 0.7971 (m) REVERT: D 335 GLU cc_start: 0.7795 (mp0) cc_final: 0.7563 (mp0) REVERT: D 341 GLU cc_start: 0.6484 (mp0) cc_final: 0.6094 (mp0) REVERT: D 912 TYR cc_start: 0.8906 (m-80) cc_final: 0.8542 (m-80) REVERT: F 44 PHE cc_start: 0.4429 (OUTLIER) cc_final: 0.3475 (m-10) outliers start: 65 outliers final: 36 residues processed: 514 average time/residue: 0.9936 time to fit residues: 812.8037 Evaluate side-chains 460 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 421 time to evaluate : 4.035 ------------------------------------------------------------------------------- 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 487 GLN 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 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 145 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 381 optimal weight: 9.9990 chunk 208 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.199738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132945 restraints weight = 157745.113| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.51 r_work: 0.3386 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35832 Z= 0.255 Angle : 0.508 6.041 48274 Z= 0.281 Chirality : 0.038 0.150 5126 Planarity : 0.004 0.063 6162 Dihedral : 5.073 59.654 4666 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 1.40 % Allowed : 17.19 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4196 helix: 1.34 (0.11), residues: 2536 sheet: -2.07 (0.32), residues: 218 loop : -0.93 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.007 0.001 HIS B 979 PHE 0.025 0.001 PHE A 440 TYR 0.029 0.001 TYR D 471 ARG 0.006 0.000 ARG D 502 *********************** 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 498 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 444 time to evaluate : 4.091 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 441 PHE cc_start: 0.8231 (m-10) cc_final: 0.7924 (m-10) REVERT: A 616 MET cc_start: 0.8735 (mmm) cc_final: 0.8350 (mmp) REVERT: A 694 GLU cc_start: 0.8205 (tp30) cc_final: 0.7917 (tp30) REVERT: A 912 TYR cc_start: 0.9182 (m-10) cc_final: 0.8922 (m-10) REVERT: B 839 PHE cc_start: 0.8769 (m-80) cc_final: 0.8330 (m-10) REVERT: B 993 ASP cc_start: 0.8427 (t0) cc_final: 0.8011 (t0) REVERT: B 996 TYR cc_start: 0.8108 (m-80) cc_final: 0.7688 (m-80) REVERT: B 998 GLU cc_start: 0.8578 (tt0) cc_final: 0.8374 (tt0) REVERT: D 134 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7237 (p90) REVERT: D 289 VAL cc_start: 0.8481 (m) cc_final: 0.8197 (m) REVERT: D 335 GLU cc_start: 0.7808 (mp0) cc_final: 0.7577 (mp0) REVERT: D 482 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7043 (t80) REVERT: E 26 ASP cc_start: 0.6262 (t0) cc_final: 0.6057 (t0) REVERT: F 44 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3466 (m-10) REVERT: F 116 VAL cc_start: 0.3678 (OUTLIER) cc_final: 0.3331 (p) outliers start: 54 outliers final: 41 residues processed: 486 average time/residue: 0.9498 time to fit residues: 738.9724 Evaluate side-chains 457 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 412 time to evaluate : 4.158 ------------------------------------------------------------------------------- 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 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 486 THR 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 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 239 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 405 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 327 optimal weight: 0.7980 chunk 395 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 D 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.196776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130803 restraints weight = 157032.287| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.47 r_work: 0.3350 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 35832 Z= 0.394 Angle : 0.568 7.123 48274 Z= 0.317 Chirality : 0.040 0.162 5126 Planarity : 0.004 0.065 6162 Dihedral : 5.224 57.826 4665 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 1.96 % Allowed : 18.02 % 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: 0.21 (0.13), residues: 4196 helix: 1.08 (0.10), residues: 2542 sheet: -2.02 (0.31), residues: 232 loop : -1.14 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 958 HIS 0.008 0.001 HIS B 979 PHE 0.023 0.002 PHE B 594 TYR 0.035 0.002 TYR D 471 ARG 0.006 0.001 ARG A 613 *********************** 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 501 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 425 time to evaluate : 4.029 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: A 482 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 694 GLU cc_start: 0.8355 (tp30) cc_final: 0.7842 (tp30) REVERT: A 760 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7282 (mmm160) REVERT: A 912 TYR cc_start: 0.9246 (m-10) cc_final: 0.8907 (m-10) REVERT: B 189 ASP cc_start: 0.8311 (m-30) cc_final: 0.8094 (m-30) REVERT: B 993 ASP cc_start: 0.8431 (t0) cc_final: 0.8003 (t0) REVERT: C 747 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7460 (mtm180) REVERT: C 940 TYR cc_start: 0.6930 (t80) cc_final: 0.6690 (t80) REVERT: D 134 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7296 (p90) REVERT: D 335 GLU cc_start: 0.7814 (mp0) cc_final: 0.7565 (mp0) REVERT: D 482 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7267 (t80) REVERT: D 625 TYR cc_start: 0.7794 (t80) cc_final: 0.7280 (t80) REVERT: D 725 TYR cc_start: 0.7415 (m-80) cc_final: 0.7198 (m-80) REVERT: D 985 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6936 (mtpp) REVERT: F 44 PHE cc_start: 0.4608 (OUTLIER) cc_final: 0.3540 (m-10) REVERT: F 116 VAL cc_start: 0.3669 (OUTLIER) cc_final: 0.3319 (p) outliers start: 76 outliers final: 55 residues processed: 484 average time/residue: 0.9014 time to fit residues: 701.7613 Evaluate side-chains 458 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 4.068 ------------------------------------------------------------------------------- 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 482 TYR 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 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 628 THR Chi-restraints excluded: chain B residue 667 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 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 410 ASN 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 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 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 Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 387 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 332 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 348 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 386 optimal weight: 20.0000 chunk 357 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 93 ASN B 332 HIS B 428 GLN ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.199520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129916 restraints weight = 157218.147| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.17 r_work: 0.3396 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35832 Z= 0.155 Angle : 0.468 7.428 48274 Z= 0.256 Chirality : 0.037 0.159 5126 Planarity : 0.003 0.062 6162 Dihedral : 4.961 57.848 4664 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 18.38 % Favored : 80.17 % 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: 0.69 (0.13), residues: 4196 helix: 1.49 (0.11), residues: 2538 sheet: -1.86 (0.32), residues: 228 loop : -0.99 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.010 0.001 HIS D 810 PHE 0.029 0.001 PHE D 708 TYR 0.029 0.001 TYR D 471 ARG 0.004 0.000 ARG A 514 *********************** 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 479 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 423 time to evaluate : 4.138 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: A 616 MET cc_start: 0.8749 (mmm) cc_final: 0.8329 (mmp) REVERT: A 694 GLU cc_start: 0.8254 (tp30) cc_final: 0.7822 (tp30) REVERT: A 950 ASP cc_start: 0.8406 (t0) cc_final: 0.8036 (t0) REVERT: B 165 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7582 (mpp80) REVERT: B 839 PHE cc_start: 0.8764 (m-80) cc_final: 0.8345 (m-10) REVERT: B 993 ASP cc_start: 0.8337 (t0) cc_final: 0.7956 (t0) REVERT: C 264 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7664 (mtpp) REVERT: C 747 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7398 (mtm180) REVERT: C 940 TYR cc_start: 0.7171 (t80) cc_final: 0.6935 (t80) REVERT: D 134 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7242 (p90) REVERT: D 143 TRP cc_start: 0.8002 (t60) cc_final: 0.7517 (t60) REVERT: D 335 GLU cc_start: 0.7789 (mp0) cc_final: 0.7566 (mp0) REVERT: D 482 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7060 (t80) REVERT: D 912 TYR cc_start: 0.8955 (m-80) cc_final: 0.8589 (m-80) REVERT: E 66 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7842 (tp) REVERT: F 44 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.3431 (m-10) outliers start: 56 outliers final: 42 residues processed: 464 average time/residue: 0.9139 time to fit residues: 681.2851 Evaluate side-chains 452 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 404 time to evaluate : 4.061 ------------------------------------------------------------------------------- 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 507 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 943 PHE 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 239 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 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 733 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU 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 346 VAL Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 526 ASP 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 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 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 66 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 194 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 276 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 93 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.196468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127961 restraints weight = 156902.620| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.34 r_work: 0.3315 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35832 Z= 0.373 Angle : 0.546 7.254 48274 Z= 0.305 Chirality : 0.040 0.176 5126 Planarity : 0.004 0.064 6162 Dihedral : 5.137 59.877 4664 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 2.28 % Allowed : 18.30 % Favored : 79.42 % 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: 0.34 (0.13), residues: 4196 helix: 1.22 (0.10), residues: 2548 sheet: -1.72 (0.33), residues: 206 loop : -1.23 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 143 HIS 0.008 0.001 HIS D 128 PHE 0.022 0.002 PHE B 100 TYR 0.034 0.002 TYR D 471 ARG 0.006 0.000 ARG D 517 *********************** 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 503 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 415 time to evaluate : 4.035 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: A 341 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 616 MET cc_start: 0.8833 (mmm) cc_final: 0.8369 (mmp) REVERT: A 993 ASP cc_start: 0.8061 (t0) cc_final: 0.7781 (t0) REVERT: B 165 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7611 (mpp80) REVERT: B 810 HIS cc_start: 0.8347 (t70) cc_final: 0.8082 (t-170) REVERT: B 839 PHE cc_start: 0.8792 (m-80) cc_final: 0.8371 (m-10) REVERT: B 993 ASP cc_start: 0.8424 (t0) cc_final: 0.7833 (t0) REVERT: B 996 TYR cc_start: 0.8343 (m-80) cc_final: 0.7889 (m-80) REVERT: C 264 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7885 (mtpp) REVERT: C 284 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: C 747 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7506 (mtm180) REVERT: C 940 TYR cc_start: 0.6981 (t80) cc_final: 0.6729 (t80) REVERT: D 134 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7319 (p90) REVERT: D 335 GLU cc_start: 0.7837 (mp0) cc_final: 0.7581 (mp0) REVERT: D 482 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7795 (t80) REVERT: D 625 TYR cc_start: 0.7794 (t80) cc_final: 0.7276 (t80) REVERT: D 725 TYR cc_start: 0.7349 (m-80) cc_final: 0.7015 (m-80) REVERT: E 66 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7964 (tp) REVERT: F 44 PHE cc_start: 0.4309 (OUTLIER) cc_final: 0.3273 (m-10) REVERT: F 116 VAL cc_start: 0.3610 (OUTLIER) cc_final: 0.3268 (p) outliers start: 88 outliers final: 71 residues processed: 484 average time/residue: 0.9301 time to fit residues: 725.8958 Evaluate side-chains 479 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 399 time to evaluate : 4.054 ------------------------------------------------------------------------------- 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 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 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 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 251 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 667 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 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 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 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 419 ASP 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 620 ILE Chi-restraints excluded: chain D residue 886 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 66 ILE 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 140 optimal weight: 0.6980 chunk 301 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 93 ASN B 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.198975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129510 restraints weight = 156664.523| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.30 r_work: 0.3369 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35832 Z= 0.160 Angle : 0.474 8.373 48274 Z= 0.258 Chirality : 0.037 0.159 5126 Planarity : 0.003 0.061 6162 Dihedral : 4.877 59.671 4658 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 1.68 % Allowed : 18.95 % Favored : 79.37 % 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: 0.73 (0.13), residues: 4196 helix: 1.53 (0.10), residues: 2556 sheet: -1.60 (0.34), residues: 202 loop : -1.11 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.007 0.001 HIS D 810 PHE 0.020 0.001 PHE D 708 TYR 0.024 0.001 TYR D 471 ARG 0.010 0.000 ARG D 629 *********************** 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 486 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 4.090 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: A 616 MET cc_start: 0.8777 (mmm) cc_final: 0.8347 (mmp) REVERT: A 694 GLU cc_start: 0.8318 (tp30) cc_final: 0.7895 (tp30) REVERT: A 744 PHE cc_start: 0.8211 (t80) cc_final: 0.7950 (t80) REVERT: A 950 ASP cc_start: 0.8414 (t0) cc_final: 0.8024 (t0) REVERT: A 993 ASP cc_start: 0.8028 (t0) cc_final: 0.7751 (t0) REVERT: B 165 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7575 (mpp80) REVERT: B 810 HIS cc_start: 0.8359 (t70) cc_final: 0.8146 (t-170) REVERT: B 839 PHE cc_start: 0.8775 (m-80) cc_final: 0.8357 (m-10) REVERT: B 993 ASP cc_start: 0.8152 (t0) cc_final: 0.7822 (t0) REVERT: C 264 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7843 (mmmm) REVERT: C 747 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7415 (mtm180) REVERT: C 940 TYR cc_start: 0.7005 (t80) cc_final: 0.6756 (t80) REVERT: D 134 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7346 (p90) REVERT: D 143 TRP cc_start: 0.8025 (t60) cc_final: 0.7563 (t60) REVERT: D 482 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7535 (t80) REVERT: D 625 TYR cc_start: 0.7638 (t80) cc_final: 0.7416 (t80) REVERT: D 912 TYR cc_start: 0.8953 (m-80) cc_final: 0.8566 (m-80) REVERT: E 66 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7947 (tp) REVERT: F 44 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.3299 (m-10) outliers start: 65 outliers final: 50 residues processed: 472 average time/residue: 0.9062 time to fit residues: 686.3961 Evaluate side-chains 458 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 4.476 ------------------------------------------------------------------------------- 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 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 943 PHE 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 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 469 CYS 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 733 LEU Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 232 VAL 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 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 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 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 886 ILE 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 66 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 151 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 402 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 308 optimal weight: 0.0870 chunk 327 optimal weight: 3.9990 chunk 387 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 93 ASN B 332 HIS ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.200299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131902 restraints weight = 156662.256| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.26 r_work: 0.3403 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35832 Z= 0.133 Angle : 0.458 7.793 48274 Z= 0.247 Chirality : 0.037 0.207 5126 Planarity : 0.003 0.060 6162 Dihedral : 4.698 58.048 4658 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.24 % Allowed : 19.36 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.13), residues: 4196 helix: 1.79 (0.11), residues: 2562 sheet: -1.27 (0.37), residues: 178 loop : -1.02 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.006 0.001 HIS A 978 PHE 0.025 0.001 PHE D 708 TYR 0.018 0.001 TYR D 471 ARG 0.012 0.000 ARG D 629 *********************** 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 463 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 415 time to evaluate : 4.186 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: A 588 LEU cc_start: 0.8838 (tt) cc_final: 0.8632 (tt) REVERT: A 616 MET cc_start: 0.8775 (mmm) cc_final: 0.8353 (mmp) REVERT: A 694 GLU cc_start: 0.8294 (tp30) cc_final: 0.7691 (tp30) REVERT: A 744 PHE cc_start: 0.8169 (t80) cc_final: 0.7866 (t80) REVERT: A 950 ASP cc_start: 0.8406 (t0) cc_final: 0.8005 (t0) REVERT: A 993 ASP cc_start: 0.8022 (t0) cc_final: 0.7729 (t0) REVERT: B 810 HIS cc_start: 0.8396 (t70) cc_final: 0.8178 (t-170) REVERT: B 839 PHE cc_start: 0.8817 (m-80) cc_final: 0.8375 (m-10) REVERT: B 936 MET cc_start: 0.5461 (mmt) cc_final: 0.5169 (mpp) REVERT: B 993 ASP cc_start: 0.8123 (t0) cc_final: 0.7710 (t0) REVERT: C 747 ARG cc_start: 0.7678 (mtm180) cc_final: 0.7450 (mtm180) REVERT: C 940 TYR cc_start: 0.7165 (t80) cc_final: 0.6895 (t80) REVERT: D 134 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7138 (p90) REVERT: D 143 TRP cc_start: 0.8047 (t60) cc_final: 0.7567 (t60) REVERT: D 482 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7398 (t80) REVERT: E 66 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7952 (tp) REVERT: F 44 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3000 (m-10) outliers start: 48 outliers final: 41 residues processed: 450 average time/residue: 0.9110 time to fit residues: 661.1867 Evaluate side-chains 441 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 396 time to evaluate : 4.033 ------------------------------------------------------------------------------- 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 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 943 PHE Chi-restraints excluded: chain B residue 181 GLU 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 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 733 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU 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 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 204 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 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 886 ILE 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 66 ILE 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 113 optimal weight: 0.9990 chunk 397 optimal weight: 0.9990 chunk 305 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 317 optimal weight: 0.8980 chunk 93 optimal weight: 0.0870 chunk 345 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 283 optimal weight: 30.0000 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.200050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130990 restraints weight = 157218.353| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.23 r_work: 0.3397 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35832 Z= 0.152 Angle : 0.460 8.832 48274 Z= 0.248 Chirality : 0.037 0.153 5126 Planarity : 0.003 0.060 6162 Dihedral : 4.471 56.333 4655 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 1.22 % Allowed : 19.57 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 4196 helix: 1.89 (0.11), residues: 2548 sheet: -1.71 (0.32), residues: 226 loop : -0.90 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.006 0.001 HIS A 978 PHE 0.018 0.001 PHE D 708 TYR 0.023 0.001 TYR D 471 ARG 0.009 0.000 ARG A 514 *********************** 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 450 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 403 time to evaluate : 4.110 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: A 616 MET cc_start: 0.8788 (mmm) cc_final: 0.8329 (mmp) REVERT: A 694 GLU cc_start: 0.8296 (tp30) cc_final: 0.7700 (tp30) REVERT: A 744 PHE cc_start: 0.8209 (t80) cc_final: 0.7876 (t80) REVERT: A 950 ASP cc_start: 0.8442 (t0) cc_final: 0.8039 (t0) REVERT: A 993 ASP cc_start: 0.8061 (t0) cc_final: 0.7785 (t0) REVERT: B 810 HIS cc_start: 0.8393 (t70) cc_final: 0.8169 (t-170) REVERT: B 839 PHE cc_start: 0.8794 (m-80) cc_final: 0.8367 (m-10) REVERT: B 936 MET cc_start: 0.5480 (mmt) cc_final: 0.5199 (mpp) REVERT: B 985 LYS cc_start: 0.8462 (ttmm) cc_final: 0.7944 (tttt) REVERT: B 993 ASP cc_start: 0.8107 (t0) cc_final: 0.7422 (t0) REVERT: B 996 TYR cc_start: 0.8341 (m-80) cc_final: 0.7618 (m-80) REVERT: C 747 ARG cc_start: 0.7680 (mtm180) cc_final: 0.7342 (mtm180) REVERT: C 940 TYR cc_start: 0.7107 (t80) cc_final: 0.6846 (t80) REVERT: D 134 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7114 (p90) REVERT: D 143 TRP cc_start: 0.8043 (t60) cc_final: 0.7557 (t60) REVERT: D 482 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7470 (t80) REVERT: E 66 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7955 (tp) REVERT: F 44 PHE cc_start: 0.3940 (OUTLIER) cc_final: 0.2874 (m-10) outliers start: 47 outliers final: 40 residues processed: 437 average time/residue: 0.9042 time to fit residues: 637.5585 Evaluate side-chains 437 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 393 time to evaluate : 4.004 ------------------------------------------------------------------------------- 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 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 A residue 966 LEU 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 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR 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 21 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU 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 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 204 MET 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 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 886 ILE 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 66 ILE 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 156 optimal weight: 0.7980 chunk 400 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 334 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.199747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131749 restraints weight = 156629.325| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.35 r_work: 0.3394 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3570 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= 0.170 Angle : 0.471 11.503 48274 Z= 0.253 Chirality : 0.037 0.172 5126 Planarity : 0.003 0.060 6162 Dihedral : 4.333 54.959 4649 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 1.19 % Allowed : 19.67 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.13), residues: 4196 helix: 1.89 (0.11), residues: 2558 sheet: -1.59 (0.34), residues: 202 loop : -0.93 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.006 0.001 HIS A 978 PHE 0.019 0.001 PHE D 708 TYR 0.025 0.001 TYR D 471 ARG 0.008 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 446 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 400 time to evaluate : 4.187 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: A 616 MET cc_start: 0.8775 (mmm) cc_final: 0.8315 (mmp) REVERT: A 694 GLU cc_start: 0.8314 (tp30) cc_final: 0.7728 (tp30) REVERT: A 744 PHE cc_start: 0.8224 (t80) cc_final: 0.7908 (t80) REVERT: A 912 TYR cc_start: 0.9192 (m-80) cc_final: 0.8961 (m-80) REVERT: A 950 ASP cc_start: 0.8447 (t0) cc_final: 0.8045 (t0) REVERT: A 993 ASP cc_start: 0.8068 (t0) cc_final: 0.7796 (t0) REVERT: B 21 MET cc_start: 0.7559 (ttm) cc_final: 0.7297 (ttm) REVERT: B 810 HIS cc_start: 0.8349 (t70) cc_final: 0.8142 (t70) REVERT: B 839 PHE cc_start: 0.8820 (m-80) cc_final: 0.8391 (m-10) REVERT: B 936 MET cc_start: 0.5700 (mmt) cc_final: 0.5420 (mpp) REVERT: B 985 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8006 (tttt) REVERT: B 993 ASP cc_start: 0.8112 (t0) cc_final: 0.7467 (t0) REVERT: B 996 TYR cc_start: 0.8386 (m-80) cc_final: 0.7696 (m-80) REVERT: C 559 PHE cc_start: 0.8650 (m-10) cc_final: 0.8437 (m-10) REVERT: C 940 TYR cc_start: 0.7192 (t80) cc_final: 0.6927 (t80) REVERT: D 134 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7171 (p90) REVERT: D 143 TRP cc_start: 0.8040 (t60) cc_final: 0.7552 (t60) REVERT: D 482 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7530 (t80) REVERT: D 629 ARG cc_start: 0.4827 (ttt-90) cc_final: 0.4606 (ttt-90) REVERT: D 866 MET cc_start: 0.7866 (mmm) cc_final: 0.7277 (mmm) REVERT: E 66 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7996 (tp) REVERT: F 44 PHE cc_start: 0.3944 (OUTLIER) cc_final: 0.2910 (m-10) outliers start: 46 outliers final: 41 residues processed: 434 average time/residue: 0.9163 time to fit residues: 643.4420 Evaluate side-chains 440 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 395 time to evaluate : 4.055 ------------------------------------------------------------------------------- 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 550 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 A residue 943 PHE Chi-restraints excluded: chain A residue 966 LEU 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 512 LEU Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 191 LEU 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 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 204 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 454 LEU Chi-restraints excluded: chain D residue 482 TYR Chi-restraints excluded: chain D residue 886 ILE 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 66 ILE 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 360 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 397 optimal weight: 0.7980 chunk 307 optimal weight: 0.5980 chunk 334 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.199964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130990 restraints weight = 156273.012| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.35 r_work: 0.3394 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35832 Z= 0.161 Angle : 0.464 10.431 48274 Z= 0.249 Chirality : 0.037 0.152 5126 Planarity : 0.003 0.058 6162 Dihedral : 4.282 52.772 4649 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 1.29 % Allowed : 19.57 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4196 helix: 1.92 (0.11), residues: 2562 sheet: -1.60 (0.34), residues: 204 loop : -0.89 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.006 0.001 HIS A 978 PHE 0.021 0.001 PHE D 708 TYR 0.026 0.001 TYR D 471 ARG 0.007 0.000 ARG A 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29228.35 seconds wall clock time: 499 minutes 21.58 seconds (29961.58 seconds total)