Starting phenix.real_space_refine on Tue Aug 26 14:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_39246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_39246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_39246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_39246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygf_39246/08_2025/8ygf_39246.map" } 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-2.0-5787/lib/python3.9/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: 8.43, per 1000 atoms: 0.22 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.53 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: 7.37 Time building geometry restraints manager: 3.56 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: 0.03 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: 6.620 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 32.130 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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 aren 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 covalent geometry : bond 0.00348 (38368) covalent geometry : angle 0.82792 (51708) hydrogen bonds : bond 0.18035 ( 1851) hydrogen bonds : angle 6.97658 ( 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 : 0.312 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: 0.0841 time to fit residues: 26.5357 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 : 0.210 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: 0.0401 time to fit residues: 1.5740 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... Flipped N/Q/H residues before XYZ refinement: 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.5636 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 aren 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 covalent geometry : bond 0.00412 (38368) covalent geometry : angle 0.90217 (51708) hydrogen bonds : bond 0.08821 ( 1851) hydrogen bonds : angle 6.35717 ( 5268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 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 : 0.301 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: 0.9140 (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: 0.0856 time to fit residues: 28.8855 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 : 0.311 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 : 0.047 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: 2.2986 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 : 0.045 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 118 HIS 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 591 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 HIS Total number of N/Q/H flips: 7 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.165679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134587 restraints weight = 19258.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139543 restraints weight = 11952.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.143088 restraints weight = 8201.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145559 restraints weight = 6007.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.147344 restraints weight = 4643.992| |-----------------------------------------------------------------------------| r_work (final): 0.3978 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.218525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181232 restraints weight = 2955.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.185893 restraints weight = 1965.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.189050 restraints weight = 1464.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.191431 restraints weight = 1179.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193212 restraints weight = 998.782| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 1.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38368 Z= 0.180 Angle : 0.836 11.167 51708 Z= 0.482 Chirality : 0.048 0.265 5500 Planarity : 0.005 0.043 6636 Dihedral : 5.920 59.307 4984 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 1.15 % Allowed : 6.47 % Favored : 92.38 % Rotamer: Outliers : 0.58 % Allowed : 4.56 % Favored : 94.86 % 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 aren not related in a simple way. whole: -1.19 (0.12), residues: 4512 helix: -0.08 (0.10), residues: 2596 sheet: -0.07 (0.29), residues: 376 loop : -2.11 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 285 TYR 0.046 0.002 TYR A 148 PHE 0.058 0.002 PHE E 44 TRP 0.027 0.004 TRP A 143 HIS 0.034 0.002 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00335 (38368) covalent geometry : angle 0.83643 (51708) hydrogen bonds : bond 0.07860 ( 1851) hydrogen bonds : angle 6.17871 ( 5268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7637 (tp) cc_final: 0.6845 (pt) REVERT: A 104 LEU cc_start: 0.8298 (mt) cc_final: 0.7841 (mt) REVERT: A 107 PHE cc_start: 0.8806 (m-10) cc_final: 0.8568 (m-10) REVERT: A 120 LYS cc_start: 0.9077 (mppt) cc_final: 0.8301 (mmtt) REVERT: A 121 ILE cc_start: 0.9054 (mt) cc_final: 0.8729 (mt) REVERT: A 124 MET cc_start: 0.8471 (tpp) cc_final: 0.7620 (tpp) REVERT: A 133 ASN cc_start: 0.8690 (m-40) cc_final: 0.8325 (m-40) REVERT: A 191 LEU cc_start: 0.9010 (pp) cc_final: 0.8696 (pp) REVERT: A 203 LEU cc_start: 0.8662 (pp) cc_final: 0.8420 (pp) REVERT: A 207 ILE cc_start: 0.8620 (mm) cc_final: 0.8377 (mm) REVERT: A 225 ILE cc_start: 0.8251 (mt) cc_final: 0.7949 (mm) REVERT: A 226 ASN cc_start: 0.8057 (m-40) cc_final: 0.7658 (m-40) REVERT: A 227 MET cc_start: 0.7723 (mpp) cc_final: 0.7333 (mpp) REVERT: A 242 LYS cc_start: 0.8892 (pttp) cc_final: 0.8237 (ttpt) REVERT: A 245 PHE cc_start: 0.7928 (t80) cc_final: 0.7711 (t80) REVERT: A 284 GLU cc_start: 0.7499 (mp0) cc_final: 0.7077 (mp0) REVERT: A 290 MET cc_start: 0.8182 (mmm) cc_final: 0.7352 (mmm) REVERT: A 291 ASP cc_start: 0.8443 (m-30) cc_final: 0.8202 (p0) REVERT: A 292 LEU cc_start: 0.9061 (mt) cc_final: 0.8644 (mt) REVERT: A 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.7915 (m-30) REVERT: A 335 GLU cc_start: 0.8630 (mp0) cc_final: 0.8412 (mp0) REVERT: A 399 ASP cc_start: 0.7801 (t0) cc_final: 0.7557 (p0) REVERT: A 404 ASN cc_start: 0.7630 (t0) cc_final: 0.7238 (t0) REVERT: A 415 HIS cc_start: 0.8443 (p-80) cc_final: 0.8052 (p-80) REVERT: A 453 ASP cc_start: 0.8526 (m-30) cc_final: 0.8311 (m-30) REVERT: A 481 ILE cc_start: 0.8494 (mm) cc_final: 0.8106 (mm) REVERT: A 483 GLN cc_start: 0.8622 (pt0) cc_final: 0.8125 (pt0) REVERT: A 485 ILE cc_start: 0.8126 (mm) cc_final: 0.7725 (mm) REVERT: A 516 GLU cc_start: 0.7830 (mp0) cc_final: 0.7561 (mp0) REVERT: A 528 PHE cc_start: 0.8096 (t80) cc_final: 0.7422 (t80) REVERT: A 536 GLN cc_start: 0.8409 (mt0) cc_final: 0.8057 (mt0) REVERT: A 552 TYR cc_start: 0.7421 (m-80) cc_final: 0.6998 (m-10) REVERT: A 596 TYR cc_start: 0.8437 (m-10) cc_final: 0.7870 (m-10) REVERT: A 607 GLU cc_start: 0.8329 (mp0) cc_final: 0.8053 (mp0) REVERT: A 608 PHE cc_start: 0.8155 (t80) cc_final: 0.7934 (t80) REVERT: A 617 SER cc_start: 0.7868 (p) cc_final: 0.7216 (p) REVERT: A 625 TYR cc_start: 0.8094 (t80) cc_final: 0.7683 (t80) REVERT: A 626 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8085 (tt0) REVERT: A 629 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.7271 (mtt-85) REVERT: A 750 ASP cc_start: 0.7966 (p0) cc_final: 0.7591 (p0) REVERT: A 754 ARG cc_start: 0.8431 (mmt180) cc_final: 0.7888 (mmm160) REVERT: A 759 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8139 (pp20) REVERT: A 836 ASP cc_start: 0.7520 (m-30) cc_final: 0.7161 (m-30) REVERT: A 837 PHE cc_start: 0.7838 (t80) cc_final: 0.7516 (t80) REVERT: A 846 SER cc_start: 0.4363 (m) cc_final: 0.4091 (t) REVERT: A 916 PHE cc_start: 0.7821 (m-80) cc_final: 0.7072 (m-10) REVERT: A 981 ILE cc_start: 0.8394 (pt) cc_final: 0.7826 (pt) REVERT: A 985 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8352 (mmtt) REVERT: A 995 ARG cc_start: 0.7034 (mpp-170) cc_final: 0.6804 (mmp80) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.0738 time to fit residues: 24.4776 Evaluate side-chains 220 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.331 Evaluate side-chains 35 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 GLN cc_start: 0.4885 (OUTLIER) cc_final: 0.4370 (tm130) REVERT: C 206 MET cc_start: 0.4614 (tpp) cc_final: 0.4343 (tpp) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.0471 time to fit residues: 1.8661 Evaluate side-chains 34 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.042 ------------------------------------------------------------------------------- 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: 0.3980 chunk 227 optimal weight: 0.3980 chunk 296 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 31 optimal weight: 0.0020 chunk 292 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 405 optimal weight: 0.1980 chunk 319 optimal weight: 0.9980 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.162970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132505 restraints weight = 19388.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137459 restraints weight = 12010.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.140979 restraints weight = 8210.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143582 restraints weight = 5981.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145408 restraints weight = 4583.887| |-----------------------------------------------------------------------------| r_work (final): 0.3989 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.224044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.190156 restraints weight = 2637.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.195246 restraints weight = 1687.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.198608 restraints weight = 1205.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.201252 restraints weight = 932.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.203212 restraints weight = 760.280| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 1.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38368 Z= 0.166 Angle : 0.799 11.775 51708 Z= 0.460 Chirality : 0.046 0.268 5500 Planarity : 0.005 0.042 6636 Dihedral : 5.842 60.887 4984 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -1.16 (0.12), residues: 4512 helix: -0.20 (0.10), residues: 2620 sheet: 0.22 (0.28), residues: 376 loop : -1.93 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 629 TYR 0.032 0.002 TYR E 134 PHE 0.032 0.002 PHE F 91 TRP 0.047 0.004 TRP B 757 HIS 0.029 0.002 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00319 (38368) covalent geometry : angle 0.79935 (51708) hydrogen bonds : bond 0.07389 ( 1851) hydrogen bonds : angle 6.12204 ( 5268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 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 42 LEU cc_start: 0.7558 (tp) cc_final: 0.6870 (pt) REVERT: A 45 PHE cc_start: 0.7212 (t80) cc_final: 0.6877 (t80) REVERT: A 104 LEU cc_start: 0.8294 (mt) cc_final: 0.7778 (mt) REVERT: A 107 PHE cc_start: 0.8803 (m-10) cc_final: 0.8572 (m-10) REVERT: A 118 HIS cc_start: 0.8667 (m170) cc_final: 0.8366 (m170) REVERT: A 120 LYS cc_start: 0.8999 (mppt) cc_final: 0.8181 (mmtt) REVERT: A 121 ILE cc_start: 0.9064 (mt) cc_final: 0.8735 (mt) REVERT: A 124 MET cc_start: 0.8430 (tpp) cc_final: 0.7575 (tpp) REVERT: A 133 ASN cc_start: 0.8808 (m-40) cc_final: 0.8571 (m-40) REVERT: A 143 TRP cc_start: 0.8356 (t-100) cc_final: 0.8044 (t-100) REVERT: A 178 PHE cc_start: 0.7197 (m-10) cc_final: 0.6985 (m-10) REVERT: A 225 ILE cc_start: 0.8205 (mt) cc_final: 0.7801 (mm) REVERT: A 226 ASN cc_start: 0.8025 (m-40) cc_final: 0.7634 (m-40) REVERT: A 227 MET cc_start: 0.7770 (mpp) cc_final: 0.7325 (mpp) REVERT: A 242 LYS cc_start: 0.8877 (pttp) cc_final: 0.8165 (ttpt) REVERT: A 245 PHE cc_start: 0.7892 (t80) cc_final: 0.7678 (t80) REVERT: A 286 TYR cc_start: 0.8071 (m-10) cc_final: 0.7820 (m-80) REVERT: A 290 MET cc_start: 0.8158 (mmm) cc_final: 0.7288 (mmm) REVERT: A 291 ASP cc_start: 0.8436 (m-30) cc_final: 0.8216 (p0) REVERT: A 292 LEU cc_start: 0.9072 (mt) cc_final: 0.8617 (mt) REVERT: A 310 ASP cc_start: 0.8296 (m-30) cc_final: 0.7922 (m-30) REVERT: A 311 TYR cc_start: 0.8171 (t80) cc_final: 0.7964 (t80) REVERT: A 384 LEU cc_start: 0.8104 (mt) cc_final: 0.7839 (mt) REVERT: A 398 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8887 (mmmt) REVERT: A 399 ASP cc_start: 0.7714 (t0) cc_final: 0.7505 (p0) REVERT: A 404 ASN cc_start: 0.7526 (t0) cc_final: 0.7165 (t0) REVERT: A 415 HIS cc_start: 0.8441 (p-80) cc_final: 0.8043 (p-80) REVERT: A 453 ASP cc_start: 0.8467 (m-30) cc_final: 0.8224 (m-30) REVERT: A 481 ILE cc_start: 0.8553 (mm) cc_final: 0.8137 (mm) REVERT: A 483 GLN cc_start: 0.8639 (pt0) cc_final: 0.8086 (pt0) REVERT: A 485 ILE cc_start: 0.8051 (mm) cc_final: 0.7677 (mm) REVERT: A 491 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 528 PHE cc_start: 0.7936 (t80) cc_final: 0.7468 (t80) REVERT: A 552 TYR cc_start: 0.7389 (m-80) cc_final: 0.6949 (m-10) REVERT: A 607 GLU cc_start: 0.8332 (mp0) cc_final: 0.8059 (mp0) REVERT: A 608 PHE cc_start: 0.8105 (t80) cc_final: 0.7829 (t80) REVERT: A 617 SER cc_start: 0.7897 (p) cc_final: 0.7206 (p) REVERT: A 622 LYS cc_start: 0.8546 (tptp) cc_final: 0.8243 (tptp) REVERT: A 626 GLU cc_start: 0.8846 (mt-10) cc_final: 0.7900 (tt0) REVERT: A 629 ARG cc_start: 0.7209 (tpp-160) cc_final: 0.6739 (mmt90) REVERT: A 694 GLU cc_start: 0.7329 (tp30) cc_final: 0.6537 (tp30) REVERT: A 750 ASP cc_start: 0.8045 (p0) cc_final: 0.7467 (p0) REVERT: A 754 ARG cc_start: 0.8411 (mmt180) cc_final: 0.8165 (mmt180) REVERT: A 759 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8117 (pp20) REVERT: A 837 PHE cc_start: 0.7844 (t80) cc_final: 0.7524 (t80) REVERT: A 916 PHE cc_start: 0.7847 (m-80) cc_final: 0.7301 (m-10) REVERT: A 981 ILE cc_start: 0.8426 (pt) cc_final: 0.7939 (pt) REVERT: A 985 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8370 (mmtt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.0844 time to fit residues: 27.1049 Evaluate side-chains 218 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.282 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 ASP cc_start: 0.6628 (m-30) cc_final: 0.6407 (m-30) REVERT: C 59 ILE cc_start: 0.7276 (mm) cc_final: 0.7030 (mm) REVERT: C 75 MET cc_start: 0.6814 (tpp) cc_final: 0.6461 (tpp) REVERT: C 76 THR cc_start: 0.7450 (t) cc_final: 0.7148 (t) REVERT: C 206 MET cc_start: 0.5155 (tpp) cc_final: 0.4382 (tpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0582 time to fit residues: 2.0829 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.052 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 166 optimal weight: 0.0980 chunk 262 optimal weight: 0.9980 chunk 326 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 381 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 269 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.164896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135048 restraints weight = 19434.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140055 restraints weight = 11978.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.143508 restraints weight = 8102.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146072 restraints weight = 5874.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147825 restraints weight = 4481.060| |-----------------------------------------------------------------------------| r_work (final): 0.4002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.206303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.169685 restraints weight = 2971.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174673 restraints weight = 1966.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.178242 restraints weight = 1454.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.180818 restraints weight = 1169.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.182223 restraints weight = 1004.205| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 1.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38368 Z= 0.166 Angle : 0.799 11.776 51708 Z= 0.460 Chirality : 0.046 0.268 5500 Planarity : 0.005 0.042 6636 Dihedral : 5.842 60.888 4984 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -1.16 (0.12), residues: 4512 helix: -0.20 (0.10), residues: 2620 sheet: 0.22 (0.28), residues: 376 loop : -1.93 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 629 TYR 0.032 0.002 TYR B 134 PHE 0.032 0.002 PHE F 91 TRP 0.047 0.004 TRP E 757 HIS 0.029 0.002 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00319 (38368) covalent geometry : angle 0.79936 (51708) hydrogen bonds : bond 0.07389 ( 1851) hydrogen bonds : angle 6.12208 ( 5268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7328 (tp) cc_final: 0.6745 (pt) REVERT: A 104 LEU cc_start: 0.8287 (mt) cc_final: 0.7798 (mt) REVERT: A 107 PHE cc_start: 0.8797 (m-10) cc_final: 0.8575 (m-10) REVERT: A 118 HIS cc_start: 0.8669 (m170) cc_final: 0.8356 (m170) REVERT: A 120 LYS cc_start: 0.9002 (mppt) cc_final: 0.8175 (mmtt) REVERT: A 121 ILE cc_start: 0.9064 (mt) cc_final: 0.8734 (mt) REVERT: A 124 MET cc_start: 0.8354 (tpp) cc_final: 0.7561 (tpp) REVERT: A 133 ASN cc_start: 0.8806 (m-40) cc_final: 0.8560 (m-40) REVERT: A 143 TRP cc_start: 0.8375 (t-100) cc_final: 0.8060 (t-100) REVERT: A 203 LEU cc_start: 0.8592 (pp) cc_final: 0.8366 (pp) REVERT: A 225 ILE cc_start: 0.8198 (mt) cc_final: 0.7806 (mm) REVERT: A 226 ASN cc_start: 0.8048 (m-40) cc_final: 0.7633 (m-40) REVERT: A 227 MET cc_start: 0.7763 (mpp) cc_final: 0.7303 (mpp) REVERT: A 242 LYS cc_start: 0.8869 (pttp) cc_final: 0.8190 (ttpt) REVERT: A 245 PHE cc_start: 0.7910 (t80) cc_final: 0.7666 (t80) REVERT: A 290 MET cc_start: 0.8130 (mmm) cc_final: 0.7267 (mmm) REVERT: A 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8198 (p0) REVERT: A 292 LEU cc_start: 0.9058 (mt) cc_final: 0.8623 (mt) REVERT: A 304 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7969 (mmmt) REVERT: A 310 ASP cc_start: 0.8346 (m-30) cc_final: 0.7919 (m-30) REVERT: A 311 TYR cc_start: 0.8179 (t80) cc_final: 0.7957 (t80) REVERT: A 384 LEU cc_start: 0.8102 (mt) cc_final: 0.7710 (mt) REVERT: A 398 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8887 (mmmt) REVERT: A 399 ASP cc_start: 0.7711 (t0) cc_final: 0.7494 (p0) REVERT: A 404 ASN cc_start: 0.7508 (t0) cc_final: 0.7164 (t0) REVERT: A 415 HIS cc_start: 0.8443 (p-80) cc_final: 0.8020 (p-80) REVERT: A 453 ASP cc_start: 0.8478 (m-30) cc_final: 0.8181 (m-30) REVERT: A 481 ILE cc_start: 0.8525 (mm) cc_final: 0.8199 (mm) REVERT: A 483 GLN cc_start: 0.8658 (pt0) cc_final: 0.8099 (pt0) REVERT: A 485 ILE cc_start: 0.8050 (mm) cc_final: 0.7667 (mm) REVERT: A 491 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 528 PHE cc_start: 0.7908 (t80) cc_final: 0.7478 (t80) REVERT: A 552 TYR cc_start: 0.7395 (m-80) cc_final: 0.6311 (m-80) REVERT: A 608 PHE cc_start: 0.8079 (t80) cc_final: 0.7825 (t80) REVERT: A 617 SER cc_start: 0.7862 (p) cc_final: 0.7366 (p) REVERT: A 625 TYR cc_start: 0.7814 (t80) cc_final: 0.7280 (t80) REVERT: A 626 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8214 (tt0) REVERT: A 629 ARG cc_start: 0.7213 (tpp-160) cc_final: 0.6679 (tpp-160) REVERT: A 677 ARG cc_start: 0.7620 (tmm160) cc_final: 0.7399 (tmm160) REVERT: A 678 PHE cc_start: 0.7999 (p90) cc_final: 0.7710 (p90) REVERT: A 694 GLU cc_start: 0.7346 (tp30) cc_final: 0.6536 (tp30) REVERT: A 750 ASP cc_start: 0.8053 (p0) cc_final: 0.7585 (p0) REVERT: A 837 PHE cc_start: 0.7835 (t80) cc_final: 0.7516 (t80) REVERT: A 913 MET cc_start: 0.7261 (mmp) cc_final: 0.6725 (mmp) REVERT: A 916 PHE cc_start: 0.7848 (m-80) cc_final: 0.7178 (m-10) REVERT: A 981 ILE cc_start: 0.8432 (pt) cc_final: 0.7940 (pt) REVERT: A 985 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8379 (mmtt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0778 time to fit residues: 24.5246 Evaluate side-chains 219 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.302 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 : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 ASP cc_start: 0.6431 (m-30) cc_final: 0.6099 (m-30) REVERT: C 59 ILE cc_start: 0.7415 (mm) cc_final: 0.7161 (mm) REVERT: C 75 MET cc_start: 0.6760 (tpp) cc_final: 0.6391 (tpp) REVERT: C 76 THR cc_start: 0.7569 (t) cc_final: 0.7249 (t) REVERT: C 206 MET cc_start: 0.4488 (tpp) cc_final: 0.3953 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0575 time to fit residues: 1.9789 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 109 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 432 optimal weight: 0.0470 chunk 7 optimal weight: 0.0570 chunk 338 optimal weight: 0.0050 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 0.2980 chunk 239 optimal weight: 0.9990 chunk 422 optimal weight: 0.8980 chunk 262 optimal weight: 0.5980 overall best weight: 0.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS ** 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 598 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.165635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135584 restraints weight = 19088.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140485 restraints weight = 11856.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143962 restraints weight = 8085.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146447 restraints weight = 5875.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148088 restraints weight = 4533.759| |-----------------------------------------------------------------------------| r_work (final): 0.3993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.222547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.184015 restraints weight = 2912.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.189316 restraints weight = 1884.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.193251 restraints weight = 1375.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.195567 restraints weight = 1084.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.197193 restraints weight = 916.386| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 1.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38368 Z= 0.163 Angle : 0.792 13.154 51708 Z= 0.452 Chirality : 0.046 0.223 5500 Planarity : 0.004 0.050 6636 Dihedral : 5.676 60.789 4984 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.65 % Favored : 92.73 % Rotamer: Outliers : 0.29 % Allowed : 2.62 % Favored : 97.09 % 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 aren not related in a simple way. whole: -0.97 (0.12), residues: 4512 helix: -0.09 (0.10), residues: 2600 sheet: 0.31 (0.28), residues: 380 loop : -1.74 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 285 TYR 0.032 0.002 TYR A 134 PHE 0.033 0.002 PHE A 91 TRP 0.062 0.004 TRP F 757 HIS 0.006 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00314 (38368) covalent geometry : angle 0.79243 (51708) hydrogen bonds : bond 0.06990 ( 1851) hydrogen bonds : angle 5.98535 ( 5268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 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: 2 poor density : 230 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8510 (m110) cc_final: 0.8277 (m110) REVERT: A 42 LEU cc_start: 0.7217 (tp) cc_final: 0.6784 (pt) REVERT: A 45 PHE cc_start: 0.7168 (t80) cc_final: 0.6796 (t80) REVERT: A 104 LEU cc_start: 0.8315 (mt) cc_final: 0.7812 (mt) REVERT: A 107 PHE cc_start: 0.8780 (m-10) cc_final: 0.8530 (m-10) REVERT: A 120 LYS cc_start: 0.9014 (mppt) cc_final: 0.8152 (mmtt) REVERT: A 121 ILE cc_start: 0.9051 (mt) cc_final: 0.8670 (mm) REVERT: A 124 MET cc_start: 0.8402 (tpp) cc_final: 0.7707 (tpp) REVERT: A 133 ASN cc_start: 0.8775 (m-40) cc_final: 0.8549 (m-40) REVERT: A 143 TRP cc_start: 0.8471 (t-100) cc_final: 0.8259 (t-100) REVERT: A 178 PHE cc_start: 0.7217 (m-10) cc_final: 0.6992 (m-10) REVERT: A 203 LEU cc_start: 0.8619 (pp) cc_final: 0.8130 (pp) REVERT: A 207 ILE cc_start: 0.8590 (mm) cc_final: 0.8385 (mm) REVERT: A 225 ILE cc_start: 0.8220 (mt) cc_final: 0.7778 (mm) REVERT: A 226 ASN cc_start: 0.8054 (m-40) cc_final: 0.7641 (m-40) REVERT: A 227 MET cc_start: 0.7727 (mpp) cc_final: 0.7267 (mpp) REVERT: A 242 LYS cc_start: 0.8886 (pttp) cc_final: 0.8293 (ttpt) REVERT: A 245 PHE cc_start: 0.7891 (t80) cc_final: 0.7645 (t80) REVERT: A 290 MET cc_start: 0.8089 (mmm) cc_final: 0.7142 (mmm) REVERT: A 291 ASP cc_start: 0.8394 (m-30) cc_final: 0.8182 (m-30) REVERT: A 304 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7995 (mmmt) REVERT: A 310 ASP cc_start: 0.8364 (m-30) cc_final: 0.7954 (m-30) REVERT: A 384 LEU cc_start: 0.8113 (mt) cc_final: 0.7808 (mt) REVERT: A 398 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8880 (mmmt) REVERT: A 404 ASN cc_start: 0.7504 (t0) cc_final: 0.7156 (t0) REVERT: A 415 HIS cc_start: 0.8384 (p-80) cc_final: 0.7957 (p-80) REVERT: A 453 ASP cc_start: 0.8393 (m-30) cc_final: 0.8139 (m-30) REVERT: A 476 ILE cc_start: 0.7722 (tp) cc_final: 0.7467 (tp) REVERT: A 478 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8255 (ptt90) REVERT: A 481 ILE cc_start: 0.8576 (mm) cc_final: 0.8132 (mm) REVERT: A 483 GLN cc_start: 0.8676 (pt0) cc_final: 0.8204 (pt0) REVERT: A 485 ILE cc_start: 0.8061 (mm) cc_final: 0.7715 (mm) REVERT: A 528 PHE cc_start: 0.7938 (t80) cc_final: 0.7482 (t80) REVERT: A 552 TYR cc_start: 0.7342 (m-80) cc_final: 0.6860 (m-10) REVERT: A 607 GLU cc_start: 0.8436 (mp0) cc_final: 0.8118 (mp0) REVERT: A 608 PHE cc_start: 0.8120 (t80) cc_final: 0.7835 (t80) REVERT: A 617 SER cc_start: 0.7962 (p) cc_final: 0.7348 (p) REVERT: A 625 TYR cc_start: 0.7773 (t80) cc_final: 0.7340 (t80) REVERT: A 626 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8167 (tt0) REVERT: A 694 GLU cc_start: 0.7284 (tp30) cc_final: 0.6526 (tp30) REVERT: A 750 ASP cc_start: 0.8130 (p0) cc_final: 0.7505 (p0) REVERT: A 913 MET cc_start: 0.7363 (mmp) cc_final: 0.6862 (mmp) REVERT: A 916 PHE cc_start: 0.7959 (m-80) cc_final: 0.7278 (m-10) REVERT: A 981 ILE cc_start: 0.8450 (pt) cc_final: 0.8082 (pt) REVERT: A 985 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8378 (mmtt) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.0754 time to fit residues: 23.9459 Evaluate side-chains 216 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.191 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6606 (mtmt) cc_final: 0.6195 (mtmm) REVERT: C 193 ILE cc_start: 0.7033 (mp) cc_final: 0.6775 (mm) REVERT: C 206 MET cc_start: 0.4267 (tpp) cc_final: 0.3786 (tpp) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.0626 time to fit residues: 2.2438 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 : 0.037 ------------------------------------------------------------------------------- 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: 0.0970 chunk 296 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 328 optimal weight: 0.8980 chunk 430 optimal weight: 3.9990 chunk 393 optimal weight: 0.6980 chunk 154 optimal weight: 0.4980 chunk 213 optimal weight: 0.0670 chunk 305 optimal weight: 0.0050 chunk 252 optimal weight: 1.9990 chunk 438 optimal weight: 0.0570 overall best weight: 0.1248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.164772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134711 restraints weight = 19021.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139675 restraints weight = 11969.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143095 restraints weight = 8200.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.145574 restraints weight = 5989.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147259 restraints weight = 4626.375| |-----------------------------------------------------------------------------| r_work (final): 0.3996 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.223581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.184770 restraints weight = 2942.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.189707 restraints weight = 1948.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.193106 restraints weight = 1442.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.195478 restraints weight = 1163.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.197109 restraints weight = 992.267| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 1.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38368 Z= 0.169 Angle : 0.804 12.563 51708 Z= 0.459 Chirality : 0.047 0.265 5500 Planarity : 0.006 0.138 6636 Dihedral : 5.749 60.660 4984 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4512 helix: -0.07 (0.10), residues: 2600 sheet: 0.26 (0.28), residues: 380 loop : -1.72 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 285 TYR 0.032 0.002 TYR A 134 PHE 0.053 0.002 PHE F 533 TRP 0.065 0.004 TRP B 757 HIS 0.068 0.003 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00332 (38368) covalent geometry : angle 0.80427 (51708) hydrogen bonds : bond 0.06926 ( 1851) hydrogen bonds : angle 6.01479 ( 5268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.223 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 42 LEU cc_start: 0.7301 (tp) cc_final: 0.6837 (pt) REVERT: A 104 LEU cc_start: 0.8294 (mt) cc_final: 0.7812 (mt) REVERT: A 107 PHE cc_start: 0.8769 (m-10) cc_final: 0.8528 (m-10) REVERT: A 120 LYS cc_start: 0.9005 (mppt) cc_final: 0.8194 (mmtt) REVERT: A 121 ILE cc_start: 0.9085 (mt) cc_final: 0.8687 (mm) REVERT: A 124 MET cc_start: 0.8410 (tpp) cc_final: 0.7731 (tpp) REVERT: A 133 ASN cc_start: 0.8774 (m-40) cc_final: 0.8549 (m-40) REVERT: A 143 TRP cc_start: 0.8410 (t-100) cc_final: 0.8116 (t-100) REVERT: A 144 LYS cc_start: 0.8864 (tttm) cc_final: 0.8613 (tttm) REVERT: A 178 PHE cc_start: 0.7216 (m-10) cc_final: 0.7014 (m-10) REVERT: A 187 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 207 ILE cc_start: 0.8546 (mm) cc_final: 0.8319 (mm) REVERT: A 225 ILE cc_start: 0.8174 (mt) cc_final: 0.7894 (mm) REVERT: A 226 ASN cc_start: 0.8040 (m-40) cc_final: 0.7734 (m-40) REVERT: A 242 LYS cc_start: 0.8822 (pttp) cc_final: 0.8158 (ttpt) REVERT: A 245 PHE cc_start: 0.7858 (t80) cc_final: 0.7612 (t80) REVERT: A 290 MET cc_start: 0.8097 (mmm) cc_final: 0.7188 (mmm) REVERT: A 291 ASP cc_start: 0.8399 (m-30) cc_final: 0.8170 (m-30) REVERT: A 304 LYS cc_start: 0.8365 (mmpt) cc_final: 0.8000 (mmmt) REVERT: A 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8028 (m-30) REVERT: A 384 LEU cc_start: 0.8136 (mt) cc_final: 0.7882 (mt) REVERT: A 404 ASN cc_start: 0.7489 (t0) cc_final: 0.7130 (t0) REVERT: A 415 HIS cc_start: 0.8365 (p-80) cc_final: 0.7940 (p-80) REVERT: A 453 ASP cc_start: 0.8376 (m-30) cc_final: 0.8130 (m-30) REVERT: A 481 ILE cc_start: 0.8568 (mm) cc_final: 0.8151 (mm) REVERT: A 483 GLN cc_start: 0.8676 (pt0) cc_final: 0.8235 (pt0) REVERT: A 485 ILE cc_start: 0.8005 (mm) cc_final: 0.7670 (mm) REVERT: A 528 PHE cc_start: 0.7929 (t80) cc_final: 0.7489 (t80) REVERT: A 552 TYR cc_start: 0.7329 (m-80) cc_final: 0.6784 (m-10) REVERT: A 607 GLU cc_start: 0.8383 (mp0) cc_final: 0.8072 (mp0) REVERT: A 608 PHE cc_start: 0.8118 (t80) cc_final: 0.7862 (t80) REVERT: A 617 SER cc_start: 0.7949 (p) cc_final: 0.7312 (p) REVERT: A 622 LYS cc_start: 0.8368 (tptp) cc_final: 0.8018 (tptp) REVERT: A 626 GLU cc_start: 0.8825 (mt-10) cc_final: 0.7821 (tt0) REVERT: A 695 ILE cc_start: 0.7826 (pt) cc_final: 0.7472 (mt) REVERT: A 750 ASP cc_start: 0.8134 (p0) cc_final: 0.7540 (p0) REVERT: A 913 MET cc_start: 0.7342 (mmp) cc_final: 0.6822 (mmp) REVERT: A 916 PHE cc_start: 0.7978 (m-80) cc_final: 0.7318 (m-10) REVERT: A 981 ILE cc_start: 0.8453 (pt) cc_final: 0.8002 (pt) REVERT: A 985 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8403 (mmmt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0713 time to fit residues: 22.0853 Evaluate side-chains 213 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.217 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 : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6584 (mtmt) cc_final: 0.6176 (mtmm) REVERT: C 75 MET cc_start: 0.6822 (tpp) cc_final: 0.6405 (tpp) REVERT: C 76 THR cc_start: 0.7594 (t) cc_final: 0.7283 (t) REVERT: C 193 ILE cc_start: 0.7073 (mp) cc_final: 0.6803 (mm) REVERT: C 206 MET cc_start: 0.4212 (tpp) cc_final: 0.3763 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0460 time to fit residues: 1.5917 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.043 ------------------------------------------------------------------------------- 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: 0.7980 chunk 101 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 41 optimal weight: 0.0370 chunk 348 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.165506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134900 restraints weight = 19357.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139801 restraints weight = 12134.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.143292 restraints weight = 8350.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145827 restraints weight = 6154.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.147683 restraints weight = 4760.230| |-----------------------------------------------------------------------------| r_work (final): 0.3993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168713 restraints weight = 3002.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.173857 restraints weight = 2033.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.177512 restraints weight = 1534.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.179820 restraints weight = 1235.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.181541 restraints weight = 1058.937| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 1.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38368 Z= 0.169 Angle : 0.804 12.564 51708 Z= 0.459 Chirality : 0.047 0.265 5500 Planarity : 0.006 0.138 6636 Dihedral : 5.749 60.660 4984 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4512 helix: -0.07 (0.10), residues: 2600 sheet: 0.26 (0.28), residues: 380 loop : -1.72 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 285 TYR 0.032 0.002 TYR B 134 PHE 0.053 0.002 PHE B 533 TRP 0.065 0.004 TRP A 757 HIS 0.068 0.003 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00332 (38368) covalent geometry : angle 0.80426 (51708) hydrogen bonds : bond 0.06926 ( 1851) hydrogen bonds : angle 6.01480 ( 5268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7307 (tp) cc_final: 0.6813 (pt) REVERT: A 45 PHE cc_start: 0.7107 (t80) cc_final: 0.6754 (t80) REVERT: A 104 LEU cc_start: 0.8305 (mt) cc_final: 0.7822 (mt) REVERT: A 107 PHE cc_start: 0.8781 (m-10) cc_final: 0.8532 (m-10) REVERT: A 120 LYS cc_start: 0.9000 (mppt) cc_final: 0.8190 (mmtt) REVERT: A 121 ILE cc_start: 0.9082 (mt) cc_final: 0.8682 (mm) REVERT: A 124 MET cc_start: 0.8428 (tpp) cc_final: 0.7729 (tpp) REVERT: A 133 ASN cc_start: 0.8780 (m-40) cc_final: 0.8543 (m-40) REVERT: A 143 TRP cc_start: 0.8404 (t-100) cc_final: 0.8111 (t-100) REVERT: A 144 LYS cc_start: 0.8867 (tttm) cc_final: 0.8610 (tttm) REVERT: A 178 PHE cc_start: 0.7204 (m-10) cc_final: 0.6998 (m-10) REVERT: A 187 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 203 LEU cc_start: 0.8456 (pp) cc_final: 0.8100 (pp) REVERT: A 207 ILE cc_start: 0.8549 (mm) cc_final: 0.8324 (mm) REVERT: A 225 ILE cc_start: 0.8250 (mt) cc_final: 0.7921 (mm) REVERT: A 226 ASN cc_start: 0.8072 (m-40) cc_final: 0.7758 (m-40) REVERT: A 242 LYS cc_start: 0.8817 (pttp) cc_final: 0.8166 (ttpt) REVERT: A 245 PHE cc_start: 0.7909 (t80) cc_final: 0.7658 (t80) REVERT: A 290 MET cc_start: 0.8120 (mmm) cc_final: 0.7192 (mmm) REVERT: A 291 ASP cc_start: 0.8402 (m-30) cc_final: 0.8171 (m-30) REVERT: A 304 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7990 (mmmt) REVERT: A 310 ASP cc_start: 0.8331 (m-30) cc_final: 0.8027 (m-30) REVERT: A 384 LEU cc_start: 0.8150 (mt) cc_final: 0.7900 (mt) REVERT: A 404 ASN cc_start: 0.7472 (t0) cc_final: 0.7131 (t0) REVERT: A 415 HIS cc_start: 0.8355 (p-80) cc_final: 0.7953 (p-80) REVERT: A 453 ASP cc_start: 0.8395 (m-30) cc_final: 0.8142 (m-30) REVERT: A 476 ILE cc_start: 0.7701 (tp) cc_final: 0.7455 (tp) REVERT: A 478 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8253 (ptt90) REVERT: A 481 ILE cc_start: 0.8574 (mm) cc_final: 0.8144 (mm) REVERT: A 483 GLN cc_start: 0.8689 (pt0) cc_final: 0.8230 (pt0) REVERT: A 485 ILE cc_start: 0.8009 (mm) cc_final: 0.7687 (mm) REVERT: A 528 PHE cc_start: 0.7940 (t80) cc_final: 0.7495 (t80) REVERT: A 552 TYR cc_start: 0.7322 (m-80) cc_final: 0.6829 (m-10) REVERT: A 607 GLU cc_start: 0.8477 (mp0) cc_final: 0.8245 (mp0) REVERT: A 608 PHE cc_start: 0.8184 (t80) cc_final: 0.7926 (t80) REVERT: A 617 SER cc_start: 0.7945 (p) cc_final: 0.7328 (p) REVERT: A 622 LYS cc_start: 0.8391 (tptp) cc_final: 0.8017 (tptp) REVERT: A 624 GLU cc_start: 0.7911 (tp30) cc_final: 0.7663 (tp30) REVERT: A 626 GLU cc_start: 0.8844 (mt-10) cc_final: 0.7873 (tt0) REVERT: A 678 PHE cc_start: 0.7896 (p90) cc_final: 0.7633 (p90) REVERT: A 695 ILE cc_start: 0.7839 (pt) cc_final: 0.7488 (mt) REVERT: A 750 ASP cc_start: 0.8146 (p0) cc_final: 0.7569 (p0) REVERT: A 757 TRP cc_start: 0.6527 (m-90) cc_final: 0.6314 (m-90) REVERT: A 913 MET cc_start: 0.7375 (mmp) cc_final: 0.6841 (mmp) REVERT: A 916 PHE cc_start: 0.7981 (m-80) cc_final: 0.7331 (m-10) REVERT: A 981 ILE cc_start: 0.8427 (pt) cc_final: 0.7982 (pt) REVERT: A 985 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8399 (mmmt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0716 time to fit residues: 22.3249 Evaluate side-chains 215 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.186 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 : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6636 (mtmt) cc_final: 0.6228 (mtmm) REVERT: C 75 MET cc_start: 0.6747 (tpp) cc_final: 0.6305 (tpp) REVERT: C 76 THR cc_start: 0.7691 (t) cc_final: 0.7378 (t) REVERT: C 193 ILE cc_start: 0.7091 (mp) cc_final: 0.6805 (mm) REVERT: C 206 MET cc_start: 0.4072 (tpp) cc_final: 0.3654 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0580 time to fit residues: 1.9949 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.039 ------------------------------------------------------------------------------- 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: 0.8980 chunk 324 optimal weight: 3.9990 chunk 367 optimal weight: 0.0970 chunk 369 optimal weight: 0.4980 chunk 269 optimal weight: 0.7980 chunk 140 optimal weight: 0.0060 chunk 233 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 chunk 104 optimal weight: 0.0570 chunk 210 optimal weight: 0.7980 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.165846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135883 restraints weight = 19171.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140786 restraints weight = 12147.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144151 restraints weight = 8385.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146665 restraints weight = 6217.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148436 restraints weight = 4829.647| |-----------------------------------------------------------------------------| r_work (final): 0.3993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.168545 restraints weight = 3047.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.173660 restraints weight = 2058.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.177230 restraints weight = 1557.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.179714 restraints weight = 1255.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.181177 restraints weight = 1070.131| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 1.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38368 Z= 0.169 Angle : 0.804 12.564 51708 Z= 0.459 Chirality : 0.047 0.265 5500 Planarity : 0.006 0.138 6636 Dihedral : 5.749 60.660 4984 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4512 helix: -0.07 (0.10), residues: 2600 sheet: 0.26 (0.28), residues: 380 loop : -1.72 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 285 TYR 0.032 0.002 TYR E 134 PHE 0.053 0.002 PHE E 533 TRP 0.065 0.004 TRP A 757 HIS 0.068 0.003 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00332 (38368) covalent geometry : angle 0.80426 (51708) hydrogen bonds : bond 0.06926 ( 1851) hydrogen bonds : angle 6.01480 ( 5268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7305 (tp) cc_final: 0.6836 (pt) REVERT: A 45 PHE cc_start: 0.7104 (t80) cc_final: 0.6751 (t80) REVERT: A 104 LEU cc_start: 0.8294 (mt) cc_final: 0.7809 (mt) REVERT: A 107 PHE cc_start: 0.8736 (m-10) cc_final: 0.8510 (m-10) REVERT: A 120 LYS cc_start: 0.8999 (mppt) cc_final: 0.8190 (mmtt) REVERT: A 121 ILE cc_start: 0.9076 (mt) cc_final: 0.8675 (mm) REVERT: A 124 MET cc_start: 0.8431 (tpp) cc_final: 0.7741 (tpp) REVERT: A 133 ASN cc_start: 0.8786 (m-40) cc_final: 0.8564 (m-40) REVERT: A 143 TRP cc_start: 0.8398 (t-100) cc_final: 0.8105 (t-100) REVERT: A 144 LYS cc_start: 0.8867 (tttm) cc_final: 0.8613 (tttm) REVERT: A 187 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 203 LEU cc_start: 0.8460 (pp) cc_final: 0.8105 (pp) REVERT: A 207 ILE cc_start: 0.8542 (mm) cc_final: 0.8312 (mm) REVERT: A 225 ILE cc_start: 0.8272 (mt) cc_final: 0.7944 (mm) REVERT: A 226 ASN cc_start: 0.8102 (m-40) cc_final: 0.7784 (m-40) REVERT: A 242 LYS cc_start: 0.8859 (pttp) cc_final: 0.8170 (ttpt) REVERT: A 245 PHE cc_start: 0.7905 (t80) cc_final: 0.7643 (t80) REVERT: A 290 MET cc_start: 0.8112 (mmm) cc_final: 0.7202 (mmm) REVERT: A 291 ASP cc_start: 0.8416 (m-30) cc_final: 0.8188 (m-30) REVERT: A 304 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7986 (mmmt) REVERT: A 310 ASP cc_start: 0.8328 (m-30) cc_final: 0.8023 (m-30) REVERT: A 384 LEU cc_start: 0.8138 (mt) cc_final: 0.7889 (mt) REVERT: A 404 ASN cc_start: 0.7489 (t0) cc_final: 0.7144 (t0) REVERT: A 415 HIS cc_start: 0.8363 (p-80) cc_final: 0.7955 (p-80) REVERT: A 453 ASP cc_start: 0.8383 (m-30) cc_final: 0.8137 (m-30) REVERT: A 476 ILE cc_start: 0.7678 (tp) cc_final: 0.7428 (tp) REVERT: A 478 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.8262 (ptt90) REVERT: A 481 ILE cc_start: 0.8569 (mm) cc_final: 0.8159 (mm) REVERT: A 483 GLN cc_start: 0.8689 (pt0) cc_final: 0.8234 (pt0) REVERT: A 485 ILE cc_start: 0.8001 (mm) cc_final: 0.7679 (mm) REVERT: A 528 PHE cc_start: 0.7933 (t80) cc_final: 0.7491 (t80) REVERT: A 552 TYR cc_start: 0.7303 (m-80) cc_final: 0.6805 (m-10) REVERT: A 607 GLU cc_start: 0.8469 (mp0) cc_final: 0.8241 (mp0) REVERT: A 608 PHE cc_start: 0.8185 (t80) cc_final: 0.7935 (t80) REVERT: A 617 SER cc_start: 0.7943 (p) cc_final: 0.7322 (p) REVERT: A 622 LYS cc_start: 0.8393 (tptp) cc_final: 0.8023 (tptp) REVERT: A 624 GLU cc_start: 0.7901 (tp30) cc_final: 0.7646 (tp30) REVERT: A 626 GLU cc_start: 0.8828 (mt-10) cc_final: 0.7870 (tt0) REVERT: A 678 PHE cc_start: 0.7879 (p90) cc_final: 0.7628 (p90) REVERT: A 695 ILE cc_start: 0.7837 (pt) cc_final: 0.7488 (mt) REVERT: A 750 ASP cc_start: 0.8211 (p0) cc_final: 0.7633 (p0) REVERT: A 913 MET cc_start: 0.7355 (mmp) cc_final: 0.6823 (mmp) REVERT: A 916 PHE cc_start: 0.7982 (m-80) cc_final: 0.7331 (m-10) REVERT: A 981 ILE cc_start: 0.8425 (pt) cc_final: 0.7982 (pt) REVERT: A 985 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8400 (mmmt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0856 time to fit residues: 26.2450 Evaluate side-chains 215 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.313 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 : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6636 (mtmt) cc_final: 0.6228 (mtmm) REVERT: C 75 MET cc_start: 0.6753 (tpp) cc_final: 0.6312 (tpp) REVERT: C 76 THR cc_start: 0.7686 (t) cc_final: 0.7374 (t) REVERT: C 193 ILE cc_start: 0.7085 (mp) cc_final: 0.6801 (mm) REVERT: C 206 MET cc_start: 0.4072 (tpp) cc_final: 0.3661 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0599 time to fit residues: 2.0865 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.044 ------------------------------------------------------------------------------- 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: 0.5980 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 315 optimal weight: 0.0970 chunk 160 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 446 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.165737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135426 restraints weight = 19068.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140343 restraints weight = 11934.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143843 restraints weight = 8188.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.146267 restraints weight = 6029.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148161 restraints weight = 4691.858| |-----------------------------------------------------------------------------| r_work (final): 0.3997 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.169022 restraints weight = 2943.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.173817 restraints weight = 2015.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.177540 restraints weight = 1532.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.179948 restraints weight = 1235.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.181418 restraints weight = 1048.654| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 1.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38368 Z= 0.169 Angle : 0.804 12.564 51708 Z= 0.459 Chirality : 0.047 0.265 5500 Planarity : 0.006 0.138 6636 Dihedral : 5.749 60.660 4984 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4512 helix: -0.07 (0.10), residues: 2600 sheet: 0.26 (0.28), residues: 380 loop : -1.72 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 285 TYR 0.032 0.002 TYR A 134 PHE 0.053 0.002 PHE B 533 TRP 0.065 0.004 TRP A 757 HIS 0.068 0.003 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00332 (38368) covalent geometry : angle 0.80426 (51708) hydrogen bonds : bond 0.06926 ( 1851) hydrogen bonds : angle 6.01480 ( 5268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9020 Ramachandran restraints generated. 4510 Oldfield, 0 Emsley, 4510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7266 (tp) cc_final: 0.6806 (pt) REVERT: A 45 PHE cc_start: 0.7107 (t80) cc_final: 0.6756 (t80) REVERT: A 104 LEU cc_start: 0.8288 (mt) cc_final: 0.7822 (mt) REVERT: A 107 PHE cc_start: 0.8781 (m-10) cc_final: 0.8533 (m-10) REVERT: A 120 LYS cc_start: 0.9003 (mppt) cc_final: 0.8192 (mmtt) REVERT: A 121 ILE cc_start: 0.9079 (mt) cc_final: 0.8680 (mm) REVERT: A 124 MET cc_start: 0.8437 (tpp) cc_final: 0.7740 (tpp) REVERT: A 133 ASN cc_start: 0.8789 (m-40) cc_final: 0.8540 (m-40) REVERT: A 143 TRP cc_start: 0.8401 (t-100) cc_final: 0.8108 (t-100) REVERT: A 144 LYS cc_start: 0.8865 (tttm) cc_final: 0.8609 (tttm) REVERT: A 187 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 203 LEU cc_start: 0.8452 (pp) cc_final: 0.8100 (pp) REVERT: A 207 ILE cc_start: 0.8555 (mm) cc_final: 0.8327 (mm) REVERT: A 225 ILE cc_start: 0.8247 (mt) cc_final: 0.7917 (mm) REVERT: A 226 ASN cc_start: 0.8071 (m-40) cc_final: 0.7756 (m-40) REVERT: A 242 LYS cc_start: 0.8853 (pttp) cc_final: 0.8158 (ttpt) REVERT: A 245 PHE cc_start: 0.7930 (t80) cc_final: 0.7670 (t80) REVERT: A 290 MET cc_start: 0.8117 (mmm) cc_final: 0.7202 (mmm) REVERT: A 291 ASP cc_start: 0.8404 (m-30) cc_final: 0.8176 (m-30) REVERT: A 304 LYS cc_start: 0.8300 (mmpt) cc_final: 0.7991 (mmmt) REVERT: A 310 ASP cc_start: 0.8332 (m-30) cc_final: 0.8027 (m-30) REVERT: A 384 LEU cc_start: 0.8149 (mt) cc_final: 0.7901 (mt) REVERT: A 404 ASN cc_start: 0.7462 (t0) cc_final: 0.7119 (t0) REVERT: A 415 HIS cc_start: 0.8352 (p-80) cc_final: 0.7951 (p-80) REVERT: A 453 ASP cc_start: 0.8395 (m-30) cc_final: 0.8142 (m-30) REVERT: A 476 ILE cc_start: 0.7700 (tp) cc_final: 0.7453 (tp) REVERT: A 478 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8252 (ptt90) REVERT: A 481 ILE cc_start: 0.8571 (mm) cc_final: 0.8141 (mm) REVERT: A 483 GLN cc_start: 0.8685 (pt0) cc_final: 0.8229 (pt0) REVERT: A 485 ILE cc_start: 0.8002 (mm) cc_final: 0.7683 (mm) REVERT: A 528 PHE cc_start: 0.7942 (t80) cc_final: 0.7492 (t80) REVERT: A 552 TYR cc_start: 0.7314 (m-80) cc_final: 0.6822 (m-10) REVERT: A 607 GLU cc_start: 0.8478 (mp0) cc_final: 0.8248 (mp0) REVERT: A 608 PHE cc_start: 0.8188 (t80) cc_final: 0.7932 (t80) REVERT: A 617 SER cc_start: 0.7951 (p) cc_final: 0.7333 (p) REVERT: A 622 LYS cc_start: 0.8399 (tptp) cc_final: 0.8023 (tptp) REVERT: A 624 GLU cc_start: 0.7915 (tp30) cc_final: 0.7662 (tp30) REVERT: A 626 GLU cc_start: 0.8850 (mt-10) cc_final: 0.7881 (tt0) REVERT: A 678 PHE cc_start: 0.7908 (p90) cc_final: 0.7638 (p90) REVERT: A 695 ILE cc_start: 0.7842 (pt) cc_final: 0.7486 (mt) REVERT: A 750 ASP cc_start: 0.8140 (p0) cc_final: 0.7566 (p0) REVERT: A 757 TRP cc_start: 0.6536 (m-90) cc_final: 0.6319 (m-90) REVERT: A 913 MET cc_start: 0.7378 (mmp) cc_final: 0.6846 (mmp) REVERT: A 916 PHE cc_start: 0.7988 (m-80) cc_final: 0.7337 (m-10) REVERT: A 981 ILE cc_start: 0.8427 (pt) cc_final: 0.7984 (pt) REVERT: A 985 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8399 (mmmt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0927 time to fit residues: 28.6794 Evaluate side-chains 215 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.402 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 : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 LYS cc_start: 0.6627 (mtmt) cc_final: 0.6221 (mtmm) REVERT: C 75 MET cc_start: 0.6752 (tpp) cc_final: 0.6312 (tpp) REVERT: C 76 THR cc_start: 0.7690 (t) cc_final: 0.7378 (t) REVERT: C 193 ILE cc_start: 0.7088 (mp) cc_final: 0.6802 (mm) REVERT: C 206 MET cc_start: 0.4066 (tpp) cc_final: 0.3652 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0670 time to fit residues: 2.3228 Evaluate side-chains 32 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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: 3.9990 chunk 291 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 447 optimal weight: 0.1980 chunk 247 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 366 optimal weight: 0.8980 chunk 321 optimal weight: 0.0870 chunk 323 optimal weight: 0.0770 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.164422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134122 restraints weight = 19103.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139039 restraints weight = 11919.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.142518 restraints weight = 8163.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145058 restraints weight = 5998.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.146806 restraints weight = 4628.950| |-----------------------------------------------------------------------------| r_work (final): 0.3993 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168700 restraints weight = 3000.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.173811 restraints weight = 2040.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.177502 restraints weight = 1537.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.179816 restraints weight = 1237.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.181304 restraints weight = 1059.837| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 1.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38368 Z= 0.169 Angle : 0.804 12.564 51708 Z= 0.459 Chirality : 0.047 0.265 5500 Planarity : 0.006 0.138 6636 Dihedral : 5.749 60.660 4984 Min Nonbonded Distance : 1.231 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4512 helix: -0.07 (0.10), residues: 2600 sheet: 0.26 (0.28), residues: 380 loop : -1.72 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 285 TYR 0.032 0.002 TYR A 134 PHE 0.053 0.002 PHE A 533 TRP 0.065 0.004 TRP A 757 HIS 0.068 0.003 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00332 (38368) covalent geometry : angle 0.80426 (51708) hydrogen bonds : bond 0.06926 ( 1851) hydrogen bonds : angle 6.01480 ( 5268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.95 seconds wall clock time: 54 minutes 10.58 seconds (3250.58 seconds total)