Starting phenix.real_space_refine on Mon Jul 6 17:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygf_39246/07_2026/8ygf_39246.cif" } resolution = 4.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 24200 2.51 5 N 6044 2.21 5 O 7140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "B" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "C" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "F" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 8183 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 963} Chain: "G" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "H" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Time building chain proxies: 7.80, per 1000 atoms: 0.21 Number of scatterers: 37524 At special positions: 0 Unit cell: (105.41, 136.12, 266.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 7140 8.00 N 6044 7.00 C 24200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8632 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 19 sheets defined 61.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.989A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.811A 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: 3.681A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.691A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.532A pdb=" N GLY A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.685A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.581A pdb=" N TYR A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.747A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.717A pdb=" N ILE A 302 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 317 removed outlier: 4.131A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.702A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.755A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.163A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.801A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 449 through 462 removed outlier: 4.524A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 495 removed outlier: 4.277A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 520 removed outlier: 3.808A pdb=" N LEU A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.782A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.703A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.922A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 629 removed outlier: 3.890A pdb=" N ARG A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.662A pdb=" N LYS A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.615A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 712 through 723 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 removed outlier: 3.512A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.538A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.505A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 812 removed outlier: 4.256A pdb=" N ASP A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 808 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.609A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.909A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.626A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 4.033A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 979 through 990 removed outlier: 3.567A pdb=" N LYS A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 removed outlier: 4.041A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.489A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.931A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.562A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.769A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.701A pdb=" N ALA B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 161 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 4.635A pdb=" N ASP B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.559A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 4.003A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.710A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.842A pdb=" N ILE B 302 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.766A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.563A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.581A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 467 through 495 removed outlier: 4.472A pdb=" N TYR B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.867A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.624A pdb=" N MET B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.930A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 570 removed outlier: 3.601A pdb=" N TYR B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.789A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.655A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 660 through 671 removed outlier: 4.227A pdb=" N ASN B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.554A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.933A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.679A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 784 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.642A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 861 through 871 removed outlier: 4.039A pdb=" N LEU B 865 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 removed outlier: 3.528A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.807A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.607A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.782A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 954 " --> pdb=" O TYR B 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 954' Processing helix chain 'B' and resid 955 through 961 removed outlier: 4.096A pdb=" N ASN B 961 " --> pdb=" O TRP B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 972 removed outlier: 3.904A pdb=" N LEU B 966 " --> pdb=" O TYR B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.603A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1005 Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.369A pdb=" N ARG D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.998A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 Processing helix chain 'E' and resid 85 through 95 removed outlier: 4.606A pdb=" N GLN E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.855A pdb=" N PHE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.658A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.654A pdb=" N ARG E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.968A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.620A pdb=" N ASN E 182 " --> pdb=" O LYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 removed outlier: 4.263A pdb=" N TYR E 197 " --> pdb=" O TYR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.695A pdb=" N SER E 201 " --> pdb=" O TYR E 197 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.520A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.541A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 302 removed outlier: 3.800A pdb=" N ILE E 302 " --> pdb=" O ASN E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.007A pdb=" N ASP E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 315 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 321 removed outlier: 3.803A pdb=" N ALA E 321 " --> pdb=" O PRO E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 321' Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 355 through 366 removed outlier: 3.945A pdb=" N PHE E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE E 361 " --> pdb=" O MET E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.581A pdb=" N LYS E 372 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 373 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 391 Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'E' and resid 411 through 416 removed outlier: 3.979A pdb=" N HIS E 415 " --> pdb=" O SER E 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 416' Processing helix chain 'E' and resid 417 through 426 removed outlier: 3.985A pdb=" N GLU E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 Processing helix chain 'E' and resid 447 through 461 removed outlier: 3.609A pdb=" N SER E 451 " --> pdb=" O ARG E 447 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP E 453 " --> pdb=" O GLU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 500 removed outlier: 4.334A pdb=" N TYR E 471 " --> pdb=" O ASN E 467 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU E 497 " --> pdb=" O ASN E 493 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 520 Processing helix chain 'E' and resid 532 through 539 Processing helix chain 'E' and resid 540 through 543 Processing helix chain 'E' and resid 548 through 572 removed outlier: 3.764A pdb=" N LYS E 557 " --> pdb=" O ASP E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 598 removed outlier: 3.724A pdb=" N ASN E 598 " --> pdb=" O PHE E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 removed outlier: 4.065A pdb=" N VAL E 603 " --> pdb=" O LEU E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 628 removed outlier: 3.559A pdb=" N ARG E 627 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR E 628 " --> pdb=" O GLU E 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 639 removed outlier: 3.596A pdb=" N PHE E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 659 removed outlier: 4.127A pdb=" N ASN E 654 " --> pdb=" O TYR E 650 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 655 " --> pdb=" O ASP E 651 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 669 removed outlier: 3.908A pdb=" N ARG E 669 " --> pdb=" O LYS E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 701 removed outlier: 4.242A pdb=" N ILE E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 711 removed outlier: 4.255A pdb=" N GLN E 711 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 723 Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'E' and resid 729 through 743 Processing helix chain 'E' and resid 750 through 765 removed outlier: 4.243A pdb=" N CYS E 764 " --> pdb=" O ARG E 760 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN E 765 " --> pdb=" O LEU E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 786 Processing helix chain 'E' and resid 799 through 812 removed outlier: 4.278A pdb=" N ASP E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 826 Processing helix chain 'E' and resid 831 through 840 Processing helix chain 'E' and resid 841 through 845 Processing helix chain 'E' and resid 846 through 855 removed outlier: 4.009A pdb=" N SER E 855 " --> pdb=" O SER E 851 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 869 Processing helix chain 'E' and resid 878 through 903 Processing helix chain 'E' and resid 912 through 922 removed outlier: 4.069A pdb=" N GLY E 917 " --> pdb=" O MET E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 934 removed outlier: 4.067A pdb=" N MET E 930 " --> pdb=" O ASN E 927 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 934 " --> pdb=" O GLU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 945 Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 958 through 962 Processing helix chain 'E' and resid 963 through 971 Processing helix chain 'E' and resid 977 through 991 removed outlier: 3.689A pdb=" N ILE E 981 " --> pdb=" O LYS E 977 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU E 982 " --> pdb=" O HIS E 978 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 989 " --> pdb=" O LYS E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1003 removed outlier: 3.765A pdb=" N LEU E 997 " --> pdb=" O ASP E 993 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E1003 " --> pdb=" O ILE E 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 39 removed outlier: 3.615A pdb=" N ASN F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 54 removed outlier: 4.090A pdb=" N SER F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.698A pdb=" N LEU F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 109 removed outlier: 4.091A pdb=" N LEU F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 7.699A pdb=" N GLU F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N MET F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 124 removed outlier: 4.108A pdb=" N ASP F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 179 through 183 removed outlier: 3.546A pdb=" N ASN F 182 " --> pdb=" O LYS F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 197 removed outlier: 3.892A pdb=" N TYR F 190 " --> pdb=" O LYS F 186 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 197 " --> pdb=" O TYR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.710A pdb=" N HIS F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 234 removed outlier: 3.689A pdb=" N ASN F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.815A pdb=" N VAL F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.778A pdb=" N ILE F 302 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 317 Processing helix chain 'F' and resid 318 through 322 removed outlier: 3.522A pdb=" N ALA F 321 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 334 removed outlier: 3.864A pdb=" N VAL F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 334' Processing helix chain 'F' and resid 355 through 365 Processing helix chain 'F' and resid 366 through 372 Processing helix chain 'F' and resid 374 through 392 Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'F' and resid 417 through 427 Processing helix chain 'F' and resid 431 through 446 Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.624A pdb=" N ASP F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 467 through 495 removed outlier: 4.044A pdb=" N TYR F 471 " --> pdb=" O ASN F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'F' and resid 508 through 519 Processing helix chain 'F' and resid 524 through 531 removed outlier: 4.363A pdb=" N PHE F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN F 529 " --> pdb=" O ASP F 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 537 removed outlier: 3.768A pdb=" N GLN F 536 " --> pdb=" O PRO F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 547 removed outlier: 3.870A pdb=" N PHE F 544 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP F 547 " --> pdb=" O PHE F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 570 removed outlier: 3.664A pdb=" N TYR F 552 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP F 554 " --> pdb=" O PHE F 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 570 " --> pdb=" O ARG F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 removed outlier: 4.188A pdb=" N ASN F 598 " --> pdb=" O PHE F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 604 removed outlier: 3.671A pdb=" N SER F 604 " --> pdb=" O TRP F 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 601 through 604' Processing helix chain 'F' and resid 605 through 628 removed outlier: 4.009A pdb=" N TYR F 611 " --> pdb=" O GLU F 607 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 612 " --> pdb=" O PHE F 608 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR F 628 " --> pdb=" O GLU F 624 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 658 Processing helix chain 'F' and resid 660 through 671 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 682 through 699 removed outlier: 3.661A pdb=" N GLU F 686 " --> pdb=" O GLU F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 723 removed outlier: 4.172A pdb=" N GLN F 711 " --> pdb=" O VAL F 707 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE F 713 " --> pdb=" O TYR F 709 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER F 714 " --> pdb=" O THR F 710 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU F 715 " --> pdb=" O GLN F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 726 No H-bonds generated for 'chain 'F' and resid 724 through 726' Processing helix chain 'F' and resid 729 through 743 Processing helix chain 'F' and resid 750 through 763 removed outlier: 3.572A pdb=" N GLU F 759 " --> pdb=" O TYR F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 787 removed outlier: 3.901A pdb=" N ILE F 787 " --> pdb=" O ALA F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 812 Processing helix chain 'F' and resid 819 through 826 Processing helix chain 'F' and resid 832 through 841 removed outlier: 3.720A pdb=" N LYS F 840 " --> pdb=" O ASP F 836 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU F 841 " --> pdb=" O PHE F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 846 through 856 Processing helix chain 'F' and resid 863 through 869 Processing helix chain 'F' and resid 881 through 903 Processing helix chain 'F' and resid 911 through 922 removed outlier: 3.686A pdb=" N THR F 915 " --> pdb=" O ASP F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 934 removed outlier: 3.596A pdb=" N GLU F 931 " --> pdb=" O SER F 928 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 934 " --> pdb=" O GLU F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 945 Processing helix chain 'F' and resid 956 through 962 removed outlier: 3.591A pdb=" N LYS F 960 " --> pdb=" O PRO F 956 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN F 961 " --> pdb=" O SER F 957 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR F 962 " --> pdb=" O TRP F 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 956 through 962' Processing helix chain 'F' and resid 964 through 972 Processing helix chain 'F' and resid 976 through 991 removed outlier: 4.327A pdb=" N VAL F 980 " --> pdb=" O MET F 976 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 981 " --> pdb=" O LYS F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1003 removed outlier: 4.021A pdb=" N TYR F1003 " --> pdb=" O ILE F 999 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'H' and resid 70 through 78 removed outlier: 3.634A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 8.832A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 4.100A pdb=" N SER C 31 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 62 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 222 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 220 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 218 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795 removed outlier: 3.757A pdb=" N ALA D 222 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE D 59 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 794 through 795 removed outlier: 4.411A pdb=" N ASN D 197 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 removed outlier: 3.848A pdb=" N SER D 189 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG D 176 " --> pdb=" O ASP D 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 removed outlier: 5.571A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS B 128 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL B 46 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 43 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 244 through 247 removed outlier: 6.331A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.775A pdb=" N VAL B 346 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.955A pdb=" N VAL C 22 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 189 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 150 through 152 removed outlier: 3.986A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB4, first strand: chain 'E' and resid 574 through 575 removed outlier: 3.589A pdb=" N GLU G 58 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 904 through 906 removed outlier: 3.621A pdb=" N SER H 189 " --> pdb=" O ALA H 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.372A pdb=" N SER F 150 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS F 169 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 152 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS F 128 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE F 44 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE F 245 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 338 through 340 Processing sheet with id=AB8, first strand: chain 'F' and resid 573 through 575 removed outlier: 3.618A pdb=" N SER H 31 " --> pdb=" O THR H 62 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE H 59 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.783A pdb=" N SER G 189 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 233 " --> pdb=" O GLN G 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 62 through 63 1853 hydrogen bonds defined for protein. 5268 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: 7.39 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10953 1.34 - 1.46: 7789 1.46 - 1.58: 19384 1.58 - 1.70: 2 1.70 - 1.82: 240 Bond restraints: 38368 Sorted by residual: bond pdb=" C ALA C 215 " pdb=" O ALA C 215 " ideal model delta sigma weight residual 1.233 1.249 -0.016 4.80e-03 4.34e+04 1.09e+01 bond pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.36e+00 bond pdb=" N GLU F 298 " pdb=" CA GLU F 298 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.06e-02 8.90e+03 7.93e+00 bond pdb=" CA ILE F 87 " pdb=" CB ILE F 87 " ideal model delta sigma weight residual 1.537 1.523 0.013 5.00e-03 4.00e+04 7.21e+00 bond pdb=" N GLN B 297 " pdb=" CA GLN B 297 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.26e-02 6.30e+03 5.92e+00 ... (remaining 38363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 51112 3.25 - 6.50: 506 6.50 - 9.76: 73 9.76 - 13.01: 13 13.01 - 16.26: 4 Bond angle restraints: 51708 Sorted by residual: angle pdb=" CA PRO F 843 " pdb=" N PRO F 843 " pdb=" CD PRO F 843 " ideal model delta sigma weight residual 112.00 102.35 9.65 1.40e+00 5.10e-01 4.75e+01 angle pdb=" C ARG F 233 " pdb=" N LYS F 234 " pdb=" CA LYS F 234 " ideal model delta sigma weight residual 123.24 113.82 9.42 1.54e+00 4.22e-01 3.74e+01 angle pdb=" CA PRO E 768 " pdb=" N PRO E 768 " pdb=" CD PRO E 768 " ideal model delta sigma weight residual 112.00 104.53 7.47 1.40e+00 5.10e-01 2.85e+01 angle pdb=" N ILE B 904 " pdb=" CA ILE B 904 " pdb=" C ILE B 904 " ideal model delta sigma weight residual 113.53 108.61 4.92 9.80e-01 1.04e+00 2.52e+01 angle pdb=" CA LYS A 120 " pdb=" CB LYS A 120 " pdb=" CG LYS A 120 " ideal model delta sigma weight residual 114.10 124.05 -9.95 2.00e+00 2.50e-01 2.47e+01 ... (remaining 51703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19745 17.96 - 35.92: 2595 35.92 - 53.88: 482 53.88 - 71.84: 63 71.84 - 89.80: 35 Dihedral angle restraints: 22920 sinusoidal: 9484 harmonic: 13436 Sorted by residual: dihedral pdb=" CA GLN E 297 " pdb=" C GLN E 297 " pdb=" N GLU E 298 " pdb=" CA GLU E 298 " ideal model delta harmonic sigma weight residual 180.00 148.35 31.65 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA LYS D 64 " pdb=" C LYS D 64 " pdb=" N ASN D 65 " pdb=" CA ASN D 65 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA TYR C 51 " pdb=" C TYR C 51 " pdb=" N ILE C 52 " pdb=" CA ILE C 52 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 22917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3994 0.047 - 0.094: 1190 0.094 - 0.140: 279 0.140 - 0.187: 30 0.187 - 0.234: 7 Chirality restraints: 5500 Sorted by residual: chirality pdb=" CA TYR B 356 " pdb=" N TYR B 356 " pdb=" C TYR B 356 " pdb=" CB TYR B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA PRO F 843 " pdb=" N PRO F 843 " pdb=" C PRO F 843 " pdb=" CB PRO F 843 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO E 532 " pdb=" N PRO E 532 " pdb=" C PRO E 532 " pdb=" CB PRO E 532 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 5497 not shown) Planarity restraints: 6636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 919 " -0.041 2.00e-02 2.50e+03 4.02e-02 4.03e+01 pdb=" CG TRP E 919 " 0.108 2.00e-02 2.50e+03 pdb=" CD1 TRP E 919 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 919 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 919 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 919 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 919 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 919 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 919 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 919 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 842 " -0.073 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F 843 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 843 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 843 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 296 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C SER A 296 " 0.062 2.00e-02 2.50e+03 pdb=" O SER A 296 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN A 297 " -0.021 2.00e-02 2.50e+03 ... (remaining 6633 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 580 2.63 - 3.20: 36874 3.20 - 3.77: 60011 3.77 - 4.33: 80120 4.33 - 4.90: 123453 Nonbonded interactions: 301038 Sorted by model distance: nonbonded pdb=" O ALA D 25 " pdb=" ND2 ASN D 65 " model vdw 2.066 3.120 nonbonded pdb=" OG SER F 817 " pdb=" OG SER F 821 " model vdw 2.077 3.040 nonbonded pdb=" O GLN F 905 " pdb=" OG1 THR F 906 " model vdw 2.113 3.040 nonbonded pdb=" OG SER A 374 " pdb=" OE1 GLN A 377 " model vdw 2.123 3.040 nonbonded pdb=" O PHE B 594 " pdb=" ND2 ASN B 598 " model vdw 2.132 3.120 ... (remaining 301033 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.080 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 38368 Z= 0.165 Angle : 0.828 16.260 51708 Z= 0.441 Chirality : 0.046 0.234 5500 Planarity : 0.004 0.104 6636 Dihedral : 16.108 89.801 14288 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.73 % Favored : 91.53 % Rotamer: Outliers : 0.58 % Allowed : 19.45 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4512 helix: 0.04 (0.10), residues: 2429 sheet: -0.76 (0.30), residues: 332 loop : -2.02 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 86 TYR 0.045 0.002 TYR F 482 PHE 0.044 0.002 PHE A 492 TRP 0.108 0.003 TRP E 919 HIS 0.016 0.001 HIS B 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (38368) covalent geometry : angle 0.82792 / 0.44 (51708) hydrogen bonds : bond 0.18035 / 11.98 ( 1851) hydrogen bonds : angle 6.97658 / 4.92 ( 5268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 227 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6755 (mtpp) REVERT: A 226 ASN cc_start: 0.8164 (m-40) cc_final: 0.7908 (m-40) REVERT: A 311 TYR cc_start: 0.8384 (t80) cc_final: 0.7760 (t80) REVERT: A 449 GLU cc_start: 0.7758 (tp30) cc_final: 0.7461 (mm-30) REVERT: A 569 MET cc_start: 0.8691 (mmm) cc_final: 0.8485 (mmt) outliers start: 5 outliers final: 1 residues processed: 229 average time/residue: 0.0752 time to fit residues: 23.9388 Evaluate side-chains 215 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.305 Evaluate side-chains 34 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: C 6 GLN cc_start: 0.6716 (pm20) cc_final: 0.6326 (pm20) REVERT: C 198 VAL cc_start: 0.6831 (t) cc_final: 0.5839 (p) REVERT: C 220 PHE cc_start: 0.7396 (m-80) cc_final: 0.7171 (t80) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0464 time to fit residues: 1.8065 Evaluate side-chains 31 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 0.0770 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 133 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN A 905 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.162340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131607 restraints weight = 19344.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.136678 restraints weight = 11894.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.140238 restraints weight = 8042.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142768 restraints weight = 5836.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144638 restraints weight = 4471.457| |-----------------------------------------------------------------------------| r_work (final): 0.3973 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.218960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.185236 restraints weight = 2635.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.189991 restraints weight = 1679.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.193597 restraints weight = 1198.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.196286 restraints weight = 911.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.198261 restraints weight = 730.222| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 1.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38368 Z= 0.211 Angle : 0.902 12.546 51708 Z= 0.523 Chirality : 0.053 0.447 5500 Planarity : 0.006 0.046 6636 Dihedral : 6.726 57.303 4984 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 3.55 % Allowed : 5.59 % Favored : 90.87 % Rotamer: Outliers : 0.97 % Allowed : 4.75 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 4512 helix: 0.07 (0.10), residues: 2624 sheet: -0.11 (0.29), residues: 376 loop : -2.32 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 819 TYR 0.023 0.002 TYR D 171 PHE 0.036 0.002 PHE E 492 TRP 0.051 0.003 TRP E 919 HIS 0.005 0.001 HIS F 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 (38368) covalent geometry : angle 0.90217 / 0.52 (51708) hydrogen bonds : bond 0.08821 / 5.67 ( 1851) hydrogen bonds : angle 6.35717 / 4.45 ( 5268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 244 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.7332 (t80) cc_final: 0.7088 (t80) REVERT: A 104 LEU cc_start: 0.8284 (mt) cc_final: 0.7925 (mt) REVERT: A 107 PHE cc_start: 0.8834 (m-10) cc_final: 0.8630 (m-10) REVERT: A 120 LYS cc_start: 0.9139 (mppt) cc_final: 0.8398 (mmtt) REVERT: A 121 ILE cc_start: 0.9091 (mt) cc_final: 0.8754 (mt) REVERT: A 124 MET cc_start: 0.8376 (tpp) cc_final: 0.7930 (tpp) REVERT: A 187 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 203 LEU cc_start: 0.8725 (pp) cc_final: 0.8454 (pp) REVERT: A 225 ILE cc_start: 0.8157 (mt) cc_final: 0.7934 (mm) REVERT: A 226 ASN cc_start: 0.8023 (m-40) cc_final: 0.7768 (m-40) REVERT: A 245 PHE cc_start: 0.7971 (t80) cc_final: 0.7703 (t80) REVERT: A 284 GLU cc_start: 0.7602 (mp0) cc_final: 0.7168 (mp0) REVERT: A 290 MET cc_start: 0.8310 (mmm) cc_final: 0.7199 (mmm) REVERT: A 310 ASP cc_start: 0.8448 (m-30) cc_final: 0.8085 (m-30) REVERT: A 335 GLU cc_start: 0.8707 (mp0) cc_final: 0.8406 (mp0) REVERT: A 384 LEU cc_start: 0.8176 (mt) cc_final: 0.7876 (mt) REVERT: A 404 ASN cc_start: 0.7702 (t0) cc_final: 0.7369 (t0) REVERT: A 415 HIS cc_start: 0.8526 (p-80) cc_final: 0.8267 (p-80) REVERT: A 481 ILE cc_start: 0.8421 (mm) cc_final: 0.8128 (mm) REVERT: A 483 GLN cc_start: 0.8594 (pt0) cc_final: 0.8170 (pt0) REVERT: A 485 ILE cc_start: 0.8121 (mm) cc_final: 0.7743 (mm) REVERT: A 528 PHE cc_start: 0.8135 (t80) cc_final: 0.7411 (t80) REVERT: A 536 GLN cc_start: 0.8208 (mt0) cc_final: 0.7939 (mt0) REVERT: A 552 TYR cc_start: 0.7583 (m-80) cc_final: 0.6615 (m-80) REVERT: A 569 MET cc_start: 0.8573 (mmm) cc_final: 0.8257 (mmt) REVERT: A 596 TYR cc_start: 0.8528 (m-10) cc_final: 0.8005 (m-10) REVERT: A 607 GLU cc_start: 0.8364 (mp0) cc_final: 0.7911 (pm20) REVERT: A 626 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8073 (tt0) REVERT: A 678 PHE cc_start: 0.7832 (p90) cc_final: 0.7631 (p90) REVERT: A 684 ILE cc_start: 0.8503 (mt) cc_final: 0.8244 (mt) REVERT: A 686 GLU cc_start: 0.8485 (pt0) cc_final: 0.8244 (pp20) REVERT: A 704 MET cc_start: 0.0121 (mmm) cc_final: -0.0676 (mmm) REVERT: A 750 ASP cc_start: 0.7942 (p0) cc_final: 0.7401 (p0) REVERT: A 754 ARG cc_start: 0.8446 (mmt180) cc_final: 0.7425 (mmm160) REVERT: A 836 ASP cc_start: 0.7443 (m-30) cc_final: 0.7107 (m-30) REVERT: A 837 PHE cc_start: 0.7912 (t80) cc_final: 0.7605 (t80) REVERT: A 846 SER cc_start: 0.4406 (m) cc_final: 0.4161 (t) REVERT: A 919 TRP cc_start: 0.6214 (m-90) cc_final: 0.5843 (m100) outliers start: 7 outliers final: 2 residues processed: 248 average time/residue: 0.0847 time to fit residues: 28.9700 Evaluate side-chains 216 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.287 Evaluate side-chains 37 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 ASP cc_start: 0.6443 (m-30) cc_final: 0.6189 (m-30) REVERT: C 57 LYS cc_start: 0.7019 (mtpt) cc_final: 0.6623 (mtmm) REVERT: C 59 ILE cc_start: 0.7356 (mm) cc_final: 0.6974 (mm) REVERT: C 75 MET cc_start: 0.6878 (tpp) cc_final: 0.6465 (tpp) REVERT: C 206 MET cc_start: 0.5356 (tpp) cc_final: 0.4962 (tpp) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.0571 time to fit residues: 2.3032 Evaluate side-chains 31 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 330 optimal weight: 0.0770 chunk 23 optimal weight: 0.0970 chunk 361 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 430 optimal weight: 0.0060 chunk 107 optimal weight: 0.1980 chunk 189 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 chunk 216 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.1952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 125 ASN A 133 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.166330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135693 restraints weight = 19325.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140575 restraints weight = 12063.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144018 restraints weight = 8303.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146417 restraints weight = 6122.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.148307 restraints weight = 4781.304| |-----------------------------------------------------------------------------| r_work (final): 0.3982 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.218167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.182316 restraints weight = 2958.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.186856 restraints weight = 1956.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.190129 restraints weight = 1447.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.192353 restraints weight = 1153.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.193720 restraints weight = 973.993| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 1.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38368 Z= 0.168 Angle : 0.799 10.867 51708 Z= 0.460 Chirality : 0.046 0.233 5500 Planarity : 0.004 0.034 6636 Dihedral : 5.823 58.721 4984 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 1.15 % Allowed : 5.85 % Favored : 93.00 % Rotamer: Outliers : 0.29 % Allowed : 4.36 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4512 helix: 0.11 (0.10), residues: 2608 sheet: -0.05 (0.28), residues: 388 loop : -2.10 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 285 TYR 0.023 0.002 TYR C 51 PHE 0.024 0.002 PHE B 492 TRP 0.022 0.003 TRP E 919 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (38368) covalent geometry : angle 0.79871 / 0.46 (51708) hydrogen bonds : bond 0.07301 / 4.67 ( 1851) hydrogen bonds : angle 6.03585 / 4.24 ( 5268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.306 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: A 42 LEU cc_start: 0.7469 (tp) cc_final: 0.6889 (pt) REVERT: A 104 LEU cc_start: 0.8267 (mt) cc_final: 0.7901 (mt) REVERT: A 107 PHE cc_start: 0.8771 (m-10) cc_final: 0.8540 (m-10) REVERT: A 118 HIS cc_start: 0.8830 (m170) cc_final: 0.8564 (m170) REVERT: A 120 LYS cc_start: 0.9097 (mppt) cc_final: 0.8295 (mmtt) REVERT: A 121 ILE cc_start: 0.9097 (mt) cc_final: 0.8776 (mt) REVERT: A 124 MET cc_start: 0.8485 (tpp) cc_final: 0.7705 (tpp) REVERT: A 203 LEU cc_start: 0.8669 (pp) cc_final: 0.8427 (pp) REVERT: A 207 ILE cc_start: 0.8649 (mm) cc_final: 0.8406 (mm) REVERT: A 225 ILE cc_start: 0.8224 (mt) cc_final: 0.7872 (mm) REVERT: A 226 ASN cc_start: 0.8031 (m-40) cc_final: 0.7746 (m-40) REVERT: A 242 LYS cc_start: 0.8848 (pttp) cc_final: 0.8293 (ttpt) REVERT: A 245 PHE cc_start: 0.7877 (t80) cc_final: 0.7676 (t80) REVERT: A 284 GLU cc_start: 0.7458 (mp0) cc_final: 0.7007 (mp0) REVERT: A 290 MET cc_start: 0.8158 (mmm) cc_final: 0.7237 (mmm) REVERT: A 291 ASP cc_start: 0.8351 (m-30) cc_final: 0.8122 (m-30) REVERT: A 310 ASP cc_start: 0.8312 (m-30) cc_final: 0.7918 (m-30) REVERT: A 311 TYR cc_start: 0.8206 (t80) cc_final: 0.7988 (t80) REVERT: A 335 GLU cc_start: 0.8621 (mp0) cc_final: 0.8408 (mp0) REVERT: A 384 LEU cc_start: 0.8145 (mt) cc_final: 0.7917 (mt) REVERT: A 399 ASP cc_start: 0.7765 (t0) cc_final: 0.7534 (p0) REVERT: A 404 ASN cc_start: 0.7643 (t0) cc_final: 0.7282 (t0) REVERT: A 415 HIS cc_start: 0.8386 (p-80) cc_final: 0.8006 (p-80) REVERT: A 453 ASP cc_start: 0.8494 (m-30) cc_final: 0.8261 (m-30) REVERT: A 467 ASN cc_start: 0.8151 (t0) cc_final: 0.7866 (m-40) REVERT: A 481 ILE cc_start: 0.8512 (mm) cc_final: 0.8115 (mm) REVERT: A 483 GLN cc_start: 0.8633 (pt0) cc_final: 0.8107 (pt0) REVERT: A 485 ILE cc_start: 0.8119 (mm) cc_final: 0.7744 (mm) REVERT: A 516 GLU cc_start: 0.7907 (mp0) cc_final: 0.7673 (mp0) REVERT: A 528 PHE cc_start: 0.8101 (t80) cc_final: 0.7445 (t80) REVERT: A 536 GLN cc_start: 0.8419 (mt0) cc_final: 0.8045 (mt0) REVERT: A 552 TYR cc_start: 0.7355 (m-80) cc_final: 0.6952 (m-10) REVERT: A 607 GLU cc_start: 0.8336 (mp0) cc_final: 0.8102 (mp0) REVERT: A 608 PHE cc_start: 0.8144 (t80) cc_final: 0.7861 (t80) REVERT: A 617 SER cc_start: 0.7897 (p) cc_final: 0.7232 (p) REVERT: A 626 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8288 (tt0) REVERT: A 750 ASP cc_start: 0.7994 (p0) cc_final: 0.7604 (p0) REVERT: A 754 ARG cc_start: 0.8421 (mmt180) cc_final: 0.7881 (mmm160) REVERT: A 759 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8145 (pp20) REVERT: A 836 ASP cc_start: 0.7441 (m-30) cc_final: 0.7085 (m-30) REVERT: A 837 PHE cc_start: 0.7827 (t80) cc_final: 0.7483 (t80) REVERT: A 913 MET cc_start: 0.7525 (mmp) cc_final: 0.7224 (mmp) REVERT: A 916 PHE cc_start: 0.7860 (m-80) cc_final: 0.7285 (m-10) REVERT: A 981 ILE cc_start: 0.8429 (pt) cc_final: 0.7925 (pt) REVERT: A 985 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8314 (mmtt) outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.0788 time to fit residues: 25.3569 Evaluate side-chains 211 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.288 Evaluate side-chains 33 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ILE cc_start: 0.7338 (mm) cc_final: 0.7097 (mm) REVERT: C 75 MET cc_start: 0.6894 (tpp) cc_final: 0.6518 (tpp) REVERT: C 206 MET cc_start: 0.4298 (tpp) cc_final: 0.3872 (tpp) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0517 time to fit residues: 1.9212 Evaluate side-chains 31 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 386 optimal weight: 0.5980 chunk 227 optimal weight: 0.3980 chunk 296 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 292 optimal weight: 0.5980 chunk 106 optimal weight: 0.0980 chunk 301 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 405 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.166579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136199 restraints weight = 19240.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.141085 restraints weight = 11879.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.144625 restraints weight = 8153.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.147242 restraints weight = 5947.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.149120 restraints weight = 4564.889| |-----------------------------------------------------------------------------| r_work (final): 0.3999 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.218027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.182598 restraints weight = 2905.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.187738 restraints weight = 1960.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.191085 restraints weight = 1439.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.193603 restraints weight = 1133.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.195515 restraints weight = 934.829| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 1.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38368 Z= 0.148 Angle : 0.756 11.353 51708 Z= 0.436 Chirality : 0.045 0.216 5500 Planarity : 0.004 0.032 6636 Dihedral : 5.536 58.388 4984 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.98 % Allowed : 6.38 % Favored : 92.64 % Rotamer: Outliers : 0.39 % Allowed : 3.59 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4512 helix: 0.16 (0.10), residues: 2600 sheet: 0.01 (0.28), residues: 392 loop : -1.76 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 285 TYR 0.019 0.001 TYR F 552 PHE 0.030 0.002 PHE F 492 TRP 0.053 0.003 TRP E 757 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (38368) covalent geometry : angle 0.75568 / 0.44 (51708) hydrogen bonds : bond 0.06600 / 4.22 ( 1851) hydrogen bonds : angle 5.82473 / 4.12 ( 5268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8542 (m110) cc_final: 0.8292 (m110) REVERT: A 42 LEU cc_start: 0.7107 (tp) cc_final: 0.6877 (pt) REVERT: A 104 LEU cc_start: 0.8293 (mt) cc_final: 0.7907 (mt) REVERT: A 107 PHE cc_start: 0.8788 (m-10) cc_final: 0.8544 (m-10) REVERT: A 120 LYS cc_start: 0.9025 (mppt) cc_final: 0.8230 (mmtt) REVERT: A 121 ILE cc_start: 0.9125 (mt) cc_final: 0.8807 (mt) REVERT: A 203 LEU cc_start: 0.8644 (pp) cc_final: 0.8129 (pp) REVERT: A 207 ILE cc_start: 0.8631 (mm) cc_final: 0.8423 (mm) REVERT: A 225 ILE cc_start: 0.8192 (mt) cc_final: 0.7785 (mm) REVERT: A 226 ASN cc_start: 0.8050 (m-40) cc_final: 0.7733 (m-40) REVERT: A 242 LYS cc_start: 0.8820 (pttp) cc_final: 0.8212 (ttpt) REVERT: A 284 GLU cc_start: 0.7512 (mp0) cc_final: 0.7068 (mp0) REVERT: A 290 MET cc_start: 0.8141 (mmm) cc_final: 0.7212 (mmm) REVERT: A 291 ASP cc_start: 0.8366 (m-30) cc_final: 0.8142 (m-30) REVERT: A 304 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7998 (mmmt) REVERT: A 310 ASP cc_start: 0.8311 (m-30) cc_final: 0.7893 (m-30) REVERT: A 384 LEU cc_start: 0.8183 (mt) cc_final: 0.7890 (mt) REVERT: A 399 ASP cc_start: 0.7740 (t0) cc_final: 0.7539 (p0) REVERT: A 404 ASN cc_start: 0.7463 (t0) cc_final: 0.7091 (t0) REVERT: A 408 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6595 (tm-30) REVERT: A 415 HIS cc_start: 0.8328 (p-80) cc_final: 0.7951 (p-80) REVERT: A 453 ASP cc_start: 0.8363 (m-30) cc_final: 0.8101 (m-30) REVERT: A 475 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7549 (mm-40) REVERT: A 478 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8327 (ptm-80) REVERT: A 481 ILE cc_start: 0.8558 (mm) cc_final: 0.8184 (mm) REVERT: A 483 GLN cc_start: 0.8659 (pt0) cc_final: 0.8145 (pt0) REVERT: A 485 ILE cc_start: 0.8097 (mm) cc_final: 0.7738 (mm) REVERT: A 528 PHE cc_start: 0.7927 (t80) cc_final: 0.7478 (t80) REVERT: A 552 TYR cc_start: 0.7379 (m-80) cc_final: 0.6297 (m-80) REVERT: A 598 ASN cc_start: 0.8365 (m-40) cc_final: 0.8147 (m110) REVERT: A 607 GLU cc_start: 0.8314 (mp0) cc_final: 0.8084 (mp0) REVERT: A 608 PHE cc_start: 0.8172 (t80) cc_final: 0.7954 (t80) REVERT: A 617 SER cc_start: 0.7994 (p) cc_final: 0.7398 (p) REVERT: A 626 GLU cc_start: 0.8841 (mt-10) cc_final: 0.7987 (tt0) REVERT: A 651 ASP cc_start: 0.8738 (m-30) cc_final: 0.8536 (m-30) REVERT: A 694 GLU cc_start: 0.7352 (tp30) cc_final: 0.6572 (tp30) REVERT: A 704 MET cc_start: -0.0241 (mmp) cc_final: -0.0473 (mmp) REVERT: A 750 ASP cc_start: 0.8068 (p0) cc_final: 0.7444 (p0) REVERT: A 754 ARG cc_start: 0.8413 (mmt180) cc_final: 0.8152 (mmt180) REVERT: A 913 MET cc_start: 0.7384 (mmp) cc_final: 0.7056 (mmp) REVERT: A 916 PHE cc_start: 0.7956 (m-80) cc_final: 0.7288 (m-10) REVERT: A 981 ILE cc_start: 0.8445 (pt) cc_final: 0.8085 (pt) REVERT: A 985 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8337 (mmtt) outliers start: 4 outliers final: 1 residues processed: 233 average time/residue: 0.0858 time to fit residues: 27.6020 Evaluate side-chains 218 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.253 Evaluate side-chains 31 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: C 10 ASP cc_start: 0.6581 (m-30) cc_final: 0.6358 (m-30) REVERT: C 59 ILE cc_start: 0.7362 (mm) cc_final: 0.7106 (mm) REVERT: C 206 MET cc_start: 0.4273 (tpp) cc_final: 0.3759 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0524 time to fit residues: 1.8193 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 3 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 166 optimal weight: 0.0970 chunk 262 optimal weight: 0.6980 chunk 326 optimal weight: 0.5980 chunk 328 optimal weight: 1.9990 chunk 381 optimal weight: 2.9990 chunk 111 optimal weight: 0.0270 chunk 269 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 133 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130000 restraints weight = 19387.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135073 restraints weight = 11915.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.138717 restraints weight = 8102.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.141347 restraints weight = 5857.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143257 restraints weight = 4457.754| |-----------------------------------------------------------------------------| r_work (final): 0.4010 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.208479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.176749 restraints weight = 2704.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.182425 restraints weight = 1633.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.186200 restraints weight = 1111.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.188968 restraints weight = 832.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.191129 restraints weight = 661.687| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 1.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38368 Z= 0.147 Angle : 0.745 12.080 51708 Z= 0.428 Chirality : 0.045 0.211 5500 Planarity : 0.004 0.033 6636 Dihedral : 5.486 56.508 4984 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.29 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.12), residues: 4512 helix: 0.14 (0.10), residues: 2628 sheet: -0.07 (0.28), residues: 392 loop : -1.64 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.016 0.001 TYR E 552 PHE 0.055 0.002 PHE F 492 TRP 0.056 0.003 TRP A 757 HIS 0.003 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (38368) covalent geometry : angle 0.74483 / 0.43 (51708) hydrogen bonds : bond 0.06342 / 4.06 ( 1851) hydrogen bonds : angle 5.74059 / 4.06 ( 5268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8243 (m) cc_final: 0.7958 (p) REVERT: A 104 LEU cc_start: 0.8314 (mt) cc_final: 0.7948 (mt) REVERT: A 107 PHE cc_start: 0.8837 (m-10) cc_final: 0.8532 (m-10) REVERT: A 114 THR cc_start: 0.8895 (m) cc_final: 0.8433 (p) REVERT: A 120 LYS cc_start: 0.9000 (mppt) cc_final: 0.8170 (mmtt) REVERT: A 121 ILE cc_start: 0.9114 (mt) cc_final: 0.8775 (mt) REVERT: A 124 MET cc_start: 0.8519 (mmp) cc_final: 0.8280 (tpt) REVERT: A 143 TRP cc_start: 0.8451 (t-100) cc_final: 0.7757 (t-100) REVERT: A 225 ILE cc_start: 0.8214 (mt) cc_final: 0.7810 (mm) REVERT: A 226 ASN cc_start: 0.8111 (m-40) cc_final: 0.7807 (m-40) REVERT: A 242 LYS cc_start: 0.8798 (pttp) cc_final: 0.8408 (pttm) REVERT: A 290 MET cc_start: 0.8082 (mmm) cc_final: 0.7209 (mmm) REVERT: A 291 ASP cc_start: 0.8466 (m-30) cc_final: 0.8250 (m-30) REVERT: A 304 LYS cc_start: 0.8315 (mmpt) cc_final: 0.8033 (mmmt) REVERT: A 310 ASP cc_start: 0.8393 (m-30) cc_final: 0.8112 (m-30) REVERT: A 311 TYR cc_start: 0.8079 (t80) cc_final: 0.7817 (t80) REVERT: A 313 TYR cc_start: 0.7270 (t80) cc_final: 0.6985 (t80) REVERT: A 380 ARG cc_start: 0.6414 (tmm160) cc_final: 0.5939 (ttp80) REVERT: A 384 LEU cc_start: 0.8183 (mt) cc_final: 0.7934 (mt) REVERT: A 404 ASN cc_start: 0.7412 (t0) cc_final: 0.7034 (t0) REVERT: A 453 ASP cc_start: 0.8278 (m-30) cc_final: 0.7960 (m-30) REVERT: A 457 ASN cc_start: 0.8142 (m110) cc_final: 0.7935 (m-40) REVERT: A 476 ILE cc_start: 0.7643 (tp) cc_final: 0.7386 (tp) REVERT: A 478 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8260 (ptt90) REVERT: A 481 ILE cc_start: 0.8578 (mm) cc_final: 0.8190 (mm) REVERT: A 483 GLN cc_start: 0.8661 (pt0) cc_final: 0.8196 (pt0) REVERT: A 485 ILE cc_start: 0.8069 (mm) cc_final: 0.7715 (mm) REVERT: A 528 PHE cc_start: 0.7942 (t80) cc_final: 0.7467 (t80) REVERT: A 563 ASN cc_start: 0.7968 (t0) cc_final: 0.7727 (t0) REVERT: A 607 GLU cc_start: 0.8334 (mp0) cc_final: 0.8097 (mp0) REVERT: A 617 SER cc_start: 0.8010 (p) cc_final: 0.7360 (p) REVERT: A 626 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8237 (tt0) REVERT: A 678 PHE cc_start: 0.8115 (p90) cc_final: 0.7698 (p90) REVERT: A 694 GLU cc_start: 0.7271 (tp30) cc_final: 0.6529 (tp30) REVERT: A 704 MET cc_start: -0.0042 (mmp) cc_final: -0.0922 (mmm) REVERT: A 750 ASP cc_start: 0.8098 (p0) cc_final: 0.7275 (p0) REVERT: A 754 ARG cc_start: 0.8409 (mmt180) cc_final: 0.7147 (mmm160) REVERT: A 757 TRP cc_start: 0.6766 (m-90) cc_final: 0.6554 (m-90) REVERT: A 913 MET cc_start: 0.7367 (mmp) cc_final: 0.6754 (mmp) REVERT: A 916 PHE cc_start: 0.8010 (m-80) cc_final: 0.7293 (m-80) REVERT: A 981 ILE cc_start: 0.8444 (pt) cc_final: 0.8156 (pt) REVERT: A 985 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8358 (mmtt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0856 time to fit residues: 27.4518 Evaluate side-chains 206 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.295 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 ILE cc_start: 0.7271 (mm) cc_final: 0.7001 (mm) REVERT: C 206 MET cc_start: 0.4623 (tpp) cc_final: 0.3943 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0593 time to fit residues: 1.9881 Evaluate side-chains 29 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 432 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 338 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 422 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.161434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131247 restraints weight = 19295.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136223 restraints weight = 12075.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.139714 restraints weight = 8296.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142213 restraints weight = 6092.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.143881 restraints weight = 4713.423| |-----------------------------------------------------------------------------| r_work (final): 0.3999 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.207843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.167671 restraints weight = 3022.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.173827 restraints weight = 2135.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.177756 restraints weight = 1582.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.180338 restraints weight = 1261.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.182359 restraints weight = 1055.752| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 1.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38368 Z= 0.147 Angle : 0.737 11.592 51708 Z= 0.423 Chirality : 0.045 0.260 5500 Planarity : 0.004 0.035 6636 Dihedral : 5.320 54.881 4984 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.85 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.13), residues: 4512 helix: 0.38 (0.10), residues: 2576 sheet: -0.02 (0.26), residues: 428 loop : -1.67 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 677 TYR 0.020 0.001 TYR E 709 PHE 0.032 0.002 PHE E 492 TRP 0.041 0.003 TRP B 757 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (38368) covalent geometry : angle 0.73706 / 0.42 (51708) hydrogen bonds : bond 0.06022 / 3.85 ( 1851) hydrogen bonds : angle 5.59432 / 3.96 ( 5268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8228 (m) cc_final: 0.7959 (p) REVERT: A 42 LEU cc_start: 0.7187 (tp) cc_final: 0.6923 (pt) REVERT: A 59 TRP cc_start: 0.6245 (t-100) cc_final: 0.5836 (t-100) REVERT: A 104 LEU cc_start: 0.8317 (mt) cc_final: 0.7943 (mt) REVERT: A 107 PHE cc_start: 0.8803 (m-10) cc_final: 0.8528 (m-10) REVERT: A 114 THR cc_start: 0.8970 (m) cc_final: 0.8528 (p) REVERT: A 120 LYS cc_start: 0.8953 (mppt) cc_final: 0.8082 (mmtt) REVERT: A 121 ILE cc_start: 0.9045 (mt) cc_final: 0.8637 (mm) REVERT: A 124 MET cc_start: 0.8320 (mmp) cc_final: 0.7328 (tpp) REVERT: A 143 TRP cc_start: 0.8404 (t-100) cc_final: 0.7713 (t-100) REVERT: A 187 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 203 LEU cc_start: 0.8327 (pp) cc_final: 0.8041 (pp) REVERT: A 225 ILE cc_start: 0.8175 (mt) cc_final: 0.7822 (mm) REVERT: A 226 ASN cc_start: 0.8086 (m-40) cc_final: 0.7774 (m-40) REVERT: A 242 LYS cc_start: 0.8821 (pttp) cc_final: 0.8496 (pttm) REVERT: A 284 GLU cc_start: 0.7596 (mp0) cc_final: 0.7209 (mp0) REVERT: A 290 MET cc_start: 0.8045 (mmm) cc_final: 0.7118 (mmm) REVERT: A 291 ASP cc_start: 0.8374 (m-30) cc_final: 0.8121 (m-30) REVERT: A 304 LYS cc_start: 0.8286 (mmpt) cc_final: 0.8034 (mmmt) REVERT: A 310 ASP cc_start: 0.8333 (m-30) cc_final: 0.8061 (m-30) REVERT: A 311 TYR cc_start: 0.8047 (t80) cc_final: 0.7803 (t80) REVERT: A 313 TYR cc_start: 0.7185 (t80) cc_final: 0.6884 (t80) REVERT: A 380 ARG cc_start: 0.6337 (tmm160) cc_final: 0.5975 (ttp80) REVERT: A 384 LEU cc_start: 0.8125 (mt) cc_final: 0.7918 (mt) REVERT: A 399 ASP cc_start: 0.7617 (p0) cc_final: 0.7138 (p0) REVERT: A 404 ASN cc_start: 0.7419 (t0) cc_final: 0.7085 (t0) REVERT: A 415 HIS cc_start: 0.8365 (p-80) cc_final: 0.8149 (p-80) REVERT: A 453 ASP cc_start: 0.8085 (m-30) cc_final: 0.7809 (m-30) REVERT: A 457 ASN cc_start: 0.8245 (m110) cc_final: 0.8007 (m-40) REVERT: A 467 ASN cc_start: 0.7651 (m-40) cc_final: 0.7400 (m-40) REVERT: A 476 ILE cc_start: 0.7596 (tp) cc_final: 0.7296 (tp) REVERT: A 478 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8275 (ptt90) REVERT: A 481 ILE cc_start: 0.8608 (mm) cc_final: 0.8184 (mm) REVERT: A 483 GLN cc_start: 0.8692 (pt0) cc_final: 0.8309 (pt0) REVERT: A 485 ILE cc_start: 0.8022 (mm) cc_final: 0.7724 (mm) REVERT: A 516 GLU cc_start: 0.7913 (mp0) cc_final: 0.7677 (mp0) REVERT: A 528 PHE cc_start: 0.7860 (t80) cc_final: 0.7357 (t80) REVERT: A 563 ASN cc_start: 0.7883 (t0) cc_final: 0.7675 (t0) REVERT: A 617 SER cc_start: 0.8063 (p) cc_final: 0.7215 (p) REVERT: A 626 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8246 (tt0) REVERT: A 678 PHE cc_start: 0.7818 (p90) cc_final: 0.7577 (p90) REVERT: A 704 MET cc_start: -0.0127 (mmp) cc_final: -0.1053 (mmp) REVERT: A 750 ASP cc_start: 0.8021 (p0) cc_final: 0.7386 (p0) REVERT: A 754 ARG cc_start: 0.8418 (mmt180) cc_final: 0.7653 (mmt180) REVERT: A 916 PHE cc_start: 0.8008 (m-80) cc_final: 0.7461 (m-10) REVERT: A 936 MET cc_start: -0.3139 (mmt) cc_final: -0.3380 (mmt) REVERT: A 981 ILE cc_start: 0.8459 (pt) cc_final: 0.7987 (pt) REVERT: A 985 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8443 (mmmt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0863 time to fit residues: 27.0169 Evaluate side-chains 207 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.304 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6670 (mtmt) cc_final: 0.6170 (ptpp) REVERT: C 59 ILE cc_start: 0.7527 (mm) cc_final: 0.7267 (mm) REVERT: C 193 ILE cc_start: 0.7221 (mp) cc_final: 0.6916 (mm) REVERT: C 206 MET cc_start: 0.3607 (tpp) cc_final: 0.3290 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0599 time to fit residues: 2.0237 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 79 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 328 optimal weight: 0.7980 chunk 430 optimal weight: 4.9990 chunk 393 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 252 optimal weight: 0.4980 chunk 438 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 133 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN C 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.162108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.132205 restraints weight = 19202.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.137163 restraints weight = 12132.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.140566 restraints weight = 8353.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.143117 restraints weight = 6196.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.144939 restraints weight = 4798.487| |-----------------------------------------------------------------------------| r_work (final): 0.4008 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.208031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.167456 restraints weight = 3069.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.173811 restraints weight = 2070.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.178067 restraints weight = 1499.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.180766 restraints weight = 1175.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.182776 restraints weight = 979.946| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5483 moved from start: 1.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38368 Z= 0.142 Angle : 0.740 11.295 51708 Z= 0.423 Chirality : 0.044 0.241 5500 Planarity : 0.004 0.058 6636 Dihedral : 5.215 53.706 4984 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.03 % Favored : 93.26 % Rotamer: Outliers : 0.10 % Allowed : 2.04 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.12), residues: 4512 helix: 0.29 (0.10), residues: 2608 sheet: -0.04 (0.26), residues: 428 loop : -1.72 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 285 TYR 0.033 0.001 TYR A 223 PHE 0.029 0.001 PHE E 492 TRP 0.078 0.004 TRP E 757 HIS 0.004 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (38368) covalent geometry : angle 0.74029 / 0.42 (51708) hydrogen bonds : bond 0.05897 / 3.76 ( 1851) hydrogen bonds : angle 5.55285 / 3.93 ( 5268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8656 (m110) cc_final: 0.8401 (m110) REVERT: A 34 THR cc_start: 0.8219 (m) cc_final: 0.7922 (p) REVERT: A 45 PHE cc_start: 0.6928 (t80) cc_final: 0.6499 (t80) REVERT: A 104 LEU cc_start: 0.8280 (mt) cc_final: 0.7907 (mt) REVERT: A 107 PHE cc_start: 0.8806 (m-10) cc_final: 0.8531 (m-10) REVERT: A 114 THR cc_start: 0.8951 (m) cc_final: 0.8543 (p) REVERT: A 120 LYS cc_start: 0.8956 (mppt) cc_final: 0.8070 (mmtt) REVERT: A 121 ILE cc_start: 0.9063 (mt) cc_final: 0.8621 (mm) REVERT: A 124 MET cc_start: 0.8462 (mmp) cc_final: 0.7551 (tpp) REVERT: A 225 ILE cc_start: 0.8150 (mt) cc_final: 0.7722 (mm) REVERT: A 226 ASN cc_start: 0.8089 (m-40) cc_final: 0.7598 (m-40) REVERT: A 227 MET cc_start: 0.7603 (mpp) cc_final: 0.7245 (mpp) REVERT: A 242 LYS cc_start: 0.8779 (pttp) cc_final: 0.8345 (pttm) REVERT: A 284 GLU cc_start: 0.7601 (mp0) cc_final: 0.7200 (mp0) REVERT: A 290 MET cc_start: 0.8016 (mmm) cc_final: 0.7055 (mmm) REVERT: A 291 ASP cc_start: 0.8420 (m-30) cc_final: 0.8122 (m-30) REVERT: A 304 LYS cc_start: 0.8286 (mmpt) cc_final: 0.8039 (mmmt) REVERT: A 310 ASP cc_start: 0.8279 (m-30) cc_final: 0.8002 (m-30) REVERT: A 313 TYR cc_start: 0.7143 (t80) cc_final: 0.6855 (t80) REVERT: A 384 LEU cc_start: 0.8087 (mt) cc_final: 0.7871 (mt) REVERT: A 399 ASP cc_start: 0.7529 (p0) cc_final: 0.7110 (p0) REVERT: A 453 ASP cc_start: 0.8043 (m-30) cc_final: 0.7767 (m-30) REVERT: A 457 ASN cc_start: 0.8247 (m110) cc_final: 0.7983 (m-40) REVERT: A 476 ILE cc_start: 0.7578 (tp) cc_final: 0.7368 (tp) REVERT: A 481 ILE cc_start: 0.8477 (mm) cc_final: 0.8043 (mm) REVERT: A 483 GLN cc_start: 0.8718 (pt0) cc_final: 0.8298 (pt0) REVERT: A 485 ILE cc_start: 0.7868 (mm) cc_final: 0.7618 (mm) REVERT: A 516 GLU cc_start: 0.7989 (mp0) cc_final: 0.7655 (mp0) REVERT: A 527 LEU cc_start: 0.8479 (tp) cc_final: 0.8107 (tp) REVERT: A 528 PHE cc_start: 0.8158 (t80) cc_final: 0.7397 (t80) REVERT: A 552 TYR cc_start: 0.7403 (m-80) cc_final: 0.6957 (m-10) REVERT: A 563 ASN cc_start: 0.7851 (t0) cc_final: 0.7632 (t0) REVERT: A 607 GLU cc_start: 0.8608 (mp0) cc_final: 0.8370 (mp0) REVERT: A 617 SER cc_start: 0.8160 (p) cc_final: 0.7379 (p) REVERT: A 622 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7196 (tmtt) REVERT: A 626 GLU cc_start: 0.8865 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 678 PHE cc_start: 0.7742 (p90) cc_final: 0.7405 (p90) REVERT: A 704 MET cc_start: -0.0400 (mmp) cc_final: -0.0728 (mmp) REVERT: A 749 LEU cc_start: 0.6156 (mp) cc_final: 0.5788 (mp) REVERT: A 750 ASP cc_start: 0.8085 (p0) cc_final: 0.7605 (p0) REVERT: A 754 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7888 (mmt180) REVERT: A 759 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 913 MET cc_start: 0.7266 (mmp) cc_final: 0.6732 (mmp) REVERT: A 916 PHE cc_start: 0.8034 (m-80) cc_final: 0.7441 (m-80) REVERT: A 936 MET cc_start: -0.3076 (mmt) cc_final: -0.3343 (mmt) REVERT: A 981 ILE cc_start: 0.8456 (pt) cc_final: 0.7986 (pt) REVERT: A 985 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8473 (mmmt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.0817 time to fit residues: 25.5692 Evaluate side-chains 209 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.256 Evaluate side-chains 31 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.042 Fit side-chains revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6217 (ptpp) REVERT: C 59 ILE cc_start: 0.7533 (mm) cc_final: 0.7273 (mm) REVERT: C 193 ILE cc_start: 0.7229 (mp) cc_final: 0.6929 (mm) REVERT: C 206 MET cc_start: 0.3591 (tpp) cc_final: 0.3364 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0613 time to fit residues: 2.1197 Evaluate side-chains 29 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 0.0060 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 0.0050 chunk 199 optimal weight: 0.4980 chunk 42 optimal weight: 0.0370 chunk 173 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 348 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.161944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133349 restraints weight = 19174.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.138088 restraints weight = 12221.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.141431 restraints weight = 8479.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.143903 restraints weight = 6262.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145659 restraints weight = 4846.513| |-----------------------------------------------------------------------------| r_work (final): 0.4017 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.209058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.168638 restraints weight = 3053.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.174730 restraints weight = 2047.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.179139 restraints weight = 1495.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.181931 restraints weight = 1175.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.184116 restraints weight = 982.275| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 1.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38368 Z= 0.143 Angle : 0.746 9.423 51708 Z= 0.425 Chirality : 0.044 0.213 5500 Planarity : 0.004 0.074 6636 Dihedral : 5.152 51.770 4984 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.85 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4512 helix: 0.31 (0.10), residues: 2584 sheet: -0.07 (0.26), residues: 424 loop : -1.49 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 285 TYR 0.030 0.001 TYR E 223 PHE 0.024 0.001 PHE B 492 TRP 0.072 0.004 TRP F 757 HIS 0.005 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (38368) covalent geometry : angle 0.74576 / 0.42 (51708) hydrogen bonds : bond 0.05813 / 3.70 ( 1851) hydrogen bonds : angle 5.49455 / 3.89 ( 5268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8566 (m110) cc_final: 0.8288 (m110) REVERT: A 34 THR cc_start: 0.8229 (m) cc_final: 0.7975 (p) REVERT: A 59 TRP cc_start: 0.6336 (t-100) cc_final: 0.5745 (t-100) REVERT: A 90 ILE cc_start: 0.8384 (mt) cc_final: 0.8127 (mm) REVERT: A 104 LEU cc_start: 0.8287 (mt) cc_final: 0.7924 (mt) REVERT: A 107 PHE cc_start: 0.8670 (m-10) cc_final: 0.8459 (m-10) REVERT: A 114 THR cc_start: 0.8910 (m) cc_final: 0.8479 (p) REVERT: A 120 LYS cc_start: 0.8956 (mppt) cc_final: 0.8077 (mmtt) REVERT: A 121 ILE cc_start: 0.9058 (mt) cc_final: 0.8678 (mm) REVERT: A 143 TRP cc_start: 0.8498 (t-100) cc_final: 0.8144 (t-100) REVERT: A 187 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 225 ILE cc_start: 0.8082 (mt) cc_final: 0.7722 (mm) REVERT: A 226 ASN cc_start: 0.7946 (m-40) cc_final: 0.7446 (m-40) REVERT: A 227 MET cc_start: 0.7417 (mpp) cc_final: 0.6972 (mpp) REVERT: A 242 LYS cc_start: 0.8740 (pttp) cc_final: 0.8369 (pttm) REVERT: A 290 MET cc_start: 0.7993 (mmm) cc_final: 0.6991 (mmm) REVERT: A 291 ASP cc_start: 0.8332 (m-30) cc_final: 0.8007 (m-30) REVERT: A 304 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7994 (mmmt) REVERT: A 310 ASP cc_start: 0.8220 (m-30) cc_final: 0.7972 (m-30) REVERT: A 311 TYR cc_start: 0.7940 (t80) cc_final: 0.7642 (t80) REVERT: A 313 TYR cc_start: 0.7080 (t80) cc_final: 0.6768 (t80) REVERT: A 384 LEU cc_start: 0.8003 (mt) cc_final: 0.7724 (mt) REVERT: A 399 ASP cc_start: 0.7646 (p0) cc_final: 0.7187 (p0) REVERT: A 415 HIS cc_start: 0.8271 (p-80) cc_final: 0.8051 (p-80) REVERT: A 453 ASP cc_start: 0.7926 (m-30) cc_final: 0.7599 (m-30) REVERT: A 457 ASN cc_start: 0.8261 (m110) cc_final: 0.7983 (m-40) REVERT: A 467 ASN cc_start: 0.7571 (m-40) cc_final: 0.7345 (m-40) REVERT: A 481 ILE cc_start: 0.8455 (mm) cc_final: 0.7950 (mm) REVERT: A 483 GLN cc_start: 0.8737 (pt0) cc_final: 0.8336 (pt0) REVERT: A 485 ILE cc_start: 0.7932 (mm) cc_final: 0.7615 (mm) REVERT: A 516 GLU cc_start: 0.7848 (mp0) cc_final: 0.7487 (mp0) REVERT: A 528 PHE cc_start: 0.7787 (t80) cc_final: 0.7376 (t80) REVERT: A 563 ASN cc_start: 0.7770 (t0) cc_final: 0.7553 (t0) REVERT: A 607 GLU cc_start: 0.8647 (mp0) cc_final: 0.8293 (mp0) REVERT: A 617 SER cc_start: 0.8228 (p) cc_final: 0.7413 (p) REVERT: A 626 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8015 (tt0) REVERT: A 749 LEU cc_start: 0.6434 (mp) cc_final: 0.6133 (mp) REVERT: A 750 ASP cc_start: 0.8220 (p0) cc_final: 0.7586 (p0) REVERT: A 754 ARG cc_start: 0.8304 (mmt180) cc_final: 0.7909 (mmt180) REVERT: A 759 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 936 MET cc_start: -0.2950 (mmt) cc_final: -0.3231 (mmt) REVERT: A 981 ILE cc_start: 0.8465 (pt) cc_final: 0.7973 (pt) REVERT: A 985 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8482 (mmmt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0869 time to fit residues: 26.2326 Evaluate side-chains 210 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.246 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.7774 (pttm) cc_final: 0.7543 (pttm) REVERT: C 57 LYS cc_start: 0.6838 (mtmt) cc_final: 0.6311 (ptpp) REVERT: C 59 ILE cc_start: 0.7568 (mm) cc_final: 0.7297 (mm) REVERT: C 193 ILE cc_start: 0.7247 (mp) cc_final: 0.6926 (mm) REVERT: C 206 MET cc_start: 0.3585 (tpp) cc_final: 0.3367 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0534 time to fit residues: 1.8104 Evaluate side-chains 28 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 340 optimal weight: 0.0040 chunk 324 optimal weight: 4.9990 chunk 367 optimal weight: 0.6980 chunk 369 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 140 optimal weight: 0.0270 chunk 233 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 317 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 overall best weight: 0.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 133 ASN A 195 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.132626 restraints weight = 18997.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137390 restraints weight = 12222.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140821 restraints weight = 8552.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.143245 restraints weight = 6369.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.145124 restraints weight = 4980.837| |-----------------------------------------------------------------------------| r_work (final): 0.4016 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.211147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.172628 restraints weight = 3246.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.178499 restraints weight = 2164.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.182604 restraints weight = 1603.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.185606 restraints weight = 1257.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.187730 restraints weight = 1029.646| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 1.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38368 Z= 0.144 Angle : 0.764 12.039 51708 Z= 0.432 Chirality : 0.044 0.221 5500 Planarity : 0.004 0.088 6636 Dihedral : 5.150 50.504 4984 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.12 % Favored : 93.17 % Rotamer: Outliers : 0.19 % Allowed : 0.48 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4512 helix: 0.28 (0.10), residues: 2584 sheet: -0.09 (0.26), residues: 424 loop : -1.46 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 285 TYR 0.030 0.001 TYR E 223 PHE 0.025 0.001 PHE B 699 TRP 0.078 0.003 TRP F 757 HIS 0.007 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (38368) covalent geometry : angle 0.76382 / 0.43 (51708) hydrogen bonds : bond 0.05769 / 3.67 ( 1851) hydrogen bonds : angle 5.54999 / 3.93 ( 5268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 THR cc_start: 0.8305 (m) cc_final: 0.8011 (p) REVERT: A 90 ILE cc_start: 0.8458 (mt) cc_final: 0.8224 (mm) REVERT: A 104 LEU cc_start: 0.8290 (mt) cc_final: 0.7994 (mt) REVERT: A 107 PHE cc_start: 0.8713 (m-10) cc_final: 0.8487 (m-10) REVERT: A 114 THR cc_start: 0.8908 (m) cc_final: 0.8502 (p) REVERT: A 120 LYS cc_start: 0.8922 (mppt) cc_final: 0.8045 (mmtt) REVERT: A 121 ILE cc_start: 0.9035 (mt) cc_final: 0.8639 (mm) REVERT: A 143 TRP cc_start: 0.8559 (t-100) cc_final: 0.7893 (t-100) REVERT: A 205 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7183 (mmtp) REVERT: A 207 ILE cc_start: 0.8608 (mm) cc_final: 0.8395 (mm) REVERT: A 225 ILE cc_start: 0.8070 (mt) cc_final: 0.7764 (mm) REVERT: A 226 ASN cc_start: 0.7830 (m-40) cc_final: 0.7475 (m-40) REVERT: A 242 LYS cc_start: 0.8577 (pttp) cc_final: 0.8314 (pttp) REVERT: A 285 ARG cc_start: 0.8811 (pmt170) cc_final: 0.7831 (pmt170) REVERT: A 290 MET cc_start: 0.7920 (mmm) cc_final: 0.6902 (mmm) REVERT: A 291 ASP cc_start: 0.8349 (m-30) cc_final: 0.8046 (m-30) REVERT: A 304 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7957 (mmmt) REVERT: A 311 TYR cc_start: 0.8020 (t80) cc_final: 0.7683 (t80) REVERT: A 313 TYR cc_start: 0.7129 (t80) cc_final: 0.6808 (t80) REVERT: A 384 LEU cc_start: 0.8065 (mt) cc_final: 0.7806 (mt) REVERT: A 399 ASP cc_start: 0.7695 (p0) cc_final: 0.7298 (p0) REVERT: A 453 ASP cc_start: 0.7956 (m-30) cc_final: 0.7645 (m-30) REVERT: A 457 ASN cc_start: 0.8257 (m110) cc_final: 0.7986 (m-40) REVERT: A 476 ILE cc_start: 0.7514 (tp) cc_final: 0.7266 (tp) REVERT: A 478 ARG cc_start: 0.8562 (ptt90) cc_final: 0.8154 (ptt90) REVERT: A 481 ILE cc_start: 0.8426 (mm) cc_final: 0.7937 (mm) REVERT: A 483 GLN cc_start: 0.8708 (pt0) cc_final: 0.8360 (pt0) REVERT: A 485 ILE cc_start: 0.7944 (mm) cc_final: 0.7633 (mm) REVERT: A 516 GLU cc_start: 0.7749 (mp0) cc_final: 0.7467 (mp0) REVERT: A 528 PHE cc_start: 0.7825 (t80) cc_final: 0.7440 (t80) REVERT: A 552 TYR cc_start: 0.7395 (m-80) cc_final: 0.6989 (m-10) REVERT: A 569 MET cc_start: 0.8994 (mmm) cc_final: 0.8637 (mmm) REVERT: A 607 GLU cc_start: 0.8578 (mp0) cc_final: 0.8262 (mp0) REVERT: A 617 SER cc_start: 0.8216 (p) cc_final: 0.7427 (p) REVERT: A 622 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7032 (tmtt) REVERT: A 625 TYR cc_start: 0.7794 (t80) cc_final: 0.7108 (t80) REVERT: A 626 GLU cc_start: 0.8863 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 678 PHE cc_start: 0.7672 (p90) cc_final: 0.7455 (p90) REVERT: A 749 LEU cc_start: 0.6437 (mp) cc_final: 0.5909 (mp) REVERT: A 750 ASP cc_start: 0.8137 (p0) cc_final: 0.7507 (p0) REVERT: A 754 ARG cc_start: 0.8299 (mmt180) cc_final: 0.7925 (mmt180) REVERT: A 759 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 913 MET cc_start: 0.7147 (mmp) cc_final: 0.6650 (mmp) REVERT: A 916 PHE cc_start: 0.8059 (m-80) cc_final: 0.7473 (m-80) REVERT: A 936 MET cc_start: -0.2936 (mmt) cc_final: -0.3258 (mmt) REVERT: A 981 ILE cc_start: 0.8459 (pt) cc_final: 0.7971 (pt) REVERT: A 985 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8466 (mmmt) outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.0833 time to fit residues: 25.6328 Evaluate side-chains 218 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.309 Evaluate side-chains 30 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6876 (mtmt) cc_final: 0.6395 (ptpp) REVERT: C 59 ILE cc_start: 0.7477 (mm) cc_final: 0.7197 (mm) REVERT: C 75 MET cc_start: 0.6888 (tpp) cc_final: 0.6407 (tpt) REVERT: C 193 ILE cc_start: 0.7233 (mp) cc_final: 0.6931 (mm) REVERT: C 206 MET cc_start: 0.3399 (tpp) cc_final: 0.3162 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0577 time to fit residues: 1.9178 Evaluate side-chains 28 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 20 optimal weight: 0.6980 chunk 225 optimal weight: 0.0170 chunk 113 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 315 optimal weight: 0.0030 chunk 160 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 446 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 133 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.162728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133869 restraints weight = 19056.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.138571 restraints weight = 12216.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.141913 restraints weight = 8523.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.144335 restraints weight = 6319.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146142 restraints weight = 4920.494| |-----------------------------------------------------------------------------| r_work (final): 0.4032 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.211314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.173313 restraints weight = 3141.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.178842 restraints weight = 2143.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.182945 restraints weight = 1604.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.185692 restraints weight = 1265.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.187768 restraints weight = 1050.176| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 1.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38368 Z= 0.144 Angle : 0.761 11.981 51708 Z= 0.432 Chirality : 0.044 0.210 5500 Planarity : 0.004 0.094 6636 Dihedral : 5.126 48.877 4984 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.94 % Favored : 93.35 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4512 helix: 0.28 (0.10), residues: 2588 sheet: -0.04 (0.27), residues: 424 loop : -1.45 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 285 TYR 0.031 0.001 TYR F 223 PHE 0.021 0.001 PHE A 492 TRP 0.083 0.004 TRP F 757 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (38368) covalent geometry : angle 0.76087 / 0.43 (51708) hydrogen bonds : bond 0.05746 / 3.67 ( 1851) hydrogen bonds : angle 5.51328 / 3.90 ( 5268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8084 (pt0) REVERT: A 34 THR cc_start: 0.8240 (m) cc_final: 0.7939 (p) REVERT: A 45 PHE cc_start: 0.6849 (t80) cc_final: 0.6625 (t80) REVERT: A 59 TRP cc_start: 0.6303 (t-100) cc_final: 0.5586 (t-100) REVERT: A 90 ILE cc_start: 0.8506 (mt) cc_final: 0.8283 (mm) REVERT: A 104 LEU cc_start: 0.8282 (mt) cc_final: 0.7973 (mt) REVERT: A 107 PHE cc_start: 0.8696 (m-10) cc_final: 0.8484 (m-10) REVERT: A 114 THR cc_start: 0.8872 (m) cc_final: 0.8489 (p) REVERT: A 120 LYS cc_start: 0.8892 (mppt) cc_final: 0.8015 (mmtt) REVERT: A 121 ILE cc_start: 0.9039 (mt) cc_final: 0.8625 (mm) REVERT: A 124 MET cc_start: 0.8419 (mmp) cc_final: 0.8180 (mmp) REVERT: A 143 TRP cc_start: 0.8562 (t-100) cc_final: 0.7944 (t-100) REVERT: A 205 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7184 (mmtt) REVERT: A 207 ILE cc_start: 0.8589 (mm) cc_final: 0.8376 (mm) REVERT: A 225 ILE cc_start: 0.8012 (mt) cc_final: 0.7714 (mm) REVERT: A 226 ASN cc_start: 0.7763 (m-40) cc_final: 0.7314 (m-40) REVERT: A 242 LYS cc_start: 0.8663 (pttp) cc_final: 0.8210 (pttp) REVERT: A 284 GLU cc_start: 0.8199 (tp30) cc_final: 0.7584 (tp30) REVERT: A 290 MET cc_start: 0.7886 (mmm) cc_final: 0.6850 (mmm) REVERT: A 291 ASP cc_start: 0.8326 (m-30) cc_final: 0.8020 (m-30) REVERT: A 304 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7977 (mmmt) REVERT: A 311 TYR cc_start: 0.7965 (t80) cc_final: 0.7643 (t80) REVERT: A 313 TYR cc_start: 0.7160 (t80) cc_final: 0.6847 (t80) REVERT: A 399 ASP cc_start: 0.7730 (p0) cc_final: 0.7352 (p0) REVERT: A 414 TYR cc_start: 0.3772 (t80) cc_final: 0.3466 (t80) REVERT: A 415 HIS cc_start: 0.8244 (p-80) cc_final: 0.7946 (p-80) REVERT: A 453 ASP cc_start: 0.7916 (m-30) cc_final: 0.7612 (m-30) REVERT: A 457 ASN cc_start: 0.8276 (m110) cc_final: 0.7999 (m-40) REVERT: A 476 ILE cc_start: 0.7491 (tp) cc_final: 0.7235 (tp) REVERT: A 478 ARG cc_start: 0.8563 (ptt90) cc_final: 0.8159 (ptt90) REVERT: A 481 ILE cc_start: 0.8417 (mm) cc_final: 0.7907 (mm) REVERT: A 483 GLN cc_start: 0.8694 (pt0) cc_final: 0.8353 (pt0) REVERT: A 485 ILE cc_start: 0.7915 (mm) cc_final: 0.7617 (mm) REVERT: A 528 PHE cc_start: 0.7794 (t80) cc_final: 0.7368 (t80) REVERT: A 534 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 607 GLU cc_start: 0.8561 (mp0) cc_final: 0.8278 (mp0) REVERT: A 617 SER cc_start: 0.8145 (p) cc_final: 0.7368 (p) REVERT: A 622 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7022 (tmtt) REVERT: A 625 TYR cc_start: 0.7825 (t80) cc_final: 0.7180 (t80) REVERT: A 626 GLU cc_start: 0.8848 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 678 PHE cc_start: 0.7633 (p90) cc_final: 0.7266 (p90) REVERT: A 749 LEU cc_start: 0.6454 (mp) cc_final: 0.6074 (mp) REVERT: A 750 ASP cc_start: 0.8154 (p0) cc_final: 0.7562 (p0) REVERT: A 754 ARG cc_start: 0.8291 (mmt180) cc_final: 0.7857 (mmt180) REVERT: A 759 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 913 MET cc_start: 0.7100 (mmp) cc_final: 0.6587 (mmp) REVERT: A 916 PHE cc_start: 0.8057 (m-80) cc_final: 0.7461 (m-80) REVERT: A 985 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8605 (mmtt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.0893 time to fit residues: 27.4928 Evaluate side-chains 212 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.307 Evaluate side-chains 29 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6905 (mtmt) cc_final: 0.6413 (ptpp) REVERT: C 59 ILE cc_start: 0.7536 (mm) cc_final: 0.7241 (mm) REVERT: C 75 MET cc_start: 0.6913 (tpp) cc_final: 0.6408 (tpt) REVERT: C 193 ILE cc_start: 0.7275 (mp) cc_final: 0.6997 (mm) REVERT: C 206 MET cc_start: 0.3200 (tpp) cc_final: 0.2975 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0473 time to fit residues: 1.5645 Evaluate side-chains 28 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 124 optimal weight: 0.2980 chunk 291 optimal weight: 5.9990 chunk 313 optimal weight: 0.3980 chunk 447 optimal weight: 0.0970 chunk 247 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 366 optimal weight: 0.3980 chunk 321 optimal weight: 0.3980 chunk 323 optimal weight: 0.4980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 133 ASN A 195 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.162863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134185 restraints weight = 18982.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.138705 restraints weight = 12240.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141998 restraints weight = 8618.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144279 restraints weight = 6402.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.146116 restraints weight = 5006.963| |-----------------------------------------------------------------------------| r_work (final): 0.4032 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.210584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.172353 restraints weight = 3167.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.178041 restraints weight = 2117.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.182274 restraints weight = 1588.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.185191 restraints weight = 1258.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.187240 restraints weight = 1051.501| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 1.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38368 Z= 0.144 Angle : 0.762 11.774 51708 Z= 0.431 Chirality : 0.044 0.211 5500 Planarity : 0.004 0.075 6636 Dihedral : 5.105 47.900 4984 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.85 % Favored : 93.44 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4512 helix: 0.26 (0.10), residues: 2588 sheet: 0.09 (0.27), residues: 420 loop : -1.40 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 285 TYR 0.034 0.001 TYR E 223 PHE 0.020 0.001 PHE A 492 TRP 0.084 0.004 TRP F 757 HIS 0.008 0.001 HIS A 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (38368) covalent geometry : angle 0.76198 / 0.43 (51708) hydrogen bonds : bond 0.05714 / 3.66 ( 1851) hydrogen bonds : angle 5.47214 / 3.87 ( 5268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3240.19 seconds wall clock time: 58 minutes 15.90 seconds (3495.90 seconds total)