Starting phenix.real_space_refine on Sun Aug 24 16:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.map" model { file = "/net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wye_37925/08_2025/8wye_37925.cif" } resolution = 2.49 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= -0.000 sd= 0.087 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 78 5.16 5 C 13748 2.51 5 N 3432 2.21 5 O 3974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s 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: 21232 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7895 Classifications: {'peptide': 945} Link IDs: {'PTRANS': 19, 'TRANS': 925} Chain breaks: 5 Chain: "B" Number of atoms: 7966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7966 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 19, 'TRANS': 933} Chain breaks: 6 Chain: "C" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2195 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "E" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2219 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Time building chain proxies: 4.07, per 1000 atoms: 0.19 Number of scatterers: 21232 At special positions: 0 Unit cell: (98.413, 126.531, 180.286, 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 78 16.00 O 3974 8.00 N 3432 7.00 C 13748 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: 1.37 Conformation dependent library (CDL) restraints added in 659.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 9 sheets defined 67.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.956A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.907A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.600A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.610A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.521A pdb=" N TYR A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.580A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.540A pdb=" N ARG A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.532A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.723A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 372' Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 495 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.607A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN A 548 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.635A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.991A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 768 through 787 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.658A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 934 removed outlier: 3.789A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.602A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1004 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.946A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.804A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.533A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.627A pdb=" N GLY B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.252A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.869A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.670A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.569A pdb=" N SER B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 495 removed outlier: 3.546A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 524 through 530 removed outlier: 4.442A pdb=" N PHE B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.241A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.555A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.837A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.734A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.541A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.937A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.688A pdb=" N ILE B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.685A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 895 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 930 through 934 removed outlier: 3.574A 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 955 through 961 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 992 Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.523A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.074A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.707A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.782A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.907A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.536A pdb=" N LYS D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 235 " --> pdb=" O TRP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.739A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.020A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 72 removed outlier: 3.607A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 95 removed outlier: 4.055A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.857A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 297 removed outlier: 3.657A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.151A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.943A pdb=" N PHE C 23 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.179A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 72 removed outlier: 7.271A pdb=" N GLU C 38 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU C 33 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN C 40 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE C 31 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE C 44 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL C 27 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU C 28 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA C 86 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP C 30 " --> pdb=" O THR C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 71 through 72 removed outlier: 10.185A pdb=" N GLU C 115 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE C 44 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL C 117 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 46 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.047A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.175A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3294 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: 3.15 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6721 1.34 - 1.46: 5244 1.46 - 1.58: 9637 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 21731 Sorted by residual: bond pdb=" CG1 ILE E 33 " pdb=" CD1 ILE E 33 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.86e+00 bond pdb=" CG1 ILE E 30 " pdb=" CD1 ILE E 30 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CB LYS B 237 " pdb=" CG LYS B 237 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CB GLU A 379 " pdb=" CG GLU A 379 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CG GLU A 379 " pdb=" CD GLU A 379 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 21726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 28935 1.77 - 3.54: 311 3.54 - 5.31: 57 5.31 - 7.08: 7 7.08 - 8.85: 8 Bond angle restraints: 29318 Sorted by residual: angle pdb=" C ILE B 835 " pdb=" N ASP B 836 " pdb=" CA ASP B 836 " ideal model delta sigma weight residual 121.58 113.91 7.67 1.95e+00 2.63e-01 1.55e+01 angle pdb=" CA ILE E 33 " pdb=" CB ILE E 33 " pdb=" CG1 ILE E 33 " ideal model delta sigma weight residual 110.40 115.98 -5.58 1.70e+00 3.46e-01 1.08e+01 angle pdb=" N ILE E 33 " pdb=" CA ILE E 33 " pdb=" CB ILE E 33 " ideal model delta sigma weight residual 110.54 114.91 -4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" C LYS D 237 " pdb=" N ASP D 238 " pdb=" CA ASP D 238 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.67e+00 angle pdb=" CB LYS B 237 " pdb=" CG LYS B 237 " pdb=" CD LYS B 237 " ideal model delta sigma weight residual 111.30 118.43 -7.13 2.30e+00 1.89e-01 9.60e+00 ... (remaining 29313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10812 17.83 - 35.66: 1538 35.66 - 53.49: 451 53.49 - 71.32: 90 71.32 - 89.16: 27 Dihedral angle restraints: 12918 sinusoidal: 5341 harmonic: 7577 Sorted by residual: dihedral pdb=" CA LYS C 19 " pdb=" C LYS C 19 " pdb=" N ILE C 20 " pdb=" CA ILE C 20 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR B 338 " pdb=" C TYR B 338 " pdb=" N HIS B 339 " pdb=" CA HIS B 339 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 12915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2304 0.040 - 0.080: 631 0.080 - 0.120: 179 0.120 - 0.160: 14 0.160 - 0.199: 4 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB ILE E 33 " pdb=" CA ILE E 33 " pdb=" CG1 ILE E 33 " pdb=" CG2 ILE E 33 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CG LEU A 922 " pdb=" CB LEU A 922 " pdb=" CD1 LEU A 922 " pdb=" CD2 LEU A 922 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CB ILE B 751 " pdb=" CA ILE B 751 " pdb=" CG1 ILE B 751 " pdb=" CG2 ILE B 751 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3129 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 249 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" CG ASP E 249 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 249 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 249 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 945 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CG ASP A 945 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP A 945 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 945 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 531 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 532 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " 0.024 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 276 2.62 - 3.19: 18519 3.19 - 3.76: 34946 3.76 - 4.33: 50284 4.33 - 4.90: 81420 Nonbonded interactions: 185445 Sorted by model distance: nonbonded pdb=" O TYR A 313 " pdb=" OG SER A 317 " model vdw 2.044 3.040 nonbonded pdb=" O VAL A 470 " pdb=" OG SER A 474 " model vdw 2.096 3.040 nonbonded pdb=" OG SER B 366 " pdb=" OE1 GLU B 369 " model vdw 2.125 3.040 nonbonded pdb=" OG SER B 37 " pdb=" O MET B 124 " model vdw 2.130 3.040 nonbonded pdb=" OH TYR B 324 " pdb=" OD1 ASP B 590 " model vdw 2.135 3.040 ... (remaining 185440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 496 or resid 502 through 565 or resid 579 throu \ gh 1005)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 26 through 297) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.580 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.077 21731 Z= 0.138 Angle : 0.518 8.848 29318 Z= 0.279 Chirality : 0.040 0.199 3132 Planarity : 0.003 0.044 3732 Dihedral : 18.235 89.156 8044 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.05 % Allowed : 27.46 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.91 (0.16), residues: 2517 helix: 1.16 (0.13), residues: 1525 sheet: -0.17 (0.56), residues: 63 loop : -0.14 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 285 TYR 0.023 0.001 TYR A 951 PHE 0.021 0.001 PHE A 921 TRP 0.015 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00321 (21731) covalent geometry : angle 0.51822 (29318) hydrogen bonds : bond 0.13823 ( 1143) hydrogen bonds : angle 5.92678 ( 3294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 282 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 ASP cc_start: 0.7649 (t0) cc_final: 0.7209 (m-30) outliers start: 95 outliers final: 86 residues processed: 370 average time/residue: 0.4987 time to fit residues: 212.7129 Evaluate side-chains 358 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 272 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 0.7980 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 591 ASN A 765 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 521 ASN B 548 ASN B 711 GLN B 765 ASN B 832 GLN B 848 ASN B 867 ASN ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 226 ASN D 297 GLN E 128 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.167107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112684 restraints weight = 23447.844| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.01 r_work: 0.3371 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21731 Z= 0.192 Angle : 0.533 9.046 29318 Z= 0.284 Chirality : 0.042 0.277 3132 Planarity : 0.004 0.042 3732 Dihedral : 7.603 74.768 2956 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.61 % Allowed : 24.39 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.16), residues: 2517 helix: 1.26 (0.13), residues: 1526 sheet: -0.89 (0.53), residues: 63 loop : 0.03 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 285 TYR 0.021 0.002 TYR A 951 PHE 0.017 0.002 PHE B 646 TRP 0.017 0.002 TRP A 757 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00459 (21731) covalent geometry : angle 0.53319 (29318) hydrogen bonds : bond 0.04078 ( 1143) hydrogen bonds : angle 4.83236 ( 3294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 311 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8213 (tttm) cc_final: 0.7880 (tppt) REVERT: A 304 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8130 (ptmm) REVERT: A 348 ARG cc_start: 0.8184 (mmt90) cc_final: 0.7905 (mmt90) REVERT: A 375 LYS cc_start: 0.8059 (tptt) cc_final: 0.7755 (ttpp) REVERT: A 434 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: A 750 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7577 (p0) REVERT: B 21 MET cc_start: 0.7871 (ppp) cc_final: 0.7634 (pmm) REVERT: B 278 ASN cc_start: 0.8209 (m-40) cc_final: 0.7990 (m-40) REVERT: B 369 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: B 454 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8217 (tp) REVERT: B 463 ILE cc_start: 0.5436 (OUTLIER) cc_final: 0.4871 (pt) REVERT: B 673 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7454 (mm) REVERT: B 759 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: B 836 ASP cc_start: 0.8181 (p0) cc_final: 0.7975 (p0) REVERT: C 26 ASP cc_start: 0.8038 (t0) cc_final: 0.7822 (t0) REVERT: C 115 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: D 187 GLU cc_start: 0.7306 (tt0) cc_final: 0.6830 (mt-10) REVERT: E 55 ASP cc_start: 0.7202 (t0) cc_final: 0.6986 (t0) REVERT: E 82 ASP cc_start: 0.7398 (m-30) cc_final: 0.7165 (m-30) REVERT: E 125 ASN cc_start: 0.7844 (m-40) cc_final: 0.7429 (t0) REVERT: E 249 ASP cc_start: 0.6336 (t0) cc_final: 0.6037 (t0) outliers start: 108 outliers final: 39 residues processed: 401 average time/residue: 0.5137 time to fit residues: 237.1001 Evaluate side-chains 330 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 198 optimal weight: 0.1980 chunk 226 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 711 GLN A 765 ASN A 797 ASN B 202 ASN B 467 ASN B 548 ASN B 711 GLN B 765 ASN B 848 ASN B 963 ASN D 226 ASN E 128 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115355 restraints weight = 23446.077| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.04 r_work: 0.3399 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21731 Z= 0.115 Angle : 0.466 6.673 29318 Z= 0.250 Chirality : 0.039 0.134 3132 Planarity : 0.003 0.042 3732 Dihedral : 6.129 73.199 2860 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.56 % Allowed : 23.20 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.17 (0.16), residues: 2517 helix: 1.40 (0.13), residues: 1531 sheet: -1.19 (0.53), residues: 63 loop : -0.01 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 870 TYR 0.013 0.001 TYR B 223 PHE 0.011 0.001 PHE B 646 TRP 0.013 0.001 TRP A 757 HIS 0.008 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00264 (21731) covalent geometry : angle 0.46643 (29318) hydrogen bonds : bond 0.03495 ( 1143) hydrogen bonds : angle 4.58070 ( 3294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 311 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8156 (tttm) cc_final: 0.7846 (tppt) REVERT: A 304 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8086 (ptmm) REVERT: A 348 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7899 (mmt180) REVERT: A 375 LYS cc_start: 0.8003 (tptt) cc_final: 0.7708 (ttpp) REVERT: A 434 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: A 519 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8072 (mmt) REVERT: A 714 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 740 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7663 (tp) REVERT: A 750 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 926 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6296 (m110) REVERT: A 940 TYR cc_start: 0.7751 (t80) cc_final: 0.7459 (t80) REVERT: B 53 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6784 (mp) REVERT: B 165 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7487 (mtm-85) REVERT: B 369 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: B 454 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8052 (tp) REVERT: B 463 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4791 (pt) REVERT: B 517 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6749 (ttp-110) REVERT: B 673 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7272 (mm) REVERT: B 832 GLN cc_start: 0.7917 (tp40) cc_final: 0.7607 (mm-40) REVERT: C 26 ASP cc_start: 0.7996 (t0) cc_final: 0.7665 (t0) REVERT: C 80 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7377 (m110) REVERT: C 115 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: D 97 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: E 34 THR cc_start: 0.7851 (m) cc_final: 0.7473 (p) REVERT: E 55 ASP cc_start: 0.7162 (t0) cc_final: 0.6906 (t0) REVERT: E 82 ASP cc_start: 0.7229 (m-30) cc_final: 0.6964 (m-30) REVERT: E 125 ASN cc_start: 0.7824 (m-40) cc_final: 0.7422 (t0) outliers start: 107 outliers final: 31 residues processed: 393 average time/residue: 0.5435 time to fit residues: 244.4861 Evaluate side-chains 330 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 947 GLU Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 217 optimal weight: 0.6980 chunk 50 optimal weight: 0.0020 chunk 97 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN B 202 ASN B 548 ASN B 765 ASN B 848 ASN B 867 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116913 restraints weight = 23423.748| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21731 Z= 0.104 Angle : 0.460 7.867 29318 Z= 0.244 Chirality : 0.039 0.183 3132 Planarity : 0.003 0.041 3732 Dihedral : 5.288 77.546 2836 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.80 % Allowed : 23.58 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.17), residues: 2517 helix: 1.49 (0.13), residues: 1539 sheet: -1.24 (0.48), residues: 82 loop : -0.01 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 870 TYR 0.015 0.001 TYR A 951 PHE 0.010 0.001 PHE B 699 TRP 0.012 0.001 TRP A 757 HIS 0.007 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00235 (21731) covalent geometry : angle 0.46043 (29318) hydrogen bonds : bond 0.03235 ( 1143) hydrogen bonds : angle 4.43917 ( 3294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 331 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7865 (mmp) cc_final: 0.7627 (mmp) REVERT: A 237 LYS cc_start: 0.8131 (tttm) cc_final: 0.7817 (tppt) REVERT: A 304 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8054 (ptmm) REVERT: A 348 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7777 (mmt180) REVERT: A 375 LYS cc_start: 0.7973 (tptt) cc_final: 0.7708 (ttpp) REVERT: A 434 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: A 519 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8027 (mmt) REVERT: A 711 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: A 714 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 750 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 840 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6720 (mttp) REVERT: A 1001 MET cc_start: 0.8384 (mmm) cc_final: 0.8156 (mmp) REVERT: B 21 MET cc_start: 0.8164 (ptp) cc_final: 0.7681 (pmm) REVERT: B 454 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8049 (tp) REVERT: B 540 LYS cc_start: 0.8644 (tptm) cc_final: 0.8441 (tptt) REVERT: B 673 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7248 (mm) REVERT: B 832 GLN cc_start: 0.7899 (tp40) cc_final: 0.7513 (mm-40) REVERT: B 836 ASP cc_start: 0.8215 (p0) cc_final: 0.7966 (p0) REVERT: C 26 ASP cc_start: 0.8015 (t0) cc_final: 0.7645 (t0) REVERT: D 97 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: E 34 THR cc_start: 0.7760 (m) cc_final: 0.7349 (p) REVERT: E 55 ASP cc_start: 0.7230 (t0) cc_final: 0.6912 (t0) REVERT: E 82 ASP cc_start: 0.7203 (m-30) cc_final: 0.6907 (m-30) REVERT: E 125 ASN cc_start: 0.7797 (m-40) cc_final: 0.7417 (t0) outliers start: 89 outliers final: 34 residues processed: 395 average time/residue: 0.4896 time to fit residues: 222.9284 Evaluate side-chains 335 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS B 202 ASN B 299 ASN B 548 ASN B 765 ASN B 848 ASN B 867 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112984 restraints weight = 24846.298| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.14 r_work: 0.3434 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21731 Z= 0.213 Angle : 0.527 10.802 29318 Z= 0.279 Chirality : 0.042 0.192 3132 Planarity : 0.003 0.040 3732 Dihedral : 5.364 85.309 2829 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.48 % Allowed : 23.33 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.16), residues: 2517 helix: 1.31 (0.13), residues: 1524 sheet: -1.43 (0.50), residues: 75 loop : 0.01 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 870 TYR 0.016 0.002 TYR A 755 PHE 0.017 0.002 PHE B 699 TRP 0.019 0.002 TRP A 757 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00515 (21731) covalent geometry : angle 0.52677 (29318) hydrogen bonds : bond 0.03856 ( 1143) hydrogen bonds : angle 4.60307 ( 3294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 302 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: A 237 LYS cc_start: 0.8097 (tttm) cc_final: 0.7753 (tppt) REVERT: A 304 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7923 (ptmm) REVERT: A 348 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7904 (mmt180) REVERT: A 375 LYS cc_start: 0.7931 (tptt) cc_final: 0.7668 (ttpp) REVERT: A 519 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8269 (mmt) REVERT: A 711 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 750 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7524 (p0) REVERT: A 840 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6608 (mttp) REVERT: A 923 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 926 ASN cc_start: 0.6879 (OUTLIER) cc_final: 0.6363 (m110) REVERT: B 21 MET cc_start: 0.8144 (ptp) cc_final: 0.7658 (ptp) REVERT: B 53 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6648 (mp) REVERT: B 454 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8103 (tp) REVERT: B 517 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6570 (ttp-110) REVERT: B 673 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7215 (mm) REVERT: B 836 ASP cc_start: 0.8168 (p0) cc_final: 0.7949 (p0) REVERT: C 26 ASP cc_start: 0.7874 (t0) cc_final: 0.7462 (t0) REVERT: C 80 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7329 (m110) REVERT: D 187 GLU cc_start: 0.7140 (tt0) cc_final: 0.6607 (mt-10) REVERT: E 34 THR cc_start: 0.7739 (m) cc_final: 0.7368 (p) REVERT: E 55 ASP cc_start: 0.7288 (t0) cc_final: 0.6913 (t0) REVERT: E 125 ASN cc_start: 0.7781 (m-40) cc_final: 0.7383 (t0) REVERT: E 285 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6332 (ttm170) outliers start: 105 outliers final: 44 residues processed: 385 average time/residue: 0.5295 time to fit residues: 234.1209 Evaluate side-chains 341 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 285 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 75 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 236 GLN A 765 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS B 202 ASN B 299 ASN B 548 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN B 939 GLN D 297 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108247 restraints weight = 25015.884| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.16 r_work: 0.3358 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 21731 Z= 0.295 Angle : 0.596 12.607 29318 Z= 0.314 Chirality : 0.045 0.208 3132 Planarity : 0.004 0.040 3732 Dihedral : 5.552 89.931 2828 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.73 % Allowed : 23.37 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.68 (0.16), residues: 2517 helix: 0.97 (0.13), residues: 1531 sheet: -1.82 (0.50), residues: 63 loop : -0.08 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 870 TYR 0.020 0.002 TYR A 148 PHE 0.019 0.002 PHE B 699 TRP 0.021 0.002 TRP A 757 HIS 0.012 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00715 (21731) covalent geometry : angle 0.59562 (29318) hydrogen bonds : bond 0.04313 ( 1143) hydrogen bonds : angle 4.80625 ( 3294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 306 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8114 (tttm) cc_final: 0.7764 (tppt) REVERT: A 304 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7711 (ptmm) REVERT: A 375 LYS cc_start: 0.7946 (tptt) cc_final: 0.7640 (ttpp) REVERT: A 750 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7573 (p0) REVERT: A 840 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6693 (mttp) REVERT: A 923 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 926 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6261 (m110) REVERT: A 928 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8743 (m) REVERT: A 938 ASP cc_start: 0.7726 (m-30) cc_final: 0.7458 (m-30) REVERT: B 122 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7805 (mm) REVERT: B 408 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 517 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6503 (ttp-110) REVERT: B 673 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7366 (mm) REVERT: B 832 GLN cc_start: 0.7919 (tp40) cc_final: 0.7584 (mm-40) REVERT: C 26 ASP cc_start: 0.7849 (t0) cc_final: 0.7374 (t0) REVERT: C 80 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7213 (m110) REVERT: D 147 LYS cc_start: 0.6656 (mmtt) cc_final: 0.6350 (mtmm) REVERT: D 187 GLU cc_start: 0.7251 (tt0) cc_final: 0.6603 (mt-10) REVERT: D 244 PHE cc_start: 0.6744 (m-80) cc_final: 0.6516 (m-80) REVERT: E 55 ASP cc_start: 0.7273 (t0) cc_final: 0.6905 (t0) REVERT: E 82 ASP cc_start: 0.7136 (m-30) cc_final: 0.6766 (m-30) REVERT: E 125 ASN cc_start: 0.7709 (m-40) cc_final: 0.7308 (t0) REVERT: E 175 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7845 (mtm-85) REVERT: E 249 ASP cc_start: 0.6276 (t70) cc_final: 0.6006 (t0) REVERT: E 280 TYR cc_start: 0.7911 (m-10) cc_final: 0.7570 (m-10) outliers start: 111 outliers final: 47 residues processed: 400 average time/residue: 0.5071 time to fit residues: 234.1061 Evaluate side-chains 346 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 926 ASN Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 51 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 0.3980 chunk 241 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN A 797 ASN A 810 HIS B 202 ASN B 548 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.168315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114827 restraints weight = 24805.983| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.14 r_work: 0.3454 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21731 Z= 0.124 Angle : 0.506 8.244 29318 Z= 0.267 Chirality : 0.040 0.286 3132 Planarity : 0.003 0.041 3732 Dihedral : 4.940 53.044 2825 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.37 % Allowed : 25.42 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.16), residues: 2517 helix: 1.28 (0.13), residues: 1533 sheet: -1.69 (0.50), residues: 75 loop : -0.06 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 870 TYR 0.020 0.001 TYR A 951 PHE 0.013 0.001 PHE B 699 TRP 0.014 0.001 TRP B 757 HIS 0.010 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00291 (21731) covalent geometry : angle 0.50564 (29318) hydrogen bonds : bond 0.03453 ( 1143) hydrogen bonds : angle 4.53712 ( 3294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LYS cc_start: 0.8091 (tttm) cc_final: 0.7745 (tppt) REVERT: A 304 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7928 (ptmm) REVERT: A 348 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7908 (mmt180) REVERT: A 375 LYS cc_start: 0.7963 (tptt) cc_final: 0.7646 (ttpp) REVERT: A 750 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 840 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6552 (mttp) REVERT: A 938 ASP cc_start: 0.7742 (m-30) cc_final: 0.7467 (m-30) REVERT: A 940 TYR cc_start: 0.7613 (t80) cc_final: 0.7354 (t80) REVERT: B 23 ASP cc_start: 0.7200 (t0) cc_final: 0.6972 (t0) REVERT: B 53 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6657 (mp) REVERT: B 278 ASN cc_start: 0.8027 (m-40) cc_final: 0.7819 (m-40) REVERT: B 454 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 517 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6535 (ttp-110) REVERT: B 673 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 832 GLN cc_start: 0.7877 (tp40) cc_final: 0.7561 (mm-40) REVERT: C 26 ASP cc_start: 0.7855 (t0) cc_final: 0.7432 (t0) REVERT: C 80 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7278 (m110) REVERT: D 187 GLU cc_start: 0.7198 (tt0) cc_final: 0.6614 (mt-10) REVERT: D 244 PHE cc_start: 0.6734 (m-80) cc_final: 0.6529 (m-80) REVERT: D 292 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6898 (tm) REVERT: E 34 THR cc_start: 0.7683 (m) cc_final: 0.7316 (p) REVERT: E 82 ASP cc_start: 0.7022 (m-30) cc_final: 0.6716 (m-30) REVERT: E 125 ASN cc_start: 0.7763 (m-40) cc_final: 0.7350 (t0) REVERT: E 175 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7880 (mtm-85) outliers start: 79 outliers final: 37 residues processed: 367 average time/residue: 0.5392 time to fit residues: 227.1206 Evaluate side-chains 332 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 204 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 810 HIS B 202 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.168323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114528 restraints weight = 24879.389| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.15 r_work: 0.3435 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21731 Z= 0.136 Angle : 0.513 9.076 29318 Z= 0.269 Chirality : 0.040 0.182 3132 Planarity : 0.003 0.041 3732 Dihedral : 4.828 50.103 2825 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.11 % Allowed : 26.01 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.16), residues: 2517 helix: 1.34 (0.13), residues: 1532 sheet: -1.66 (0.50), residues: 75 loop : -0.04 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 870 TYR 0.019 0.001 TYR A 951 PHE 0.013 0.001 PHE B 699 TRP 0.015 0.001 TRP C 121 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00325 (21731) covalent geometry : angle 0.51319 (29318) hydrogen bonds : bond 0.03478 ( 1143) hydrogen bonds : angle 4.50617 ( 3294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 295 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7607 (mmp) cc_final: 0.7383 (mmp) REVERT: A 237 LYS cc_start: 0.8105 (tttm) cc_final: 0.7744 (tppt) REVERT: A 304 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7876 (ptmm) REVERT: A 375 LYS cc_start: 0.7949 (tptt) cc_final: 0.7666 (ttpp) REVERT: A 714 SER cc_start: 0.8450 (t) cc_final: 0.8112 (p) REVERT: A 813 LYS cc_start: 0.8651 (tppt) cc_final: 0.8376 (mmtp) REVERT: A 831 LYS cc_start: 0.5772 (OUTLIER) cc_final: 0.5424 (pmtt) REVERT: A 840 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6560 (mttp) REVERT: A 940 TYR cc_start: 0.7653 (t80) cc_final: 0.7340 (t80) REVERT: B 23 ASP cc_start: 0.7219 (t0) cc_final: 0.6950 (t0) REVERT: B 278 ASN cc_start: 0.7973 (m-40) cc_final: 0.7766 (m-40) REVERT: B 454 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 517 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6502 (ttp-110) REVERT: B 673 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7096 (mm) REVERT: B 890 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8312 (mm-30) REVERT: C 26 ASP cc_start: 0.7740 (t0) cc_final: 0.7266 (t0) REVERT: C 80 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7282 (m110) REVERT: D 187 GLU cc_start: 0.7164 (tt0) cc_final: 0.6579 (mt-10) REVERT: D 292 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6880 (tm) REVERT: E 34 THR cc_start: 0.7666 (m) cc_final: 0.7281 (p) REVERT: E 82 ASP cc_start: 0.6885 (m-30) cc_final: 0.6504 (m-30) REVERT: E 147 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7195 (ptmt) REVERT: E 175 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7892 (mtm-85) REVERT: E 255 ASN cc_start: 0.6756 (p0) cc_final: 0.5778 (t0) outliers start: 73 outliers final: 35 residues processed: 358 average time/residue: 0.5146 time to fit residues: 211.4951 Evaluate side-chains 328 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 103 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 234 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 765 ASN A 810 HIS B 202 ASN B 467 ASN B 711 GLN B 765 ASN B 848 ASN B 867 ASN D 297 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.168889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115341 restraints weight = 24773.629| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.15 r_work: 0.3443 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21731 Z= 0.129 Angle : 0.511 10.999 29318 Z= 0.267 Chirality : 0.040 0.267 3132 Planarity : 0.003 0.041 3732 Dihedral : 4.635 48.796 2821 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.77 % Allowed : 26.44 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.16), residues: 2517 helix: 1.35 (0.13), residues: 1539 sheet: -1.59 (0.50), residues: 75 loop : -0.07 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 870 TYR 0.018 0.001 TYR C 43 PHE 0.013 0.001 PHE B 921 TRP 0.015 0.001 TRP C 121 HIS 0.010 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00308 (21731) covalent geometry : angle 0.51113 (29318) hydrogen bonds : bond 0.03380 ( 1143) hydrogen bonds : angle 4.47279 ( 3294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7608 (mmp) cc_final: 0.7378 (mmp) REVERT: A 237 LYS cc_start: 0.8088 (tttm) cc_final: 0.7733 (tppt) REVERT: A 304 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7893 (ptmm) REVERT: A 348 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7803 (mmt180) REVERT: A 363 LEU cc_start: 0.7630 (mt) cc_final: 0.7417 (mt) REVERT: A 372 LYS cc_start: 0.6915 (tmtt) cc_final: 0.6662 (mttp) REVERT: A 375 LYS cc_start: 0.7932 (tptt) cc_final: 0.7663 (ttpp) REVERT: A 714 SER cc_start: 0.8444 (t) cc_final: 0.8119 (p) REVERT: A 813 LYS cc_start: 0.8625 (tppt) cc_final: 0.8368 (mmtp) REVERT: A 840 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6544 (mttp) REVERT: A 940 TYR cc_start: 0.7723 (t80) cc_final: 0.7485 (t80) REVERT: B 23 ASP cc_start: 0.7254 (t0) cc_final: 0.6946 (t0) REVERT: B 69 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6989 (mp0) REVERT: B 181 GLU cc_start: 0.8443 (pt0) cc_final: 0.8037 (pm20) REVERT: B 454 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7954 (tp) REVERT: B 517 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6561 (ttp-110) REVERT: B 673 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7086 (mm) REVERT: B 890 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8346 (mm-30) REVERT: C 26 ASP cc_start: 0.7749 (t0) cc_final: 0.7268 (t0) REVERT: C 80 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7297 (m110) REVERT: D 183 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7594 (m) REVERT: D 187 GLU cc_start: 0.7095 (tt0) cc_final: 0.6540 (mt-10) REVERT: E 34 THR cc_start: 0.7539 (m) cc_final: 0.7177 (p) REVERT: E 82 ASP cc_start: 0.6911 (m-30) cc_final: 0.6584 (m-30) REVERT: E 147 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7164 (ptmt) REVERT: E 175 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7862 (mtm-85) REVERT: E 255 ASN cc_start: 0.6730 (p0) cc_final: 0.5752 (t0) outliers start: 65 outliers final: 36 residues processed: 358 average time/residue: 0.5139 time to fit residues: 210.9290 Evaluate side-chains 330 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 234 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 120 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 810 HIS B 202 ASN B 467 ASN B 765 ASN B 848 ASN B 867 ASN E 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.168841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115284 restraints weight = 24899.658| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.16 r_work: 0.3443 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 21731 Z= 0.146 Angle : 0.671 59.183 29318 Z= 0.378 Chirality : 0.040 0.280 3132 Planarity : 0.003 0.065 3732 Dihedral : 4.663 48.796 2821 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.52 % Allowed : 26.52 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.16), residues: 2517 helix: 1.34 (0.13), residues: 1539 sheet: -1.59 (0.50), residues: 75 loop : -0.08 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 285 TYR 0.017 0.001 TYR C 43 PHE 0.013 0.001 PHE B 699 TRP 0.014 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00341 (21731) covalent geometry : angle 0.67147 (29318) hydrogen bonds : bond 0.03389 ( 1143) hydrogen bonds : angle 4.47462 ( 3294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7616 (mmp) cc_final: 0.7385 (mmp) REVERT: A 237 LYS cc_start: 0.8086 (tttm) cc_final: 0.7730 (tppt) REVERT: A 304 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7890 (ptmm) REVERT: A 348 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7699 (mmt90) REVERT: A 363 LEU cc_start: 0.7628 (mt) cc_final: 0.7413 (mt) REVERT: A 372 LYS cc_start: 0.6911 (tmtt) cc_final: 0.6658 (mttp) REVERT: A 375 LYS cc_start: 0.7934 (tptt) cc_final: 0.7664 (ttpp) REVERT: A 404 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7721 (p0) REVERT: A 714 SER cc_start: 0.8449 (t) cc_final: 0.8125 (p) REVERT: A 813 LYS cc_start: 0.8626 (tppt) cc_final: 0.8369 (mmtp) REVERT: A 840 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6577 (mttp) REVERT: A 940 TYR cc_start: 0.7707 (t80) cc_final: 0.7452 (t80) REVERT: B 23 ASP cc_start: 0.7273 (t0) cc_final: 0.6997 (t0) REVERT: B 53 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6490 (mp) REVERT: B 69 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6995 (mp0) REVERT: B 181 GLU cc_start: 0.8444 (pt0) cc_final: 0.8037 (pm20) REVERT: B 454 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7958 (tp) REVERT: B 517 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6555 (ttp-110) REVERT: B 673 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7076 (mm) REVERT: B 890 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8345 (mm-30) REVERT: C 26 ASP cc_start: 0.7752 (t0) cc_final: 0.7271 (t0) REVERT: C 80 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7311 (m110) REVERT: D 183 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7610 (m) REVERT: D 187 GLU cc_start: 0.7105 (tt0) cc_final: 0.6552 (mt-10) REVERT: E 34 THR cc_start: 0.7563 (m) cc_final: 0.7199 (p) REVERT: E 82 ASP cc_start: 0.6912 (m-30) cc_final: 0.6527 (m-30) REVERT: E 147 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7168 (ptmt) REVERT: E 175 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7861 (mtm-85) REVERT: E 255 ASN cc_start: 0.6799 (p0) cc_final: 0.5796 (t0) outliers start: 59 outliers final: 38 residues processed: 334 average time/residue: 0.5361 time to fit residues: 204.8347 Evaluate side-chains 333 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 505 LYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 801 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 927 ASN Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 147 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 234 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 141 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A 797 ASN A 810 HIS B 202 ASN B 765 ASN B 848 ASN B 867 ASN E 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.168854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115330 restraints weight = 24851.634| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.15 r_work: 0.3446 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 21731 Z= 0.163 Angle : 0.683 59.017 29318 Z= 0.388 Chirality : 0.040 0.275 3132 Planarity : 0.004 0.139 3732 Dihedral : 4.662 48.796 2821 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 26.78 % Favored : 70.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.16), residues: 2517 helix: 1.34 (0.13), residues: 1539 sheet: -1.59 (0.50), residues: 75 loop : -0.08 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 285 TYR 0.017 0.001 TYR C 43 PHE 0.013 0.001 PHE B 699 TRP 0.014 0.001 TRP A 757 HIS 0.009 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00370 (21731) covalent geometry : angle 0.68254 (29318) hydrogen bonds : bond 0.03389 ( 1143) hydrogen bonds : angle 4.47482 ( 3294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9306.50 seconds wall clock time: 158 minutes 38.76 seconds (9518.76 seconds total)