Starting phenix.real_space_refine on Mon Oct 13 10:25:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wya_37921/10_2025/8wya_37921.map" } resolution = 3.62 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= 0.044 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 124 5.16 5 C 21149 2.51 5 N 5240 2.21 5 O 6108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32621 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7655 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 19, 'TRANS': 895} Chain breaks: 10 Chain: "B" Number of atoms: 7706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7706 Classifications: {'peptide': 923} Link IDs: {'PTRANS': 19, 'TRANS': 903} Chain breaks: 9 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "D" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7705 Classifications: {'peptide': 921} Link IDs: {'PTRANS': 19, 'TRANS': 901} Chain breaks: 9 Chain: "E" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7677 Classifications: {'peptide': 919} Link IDs: {'PTRANS': 18, 'TRANS': 900} Chain breaks: 9 Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Time building chain proxies: 8.71, per 1000 atoms: 0.27 Number of scatterers: 32621 At special positions: 0 Unit cell: (100.776, 131.404, 276.64, 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 124 16.00 O 6108 8.00 N 5240 7.00 C 21149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7484 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 13 sheets defined 68.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.625A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.668A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.570A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.648A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.871A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.534A pdb=" N THR A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.343A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.763A pdb=" N ASN A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 183 " --> pdb=" O GLY A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.604A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.768A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.812A 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 322 removed outlier: 3.630A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) 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: 3.529A 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 367 through 372 removed outlier: 3.904A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 411 through 416 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 removed outlier: 3.553A pdb=" N SER A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.580A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.525A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.613A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 699 removed outlier: 3.545A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 723 removed outlier: 4.092A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.656A 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 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.177A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.639A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 811 removed outlier: 3.779A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.790A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 857 removed outlier: 4.120A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 913 through 922 removed outlier: 3.785A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 955 removed outlier: 3.969A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 954 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 955 " --> pdb=" O LYS A 952 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 955' Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.636A pdb=" N LYS A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.817A pdb=" N LYS A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.503A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.597A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.710A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.708A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.567A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.714A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.710A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.521A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.098A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.753A pdb=" N ARG B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.780A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.866A pdb=" N THR B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.984A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.528A pdb=" N GLU B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 628 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 removed outlier: 3.602A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.684A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.924A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.760A 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 742 Processing helix chain 'B' and resid 750 through 765 removed outlier: 4.292A pdb=" N CYS B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.556A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 813 removed outlier: 3.572A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 831 through 840 removed outlier: 4.015A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 856 removed outlier: 4.046A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 897 removed outlier: 3.866A pdb=" N ILE B 897 " --> pdb=" O LYS B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 removed outlier: 4.043A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 945 removed outlier: 3.712A pdb=" N VAL B 944 " --> pdb=" O TYR B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 949 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 956 No H-bonds generated for 'chain 'B' and resid 955 through 956' Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.751A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 962 " --> pdb=" O TRP B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 962' Processing helix chain 'B' and resid 963 through 974 removed outlier: 4.081A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 Processing helix chain 'B' and resid 995 through 1004 removed outlier: 4.157A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.751A pdb=" N LEU C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.864A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.701A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.943A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.583A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.535A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.761A pdb=" N GLY D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 329 through 334 removed outlier: 3.544A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.710A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.985A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.778A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.666A pdb=" N ASN D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 494 Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.509A pdb=" N GLU D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN D 521 " --> pdb=" O ARG D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 551 through 572 removed outlier: 3.581A pdb=" N VAL D 556 " --> pdb=" O TYR D 552 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 570 " --> pdb=" O ARG D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 Processing helix chain 'D' and resid 600 through 604 Processing helix chain 'D' and resid 605 through 628 removed outlier: 3.665A pdb=" N LEU D 618 " --> pdb=" O ASN D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 4.007A pdb=" N ASN D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 680 through 699 removed outlier: 3.844A pdb=" N GLU D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D 699 " --> pdb=" O ILE D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 722 removed outlier: 3.584A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 720 " --> pdb=" O ALA D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 726 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 765 removed outlier: 3.602A pdb=" N LEU D 761 " --> pdb=" O TRP D 757 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 removed outlier: 3.649A pdb=" N LYS D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 811 removed outlier: 4.011A pdb=" N ILE D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 3.633A pdb=" N CYS D 826 " --> pdb=" O GLU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 841 removed outlier: 3.562A pdb=" N ILE D 835 " --> pdb=" O LYS D 831 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 841 " --> pdb=" O PHE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 857 removed outlier: 4.142A pdb=" N HIS D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 872 removed outlier: 3.552A pdb=" N ASN D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 897 removed outlier: 3.640A pdb=" N LEU D 889 " --> pdb=" O ILE D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 914 removed outlier: 4.177A pdb=" N SER D 914 " --> pdb=" O ASP D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 911 through 914' Processing helix chain 'D' and resid 915 through 922 removed outlier: 3.564A pdb=" N TRP D 919 " --> pdb=" O THR D 915 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR D 920 " --> pdb=" O PHE D 916 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 934 removed outlier: 3.867A pdb=" N PHE D 933 " --> pdb=" O MET D 930 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE D 934 " --> pdb=" O GLU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 956 through 962 removed outlier: 4.062A pdb=" N LYS D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 974 removed outlier: 4.516A pdb=" N LYS D 974 " --> pdb=" O ILE D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.908A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 981 " --> pdb=" O LYS D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1004 Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 47 through 52 removed outlier: 4.415A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.827A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 108 removed outlier: 3.884A pdb=" N TYR E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 7.441A pdb=" N GLU E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N MET E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.825A 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 211 Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.594A pdb=" N ARG E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.842A pdb=" N GLY E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 298 removed outlier: 3.624A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 317 removed outlier: 3.586A pdb=" N LYS E 315 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 355 through 366 removed outlier: 3.593A pdb=" N ARG E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 391 removed outlier: 3.668A pdb=" N PHE E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 427 removed outlier: 3.706A pdb=" N LYS E 423 " --> pdb=" O ASP E 419 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.577A pdb=" N CYS E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 462 Processing helix chain 'E' and resid 468 through 495 removed outlier: 3.740A pdb=" N TYR E 472 " --> pdb=" O GLY E 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 473 " --> pdb=" O CYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'E' and resid 508 through 520 removed outlier: 3.579A pdb=" N ARG E 517 " --> pdb=" O ALA E 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 518 " --> pdb=" O ARG E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 539 Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.717A pdb=" N PHE E 544 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 545 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 561 removed outlier: 3.734A pdb=" N VAL E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 557 " --> pdb=" O ASP E 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 561 " --> pdb=" O LYS E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 596 removed outlier: 4.031A pdb=" N ARG E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 589 " --> pdb=" O LEU E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 604 Processing helix chain 'E' and resid 605 through 628 Processing helix chain 'E' and resid 649 through 659 removed outlier: 3.655A pdb=" N VAL E 653 " --> pdb=" O TYR E 649 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN E 654 " --> pdb=" O TYR E 650 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 655 " --> pdb=" O ASP E 651 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 659 " --> pdb=" O ILE E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 671 Processing helix chain 'E' and resid 680 through 700 removed outlier: 3.617A pdb=" N GLU E 686 " --> pdb=" O GLU E 682 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 695 " --> pdb=" O ILE E 691 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 696 " --> pdb=" O ALA E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 723 removed outlier: 3.642A pdb=" N THR E 710 " --> pdb=" O VAL E 706 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN E 711 " --> pdb=" O VAL E 707 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER E 714 " --> pdb=" O THR E 710 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU E 715 " --> pdb=" O GLN E 711 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 718 " --> pdb=" O SER E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 750 through 762 removed outlier: 3.626A pdb=" N LEU E 761 " --> pdb=" O TRP E 757 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 762 " --> pdb=" O LEU E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 786 Processing helix chain 'E' and resid 800 through 813 removed outlier: 3.987A pdb=" N TYR E 804 " --> pdb=" O TYR E 800 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 826 Processing helix chain 'E' and resid 831 through 841 removed outlier: 3.567A pdb=" N ASP E 836 " --> pdb=" O GLN E 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 837 " --> pdb=" O LYS E 833 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 840 " --> pdb=" O ASP E 836 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 841 " --> pdb=" O PHE E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 856 removed outlier: 4.314A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 872 removed outlier: 3.808A pdb=" N LEU E 865 " --> pdb=" O ASN E 861 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 866 " --> pdb=" O ILE E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 897 removed outlier: 3.708A pdb=" N LEU E 884 " --> pdb=" O GLU E 880 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 885 " --> pdb=" O HIS E 881 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 886 " --> pdb=" O GLU E 882 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 922 removed outlier: 3.794A pdb=" N THR E 915 " --> pdb=" O ASP E 911 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 920 " --> pdb=" O PHE E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 929 through 934 removed outlier: 4.104A pdb=" N GLU E 932 " --> pdb=" O LYS E 929 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 934 " --> pdb=" O GLU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 945 Processing helix chain 'E' and resid 946 through 949 Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 955 through 962 removed outlier: 3.703A pdb=" N LEU E 959 " --> pdb=" O PRO E 956 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 960 " --> pdb=" O SER E 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 974 removed outlier: 4.030A pdb=" N LYS E 974 " --> pdb=" O ILE E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 991 removed outlier: 3.908A pdb=" N ARG E 987 " --> pdb=" O VAL E 983 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 988 " --> pdb=" O LEU E 984 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 989 " --> pdb=" O LYS E 985 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1003 removed outlier: 3.603A pdb=" N GLU E 998 " --> pdb=" O LYS E 994 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR E1003 " --> pdb=" O ILE E 999 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 4.083A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.037A 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 574 through 575 removed outlier: 6.900A pdb=" N PHE C 23 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE C 68 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 25 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA C 66 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ALA C 27 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS C 219 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR C 171 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG C 15 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 21 " --> pdb=" O ARG C 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.070A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 43 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 216 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE B 45 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 244 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.254A 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 'B' and resid 794 through 795 Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.570A pdb=" N PHE D 44 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 338 through 340 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: 7.265A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU E 42 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ILE E 130 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE E 44 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE E 245 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 646 through 647 removed outlier: 3.941A pdb=" N MET E 647 " --> pdb=" O ARG E 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AB4, first strand: chain 'E' and resid 906 through 907 removed outlier: 4.052A pdb=" N VAL F 233 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE F 235 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR F 192 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 10 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG F 15 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU F 21 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU F 26 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) 1689 hydrogen bonds defined for protein. 4902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 3.84 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: 10167 1.34 - 1.46: 7415 1.46 - 1.58: 15557 1.58 - 1.70: 1 1.70 - 1.83: 208 Bond restraints: 33348 Sorted by residual: bond pdb=" CB PRO B 956 " pdb=" CG PRO B 956 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.72e+00 bond pdb=" CA ASN B 160 " pdb=" CB ASN B 160 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.53e-02 4.27e+03 2.84e+00 bond pdb=" CB LYS D 540 " pdb=" CG LYS D 540 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB GLN B 832 " pdb=" CG GLN B 832 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG1 ILE B 808 " pdb=" CD1 ILE B 808 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 ... (remaining 33343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 44435 2.77 - 5.54: 374 5.54 - 8.31: 59 8.31 - 11.08: 25 11.08 - 13.85: 8 Bond angle restraints: 44901 Sorted by residual: angle pdb=" CA PRO B 956 " pdb=" N PRO B 956 " pdb=" CD PRO B 956 " ideal model delta sigma weight residual 112.00 98.32 13.68 1.40e+00 5.10e-01 9.55e+01 angle pdb=" N VAL A 706 " pdb=" CA VAL A 706 " pdb=" C VAL A 706 " ideal model delta sigma weight residual 113.53 109.25 4.28 9.80e-01 1.04e+00 1.90e+01 angle pdb=" CB LYS D 540 " pdb=" CG LYS D 540 " pdb=" CD LYS D 540 " ideal model delta sigma weight residual 111.30 121.07 -9.77 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA MET B 866 " pdb=" CB MET B 866 " pdb=" CG MET B 866 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CB MET E 616 " pdb=" CG MET E 616 " pdb=" SD MET E 616 " ideal model delta sigma weight residual 112.70 125.16 -12.46 3.00e+00 1.11e-01 1.72e+01 ... (remaining 44896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16558 17.92 - 35.85: 2527 35.85 - 53.77: 607 53.77 - 71.69: 113 71.69 - 89.62: 48 Dihedral angle restraints: 19853 sinusoidal: 8253 harmonic: 11600 Sorted by residual: dihedral pdb=" CA ARG E 267 " pdb=" C ARG E 267 " pdb=" N ILE E 268 " pdb=" CA ILE E 268 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 803 " pdb=" C ASP A 803 " pdb=" N TYR A 804 " pdb=" CA TYR A 804 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG D 267 " pdb=" C ARG D 267 " pdb=" N ILE D 268 " pdb=" CA ILE D 268 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 19850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4446 0.075 - 0.151: 342 0.151 - 0.226: 7 0.226 - 0.301: 0 0.301 - 0.377: 1 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CG LEU B 781 " pdb=" CB LEU B 781 " pdb=" CD1 LEU B 781 " pdb=" CD2 LEU B 781 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE B 808 " pdb=" CA ILE B 808 " pdb=" CG1 ILE B 808 " pdb=" CG2 ILE B 808 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU A 363 " pdb=" CB LEU A 363 " pdb=" CD1 LEU A 363 " pdb=" CD2 LEU A 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 4793 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 955 " -0.119 5.00e-02 4.00e+02 1.68e-01 4.54e+01 pdb=" N PRO B 956 " 0.291 5.00e-02 4.00e+02 pdb=" CA PRO B 956 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 956 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 287 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C SER B 287 " -0.045 2.00e-02 2.50e+03 pdb=" O SER B 287 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 288 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 291 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.88e+00 pdb=" CG ASP E 291 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 291 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 291 " 0.015 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 434 2.60 - 3.18: 30101 3.18 - 3.75: 54061 3.75 - 4.33: 71260 4.33 - 4.90: 113493 Nonbonded interactions: 269349 Sorted by model distance: nonbonded pdb=" O TRP C 72 " pdb=" OG1 THR C 76 " model vdw 2.026 3.040 nonbonded pdb=" OG SER D 80 " pdb=" OD1 ASP D 82 " model vdw 2.094 3.040 nonbonded pdb=" O TYR A 912 " pdb=" OG1 THR A 915 " model vdw 2.132 3.040 nonbonded pdb=" O MET D 930 " pdb=" OH TYR D 940 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR D 324 " pdb=" OD1 ASP D 590 " model vdw 2.138 3.040 ... (remaining 269344 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 23 through 71 or resid 80 through 367 or resid 373 through \ 399 or resid 406 through 546 or resid 551 through 562 or resid 579 through 628 \ or resid 645 through 1005)) selection = (chain 'B' and (resid 23 through 71 or resid 80 through 144 or resid 148 through \ 296 or resid 303 through 462 or resid 468 through 494 or resid 504 through 628 \ or resid 645 through 699 or resid 705 through 788 or resid 793 through 857 or re \ sid 862 through 897 or resid 911 through 1005)) selection = (chain 'D' and (resid 23 through 71 or resid 80 through 144 or resid 148 through \ 296 or resid 303 through 367 or resid 373 through 399 or resid 406 through 546 \ or resid 551 through 562 or resid 579 through 628 or resid 645 through 1005)) selection = (chain 'E' and (resid 23 through 144 or resid 148 through 296 or resid 303 throu \ gh 462 or resid 468 through 494 or resid 504 through 628 or resid 645 through 69 \ 9 or resid 705 through 788 or resid 793 through 857 or resid 862 through 897 or \ resid 911 through 1005)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.070 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: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 33.380 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1583 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 0.139 33348 Z= 0.140 Angle : 0.711 13.848 44901 Z= 0.365 Chirality : 0.041 0.377 4796 Planarity : 0.004 0.168 5697 Dihedral : 18.133 89.618 12369 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 33.83 % Favored : 64.50 % 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: -0.20 (0.13), residues: 3808 helix: 0.39 (0.11), residues: 2287 sheet: -0.61 (0.45), residues: 120 loop : -0.82 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 359 TYR 0.027 0.001 TYR E 709 PHE 0.032 0.001 PHE D 742 TRP 0.039 0.002 TRP D 601 HIS 0.005 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00321 (33348) covalent geometry : angle 0.71071 (44901) hydrogen bonds : bond 0.19805 ( 1689) hydrogen bonds : angle 6.86419 ( 4902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 570 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.5828 (p0) cc_final: 0.5619 (t70) REVERT: A 551 LEU cc_start: 0.1752 (mt) cc_final: 0.1401 (tp) REVERT: A 758 LEU cc_start: 0.6029 (pp) cc_final: 0.5053 (tp) REVERT: A 804 TYR cc_start: 0.7452 (m-10) cc_final: 0.7017 (m-80) REVERT: A 930 MET cc_start: 0.5168 (mpt) cc_final: 0.3299 (ppp) REVERT: A 940 TYR cc_start: 0.6534 (t80) cc_final: 0.5501 (t80) REVERT: A 996 TYR cc_start: 0.4947 (m-80) cc_final: 0.4288 (m-80) REVERT: B 124 MET cc_start: 0.2646 (mmt) cc_final: 0.2239 (mmt) REVERT: B 160 ASN cc_start: 0.1739 (OUTLIER) cc_final: 0.1298 (m110) REVERT: B 476 ILE cc_start: 0.5317 (mm) cc_final: 0.5036 (pt) REVERT: B 491 GLN cc_start: 0.7998 (tt0) cc_final: 0.7770 (tm-30) REVERT: B 757 TRP cc_start: -0.1791 (OUTLIER) cc_final: -0.2291 (m-90) REVERT: B 930 MET cc_start: 0.1446 (ppp) cc_final: 0.1000 (ptp) REVERT: C 8 THR cc_start: -0.1232 (OUTLIER) cc_final: -0.2004 (t) REVERT: C 231 MET cc_start: 0.1256 (tpt) cc_final: -0.0002 (ppp) REVERT: D 240 PHE cc_start: -0.1098 (p90) cc_final: -0.1842 (p90) REVERT: D 409 ILE cc_start: 0.1396 (mm) cc_final: 0.1179 (mt) REVERT: D 418 TYR cc_start: 0.3611 (m-80) cc_final: 0.2556 (m-80) REVERT: D 507 PHE cc_start: 0.2218 (OUTLIER) cc_final: 0.1075 (m-80) REVERT: D 592 LEU cc_start: 0.8623 (tm) cc_final: 0.8085 (tt) REVERT: D 837 PHE cc_start: 0.2808 (t80) cc_final: 0.2282 (t80) REVERT: D 930 MET cc_start: 0.4379 (tpt) cc_final: 0.1996 (tpt) REVERT: D 933 PHE cc_start: 0.3241 (m-10) cc_final: 0.2760 (m-10) REVERT: D 936 MET cc_start: 0.0945 (ptt) cc_final: -0.0198 (tpp) REVERT: E 114 THR cc_start: -0.0328 (OUTLIER) cc_final: -0.0800 (p) REVERT: E 419 ASP cc_start: -0.1567 (OUTLIER) cc_final: -0.1987 (m-30) REVERT: E 445 LEU cc_start: 0.4106 (mt) cc_final: 0.3522 (mp) REVERT: E 553 ASP cc_start: 0.2938 (m-30) cc_final: 0.2555 (t70) REVERT: E 764 CYS cc_start: 0.5259 (m) cc_final: 0.5026 (t) REVERT: E 861 ASN cc_start: 0.2761 (p0) cc_final: 0.2530 (p0) REVERT: E 936 MET cc_start: 0.3289 (mmp) cc_final: 0.2509 (tpp) REVERT: E 975 HIS cc_start: 0.5488 (m90) cc_final: 0.5269 (m90) REVERT: E 1001 MET cc_start: 0.4369 (mtt) cc_final: 0.3833 (mmt) REVERT: E 1004 PHE cc_start: 0.3472 (t80) cc_final: 0.3037 (m-10) REVERT: F 172 GLU cc_start: 0.6499 (tt0) cc_final: 0.5942 (pp20) outliers start: 60 outliers final: 13 residues processed: 622 average time/residue: 0.2364 time to fit residues: 230.1115 Evaluate side-chains 355 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 336 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 757 TRP Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 202 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 591 ASN A 654 ASN A 829 GLN A 863 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 58 GLN D 332 HIS D 591 ASN ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN D 786 HIS D 973 ASN D 975 HIS ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 115 ASN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 ASN E 698 GLN E 834 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.156973 restraints weight = 135986.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.155489 restraints weight = 110935.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.156059 restraints weight = 78893.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.156537 restraints weight = 62710.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.156608 restraints weight = 54671.194| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1956 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33348 Z= 0.192 Angle : 0.751 13.646 44901 Z= 0.389 Chirality : 0.045 0.267 4796 Planarity : 0.005 0.083 5697 Dihedral : 5.379 54.088 4305 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.98 % Allowed : 28.23 % Favored : 66.79 % 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: -0.39 (0.13), residues: 3808 helix: 0.26 (0.10), residues: 2377 sheet: -0.76 (0.52), residues: 86 loop : -1.01 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 870 TYR 0.032 0.002 TYR A 223 PHE 0.026 0.002 PHE E 107 TRP 0.018 0.003 TRP B 448 HIS 0.019 0.002 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00419 (33348) covalent geometry : angle 0.75150 (44901) hydrogen bonds : bond 0.04867 ( 1689) hydrogen bonds : angle 5.22414 ( 4902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 376 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.3918 (pmm) cc_final: 0.3284 (pmm) REVERT: A 267 ARG cc_start: 0.3223 (OUTLIER) cc_final: 0.2781 (mtm180) REVERT: A 309 ILE cc_start: 0.1752 (OUTLIER) cc_final: 0.0415 (mt) REVERT: A 310 ASP cc_start: 0.4139 (OUTLIER) cc_final: 0.3855 (t0) REVERT: A 493 ASN cc_start: 0.4930 (OUTLIER) cc_final: 0.3317 (t0) REVERT: A 683 LYS cc_start: 0.4093 (tttp) cc_final: 0.3528 (tttt) REVERT: A 731 GLU cc_start: 0.7712 (pm20) cc_final: 0.7191 (pm20) REVERT: A 785 LYS cc_start: 0.2656 (OUTLIER) cc_final: 0.2218 (tttt) REVERT: A 842 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6778 (mt) REVERT: A 930 MET cc_start: 0.3883 (mpt) cc_final: 0.1542 (ptm) REVERT: B 124 MET cc_start: 0.3610 (mmt) cc_final: 0.3155 (mmt) REVERT: B 160 ASN cc_start: 0.2038 (OUTLIER) cc_final: 0.0412 (p0) REVERT: B 447 ARG cc_start: 0.5355 (mmp-170) cc_final: 0.4919 (mmp-170) REVERT: B 476 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5033 (tp) REVERT: B 524 ILE cc_start: 0.5321 (OUTLIER) cc_final: 0.4869 (pt) REVERT: B 647 MET cc_start: -0.2305 (ptm) cc_final: -0.2961 (ptp) REVERT: B 930 MET cc_start: 0.1258 (ppp) cc_final: 0.0350 (ptp) REVERT: B 976 MET cc_start: 0.3025 (mmp) cc_final: 0.1526 (tpt) REVERT: C 34 GLN cc_start: -0.1446 (OUTLIER) cc_final: -0.2292 (mt0) REVERT: C 173 VAL cc_start: -0.2067 (OUTLIER) cc_final: -0.2333 (m) REVERT: C 206 MET cc_start: 0.3546 (pmm) cc_final: 0.2979 (mpp) REVERT: C 231 MET cc_start: 0.0424 (tpt) cc_final: -0.0599 (ptm) REVERT: D 204 MET cc_start: -0.0053 (OUTLIER) cc_final: -0.2835 (mmm) REVERT: D 240 PHE cc_start: -0.1371 (p90) cc_final: -0.2559 (p90) REVERT: D 507 PHE cc_start: 0.1844 (m-80) cc_final: 0.1266 (m-10) REVERT: D 837 PHE cc_start: 0.2599 (t80) cc_final: 0.2329 (t80) REVERT: D 912 TYR cc_start: 0.2810 (OUTLIER) cc_final: 0.2211 (m-80) REVERT: D 997 LEU cc_start: 0.4929 (tp) cc_final: 0.4645 (tt) REVERT: E 79 TYR cc_start: 0.0730 (OUTLIER) cc_final: 0.0505 (t80) REVERT: E 97 GLU cc_start: 0.1063 (OUTLIER) cc_final: 0.0037 (mm-30) REVERT: E 133 ASN cc_start: 0.6278 (m-40) cc_final: 0.5668 (t0) REVERT: E 290 MET cc_start: 0.6286 (tpp) cc_final: 0.5819 (tpt) REVERT: E 554 ASP cc_start: -0.2901 (OUTLIER) cc_final: -0.3255 (t0) REVERT: E 646 PHE cc_start: 0.4026 (OUTLIER) cc_final: 0.3536 (p90) REVERT: E 819 ARG cc_start: 0.5238 (mtp180) cc_final: 0.4964 (mtm110) REVERT: E 936 MET cc_start: 0.1749 (mmp) cc_final: 0.1412 (tpp) REVERT: F 172 GLU cc_start: 0.6153 (tt0) cc_final: 0.5901 (pm20) REVERT: F 219 LYS cc_start: 0.1707 (OUTLIER) cc_final: 0.1255 (mttt) REVERT: F 231 MET cc_start: 0.1607 (pmm) cc_final: 0.0434 (mtm) outliers start: 179 outliers final: 65 residues processed: 523 average time/residue: 0.2136 time to fit residues: 181.4215 Evaluate side-chains 392 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 309 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 128 HIS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 684 ILE Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 982 GLU Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 52 optimal weight: 6.9990 chunk 364 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 335 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 355 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 182 ASN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS A 386 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 834 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 332 HIS B 339 HIS B 477 ASN B 493 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 89 GLN D 133 ASN D 196 ASN D 698 GLN D 765 ASN E 339 HIS ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.176268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.158636 restraints weight = 136342.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.157807 restraints weight = 97645.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.158197 restraints weight = 67827.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.158627 restraints weight = 54892.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.158673 restraints weight = 48231.725| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2004 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33348 Z= 0.149 Angle : 0.654 12.239 44901 Z= 0.337 Chirality : 0.042 0.228 4796 Planarity : 0.004 0.061 5697 Dihedral : 4.864 52.424 4283 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.40 % Allowed : 27.84 % Favored : 67.76 % 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: -0.25 (0.13), residues: 3808 helix: 0.38 (0.10), residues: 2383 sheet: -0.97 (0.47), residues: 110 loop : -0.94 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.032 0.002 TYR A 223 PHE 0.025 0.002 PHE A 522 TRP 0.026 0.002 TRP E 231 HIS 0.010 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00318 (33348) covalent geometry : angle 0.65439 (44901) hydrogen bonds : bond 0.04143 ( 1689) hydrogen bonds : angle 4.86765 ( 4902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 339 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.0336 (OUTLIER) cc_final: -0.0892 (m-40) REVERT: A 608 PHE cc_start: 0.2568 (t80) cc_final: 0.1506 (t80) REVERT: A 665 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8280 (tptp) REVERT: A 683 LYS cc_start: 0.4447 (tttp) cc_final: 0.3829 (tttt) REVERT: A 731 GLU cc_start: 0.7703 (pm20) cc_final: 0.7407 (pm20) REVERT: A 765 ASN cc_start: 0.5448 (t0) cc_final: 0.5208 (t0) REVERT: A 785 LYS cc_start: 0.2818 (OUTLIER) cc_final: 0.2526 (tttt) REVERT: A 842 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6788 (mt) REVERT: A 930 MET cc_start: 0.3708 (mpt) cc_final: 0.1492 (ppp) REVERT: A 998 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8686 (tm-30) REVERT: B 124 MET cc_start: 0.4190 (OUTLIER) cc_final: 0.3402 (mmt) REVERT: B 160 ASN cc_start: 0.1618 (OUTLIER) cc_final: -0.0784 (p0) REVERT: B 339 HIS cc_start: -0.0557 (OUTLIER) cc_final: -0.0887 (p90) REVERT: B 447 ARG cc_start: 0.5676 (mmp-170) cc_final: 0.5053 (mmp-170) REVERT: B 476 ILE cc_start: 0.5590 (OUTLIER) cc_final: 0.5105 (tp) REVERT: B 647 MET cc_start: -0.2347 (ptm) cc_final: -0.2798 (ptp) REVERT: B 930 MET cc_start: 0.0950 (ppp) cc_final: -0.0015 (ptp) REVERT: B 976 MET cc_start: 0.2950 (mmp) cc_final: 0.1487 (tpt) REVERT: C 34 GLN cc_start: -0.2376 (OUTLIER) cc_final: -0.3360 (mt0) REVERT: C 206 MET cc_start: 0.3359 (pmm) cc_final: 0.2859 (mpp) REVERT: C 231 MET cc_start: 0.0635 (tpt) cc_final: -0.0759 (ptm) REVERT: D 71 TYR cc_start: -0.2937 (OUTLIER) cc_final: -0.3290 (m-80) REVERT: D 204 MET cc_start: -0.0584 (tpp) cc_final: -0.4420 (mtp) REVERT: D 326 ARG cc_start: -0.1153 (mtm180) cc_final: -0.1768 (mtm180) REVERT: D 343 ASN cc_start: 0.0401 (p0) cc_final: 0.0066 (p0) REVERT: D 361 PHE cc_start: -0.3385 (OUTLIER) cc_final: -0.4756 (m-80) REVERT: D 507 PHE cc_start: 0.1502 (m-80) cc_final: 0.1106 (m-10) REVERT: D 578 MET cc_start: -0.1394 (ttt) cc_final: -0.1943 (ttt) REVERT: D 837 PHE cc_start: 0.2563 (t80) cc_final: 0.2125 (t80) REVERT: D 866 MET cc_start: -0.1530 (mtt) cc_final: -0.1943 (mpp) REVERT: D 912 TYR cc_start: 0.3065 (OUTLIER) cc_final: 0.2243 (m-80) REVERT: E 79 TYR cc_start: 0.0630 (OUTLIER) cc_final: 0.0304 (t80) REVERT: E 646 PHE cc_start: 0.3906 (OUTLIER) cc_final: 0.3347 (p90) REVERT: E 647 MET cc_start: 0.3661 (OUTLIER) cc_final: 0.3053 (ppp) REVERT: E 819 ARG cc_start: 0.5479 (mtp180) cc_final: 0.5108 (mtm110) REVERT: F 172 GLU cc_start: 0.6168 (tt0) cc_final: 0.5909 (pm20) REVERT: F 219 LYS cc_start: 0.1345 (OUTLIER) cc_final: 0.0946 (mttt) REVERT: F 231 MET cc_start: 0.1552 (pmm) cc_final: 0.0365 (mtm) outliers start: 158 outliers final: 79 residues processed: 465 average time/residue: 0.2171 time to fit residues: 163.1226 Evaluate side-chains 393 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 299 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 803 ASP Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 107 PHE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 684 ILE Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 249 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 356 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 370 optimal weight: 0.0570 chunk 382 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 832 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN B 415 HIS ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 211 HIS D 475 GLN E 133 ASN E 377 GLN E 391 ASN ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.175977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.156673 restraints weight = 137034.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.156724 restraints weight = 100157.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.157878 restraints weight = 64070.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.157695 restraints weight = 49869.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.157939 restraints weight = 45799.460| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2283 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33348 Z= 0.166 Angle : 0.684 14.096 44901 Z= 0.354 Chirality : 0.043 0.251 4796 Planarity : 0.005 0.083 5697 Dihedral : 5.044 51.543 4281 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.87 % Allowed : 27.20 % Favored : 67.93 % 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: -0.40 (0.13), residues: 3808 helix: 0.30 (0.10), residues: 2370 sheet: -1.12 (0.46), residues: 116 loop : -1.05 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 285 TYR 0.036 0.002 TYR A 223 PHE 0.024 0.002 PHE B 492 TRP 0.018 0.002 TRP B 60 HIS 0.036 0.002 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00365 (33348) covalent geometry : angle 0.68444 (44901) hydrogen bonds : bond 0.04089 ( 1689) hydrogen bonds : angle 4.90523 ( 4902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 335 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.2177 (OUTLIER) cc_final: 0.0619 (t80) REVERT: A 169 LYS cc_start: -0.0981 (OUTLIER) cc_final: -0.1740 (mtmm) REVERT: A 223 TYR cc_start: 0.1701 (t80) cc_final: -0.0026 (p90) REVERT: A 267 ARG cc_start: 0.3845 (OUTLIER) cc_final: 0.3239 (mtm180) REVERT: A 391 ASN cc_start: 0.0286 (OUTLIER) cc_final: -0.1140 (m-40) REVERT: A 665 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8344 (tptp) REVERT: A 683 LYS cc_start: 0.4641 (tttp) cc_final: 0.4357 (tttt) REVERT: A 765 ASN cc_start: 0.5767 (t0) cc_final: 0.5415 (t0) REVERT: A 842 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6922 (mt) REVERT: A 930 MET cc_start: 0.4165 (mpt) cc_final: 0.1804 (ptm) REVERT: A 936 MET cc_start: 0.2575 (mmm) cc_final: 0.1623 (mtt) REVERT: A 998 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8576 (tm-30) REVERT: B 98 MET cc_start: 0.0457 (tpp) cc_final: 0.0226 (tpp) REVERT: B 160 ASN cc_start: 0.2266 (OUTLIER) cc_final: 0.0814 (p0) REVERT: B 204 MET cc_start: -0.0806 (tmm) cc_final: -0.1064 (tmm) REVERT: B 447 ARG cc_start: 0.5639 (mmp-170) cc_final: 0.5198 (mmp-170) REVERT: B 476 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5339 (tp) REVERT: B 611 TYR cc_start: 0.2513 (t80) cc_final: 0.1834 (m-80) REVERT: B 647 MET cc_start: -0.2289 (ptm) cc_final: -0.2620 (ptp) REVERT: B 913 MET cc_start: 0.0971 (tpp) cc_final: 0.0563 (tpp) REVERT: B 930 MET cc_start: 0.0862 (ppp) cc_final: -0.0289 (ptp) REVERT: B 976 MET cc_start: 0.3433 (mmp) cc_final: 0.1639 (tpt) REVERT: C 26 GLU cc_start: 0.6593 (mp0) cc_final: 0.5932 (pm20) REVERT: C 34 GLN cc_start: -0.1965 (OUTLIER) cc_final: -0.3287 (mp-120) REVERT: C 206 MET cc_start: 0.3657 (pmm) cc_final: 0.3134 (mpp) REVERT: C 231 MET cc_start: 0.1185 (tpt) cc_final: -0.0890 (ptp) REVERT: D 41 LYS cc_start: 0.0307 (OUTLIER) cc_final: -0.0954 (mtmt) REVERT: D 204 MET cc_start: -0.0146 (tpp) cc_final: -0.1195 (tpp) REVERT: D 241 HIS cc_start: -0.1661 (OUTLIER) cc_final: -0.2673 (m90) REVERT: D 357 MET cc_start: -0.4505 (mtp) cc_final: -0.4785 (mtp) REVERT: D 361 PHE cc_start: -0.3243 (OUTLIER) cc_final: -0.4476 (m-80) REVERT: D 507 PHE cc_start: 0.1562 (m-80) cc_final: 0.1323 (m-80) REVERT: D 578 MET cc_start: -0.2018 (ttt) cc_final: -0.2335 (ttt) REVERT: D 837 PHE cc_start: 0.2666 (t80) cc_final: 0.2165 (t80) REVERT: D 920 TYR cc_start: 0.5373 (t80) cc_final: 0.5129 (t80) REVERT: D 930 MET cc_start: -0.0625 (tpt) cc_final: -0.0996 (tpt) REVERT: E 79 TYR cc_start: 0.1143 (OUTLIER) cc_final: 0.0761 (t80) REVERT: E 97 GLU cc_start: 0.0836 (OUTLIER) cc_final: 0.0034 (mm-30) REVERT: E 124 MET cc_start: -0.1808 (tmm) cc_final: -0.4957 (mtt) REVERT: E 616 MET cc_start: -0.3307 (mmm) cc_final: -0.3761 (mtp) REVERT: E 646 PHE cc_start: 0.4215 (OUTLIER) cc_final: 0.3728 (p90) REVERT: E 647 MET cc_start: 0.3852 (OUTLIER) cc_final: 0.3349 (ppp) REVERT: E 866 MET cc_start: 0.1393 (tmm) cc_final: -0.0324 (mmt) REVERT: E 876 GLU cc_start: 0.7082 (pp20) cc_final: 0.6843 (pm20) REVERT: F 172 GLU cc_start: 0.6447 (tt0) cc_final: 0.6022 (pm20) REVERT: F 219 LYS cc_start: 0.1582 (OUTLIER) cc_final: 0.1113 (mttt) REVERT: F 231 MET cc_start: 0.1325 (pmm) cc_final: 0.0967 (mtp) outliers start: 175 outliers final: 100 residues processed: 472 average time/residue: 0.2192 time to fit residues: 167.1885 Evaluate side-chains 419 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 303 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 376 LYS Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 803 ASP Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 684 ILE Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 884 LEU Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 384 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 133 ASN A 351 ASN A 415 HIS A 475 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 HIS C 34 GLN D 39 ASN D 171 HIS D 196 ASN ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN ** E 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.159093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.127605 restraints weight = 112861.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.130470 restraints weight = 57280.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.132242 restraints weight = 35061.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.133173 restraints weight = 24812.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.133931 restraints weight = 20156.136| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2620 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33348 Z= 0.181 Angle : 0.733 13.881 44901 Z= 0.380 Chirality : 0.045 0.261 4796 Planarity : 0.005 0.075 5697 Dihedral : 5.303 51.493 4281 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.23 % Allowed : 27.26 % Favored : 67.51 % 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: -0.69 (0.13), residues: 3808 helix: 0.08 (0.10), residues: 2365 sheet: -1.70 (0.39), residues: 145 loop : -1.12 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 285 TYR 0.041 0.002 TYR A 223 PHE 0.024 0.002 PHE A 652 TRP 0.054 0.003 TRP B 601 HIS 0.011 0.002 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00406 (33348) covalent geometry : angle 0.73252 (44901) hydrogen bonds : bond 0.04233 ( 1689) hydrogen bonds : angle 5.08311 ( 4902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 332 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.2294 (OUTLIER) cc_final: 0.0457 (t80) REVERT: A 169 LYS cc_start: -0.0819 (OUTLIER) cc_final: -0.1595 (mtmm) REVERT: A 223 TYR cc_start: 0.1355 (OUTLIER) cc_final: -0.1354 (t80) REVERT: A 475 GLN cc_start: -0.2351 (OUTLIER) cc_final: -0.3320 (tt0) REVERT: A 563 ASN cc_start: 0.1728 (OUTLIER) cc_final: 0.1191 (t0) REVERT: A 665 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8419 (tptp) REVERT: A 683 LYS cc_start: 0.6311 (tttp) cc_final: 0.6051 (tttt) REVERT: A 735 LYS cc_start: 0.5842 (tptt) cc_final: 0.5110 (tptt) REVERT: A 765 ASN cc_start: 0.5558 (t0) cc_final: 0.5161 (t0) REVERT: A 785 LYS cc_start: 0.3851 (OUTLIER) cc_final: 0.3377 (tttt) REVERT: A 930 MET cc_start: 0.4484 (mpt) cc_final: 0.1987 (ptm) REVERT: A 936 MET cc_start: 0.2653 (mmm) cc_final: 0.1842 (mtt) REVERT: B 32 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: B 98 MET cc_start: 0.0505 (tpp) cc_final: 0.0273 (tpp) REVERT: B 160 ASN cc_start: 0.1872 (OUTLIER) cc_final: 0.0510 (p0) REVERT: B 275 ILE cc_start: -0.1632 (OUTLIER) cc_final: -0.2014 (mp) REVERT: B 447 ARG cc_start: 0.5737 (mmp-170) cc_final: 0.5273 (mmp80) REVERT: B 485 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7099 (tt) REVERT: B 491 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7549 (tm-30) REVERT: B 647 MET cc_start: -0.1945 (ptm) cc_final: -0.2316 (ptp) REVERT: B 930 MET cc_start: 0.1428 (ppp) cc_final: -0.0063 (ptp) REVERT: C 34 GLN cc_start: -0.2307 (OUTLIER) cc_final: -0.3678 (mp-120) REVERT: C 206 MET cc_start: 0.3714 (pmm) cc_final: 0.3128 (tpt) REVERT: C 231 MET cc_start: 0.1573 (tpt) cc_final: -0.1193 (ptp) REVERT: D 41 LYS cc_start: 0.0565 (OUTLIER) cc_final: -0.0770 (mtmt) REVERT: D 124 MET cc_start: -0.2619 (tpt) cc_final: -0.3090 (tpt) REVERT: D 204 MET cc_start: -0.0404 (tpp) cc_final: -0.1706 (tpp) REVERT: D 361 PHE cc_start: -0.2779 (OUTLIER) cc_final: -0.3929 (m-80) REVERT: D 619 LEU cc_start: 0.1058 (OUTLIER) cc_final: 0.0828 (tp) REVERT: D 625 TYR cc_start: 0.5853 (t80) cc_final: 0.5613 (t80) REVERT: D 695 ILE cc_start: 0.4582 (mm) cc_final: 0.4378 (mm) REVERT: D 837 PHE cc_start: 0.3066 (t80) cc_final: 0.2458 (t80) REVERT: D 920 TYR cc_start: 0.6078 (t80) cc_final: 0.5868 (t80) REVERT: D 930 MET cc_start: 0.1416 (tpt) cc_final: 0.1033 (tpt) REVERT: E 79 TYR cc_start: 0.1904 (OUTLIER) cc_final: 0.1521 (t80) REVERT: E 97 GLU cc_start: 0.1322 (OUTLIER) cc_final: 0.0387 (mm-30) REVERT: E 124 MET cc_start: -0.1729 (tmm) cc_final: -0.4295 (mtt) REVERT: E 202 ASN cc_start: -0.3688 (OUTLIER) cc_final: -0.4417 (m-40) REVERT: E 205 LYS cc_start: 0.1998 (OUTLIER) cc_final: 0.0728 (mmtp) REVERT: E 264 LYS cc_start: -0.1148 (OUTLIER) cc_final: -0.3203 (ttpt) REVERT: E 373 LEU cc_start: 0.1673 (OUTLIER) cc_final: 0.1324 (mm) REVERT: E 947 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5263 (pm20) REVERT: E 948 ASN cc_start: 0.4242 (OUTLIER) cc_final: 0.3687 (t0) REVERT: F 172 GLU cc_start: 0.6508 (tt0) cc_final: 0.6243 (pm20) REVERT: F 219 LYS cc_start: 0.1439 (OUTLIER) cc_final: 0.0979 (mttt) outliers start: 188 outliers final: 106 residues processed: 484 average time/residue: 0.2151 time to fit residues: 167.7107 Evaluate side-chains 429 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 300 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 763 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 803 ASP Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 947 GLU Chi-restraints excluded: chain E residue 948 ASN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 216 optimal weight: 0.7980 chunk 357 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 382 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 765 ASN E 263 ASN E 457 ASN E 975 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.159896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.128184 restraints weight = 110169.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.131065 restraints weight = 55690.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.132836 restraints weight = 34028.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.134041 restraints weight = 24168.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.134696 restraints weight = 19229.828| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2571 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33348 Z= 0.145 Angle : 0.667 14.438 44901 Z= 0.342 Chirality : 0.043 0.243 4796 Planarity : 0.004 0.077 5697 Dihedral : 5.108 53.773 4281 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.84 % Allowed : 27.34 % Favored : 67.82 % 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: -0.50 (0.13), residues: 3808 helix: 0.23 (0.11), residues: 2358 sheet: -1.30 (0.43), residues: 131 loop : -1.09 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 819 TYR 0.033 0.002 TYR A 649 PHE 0.026 0.002 PHE A 722 TRP 0.030 0.002 TRP B 601 HIS 0.024 0.001 HIS E 975 Details of bonding type rmsd covalent geometry : bond 0.00312 (33348) covalent geometry : angle 0.66743 (44901) hydrogen bonds : bond 0.03856 ( 1689) hydrogen bonds : angle 4.86273 ( 4902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 315 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.0576 (OUTLIER) cc_final: -0.1457 (t80) REVERT: A 391 ASN cc_start: 0.0439 (OUTLIER) cc_final: 0.0120 (t0) REVERT: A 665 LYS cc_start: 0.8670 (ptpp) cc_final: 0.8440 (tptp) REVERT: A 735 LYS cc_start: 0.5968 (tptt) cc_final: 0.5254 (tptt) REVERT: A 765 ASN cc_start: 0.5645 (t0) cc_final: 0.5220 (t0) REVERT: A 785 LYS cc_start: 0.3614 (OUTLIER) cc_final: 0.3379 (tttt) REVERT: A 930 MET cc_start: 0.4728 (mpt) cc_final: 0.2215 (ptm) REVERT: A 936 MET cc_start: 0.2513 (mmm) cc_final: 0.1850 (mtt) REVERT: B 32 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7159 (pp20) REVERT: B 98 MET cc_start: 0.0635 (OUTLIER) cc_final: 0.0327 (tpp) REVERT: B 160 ASN cc_start: 0.1814 (OUTLIER) cc_final: 0.0360 (p0) REVERT: B 275 ILE cc_start: -0.1616 (OUTLIER) cc_final: -0.1905 (mp) REVERT: B 447 ARG cc_start: 0.5689 (mmp-170) cc_final: 0.4853 (mmp-170) REVERT: B 647 MET cc_start: -0.2162 (ptm) cc_final: -0.2568 (ptp) REVERT: B 704 MET cc_start: 0.1012 (pmm) cc_final: 0.0699 (pmm) REVERT: B 930 MET cc_start: 0.0957 (ppp) cc_final: -0.0424 (ptp) REVERT: B 976 MET cc_start: 0.3466 (mmp) cc_final: 0.1965 (tpt) REVERT: C 206 MET cc_start: 0.3358 (pmm) cc_final: 0.3073 (mpp) REVERT: C 231 MET cc_start: 0.1573 (tpt) cc_final: -0.0399 (mtm) REVERT: D 32 GLU cc_start: -0.2126 (OUTLIER) cc_final: -0.3803 (mm-30) REVERT: D 41 LYS cc_start: 0.0731 (OUTLIER) cc_final: -0.0490 (mtmt) REVERT: D 71 TYR cc_start: -0.2067 (OUTLIER) cc_final: -0.3080 (m-80) REVERT: D 204 MET cc_start: -0.0479 (tpp) cc_final: -0.1281 (mmm) REVERT: D 267 ARG cc_start: 0.1853 (OUTLIER) cc_final: 0.1527 (ttt180) REVERT: D 361 PHE cc_start: -0.2857 (OUTLIER) cc_final: -0.3755 (m-80) REVERT: D 837 PHE cc_start: 0.3027 (t80) cc_final: 0.2465 (t80) REVERT: D 920 TYR cc_start: 0.6064 (t80) cc_final: 0.5829 (t80) REVERT: D 930 MET cc_start: 0.1209 (tpt) cc_final: 0.0610 (tpt) REVERT: E 79 TYR cc_start: 0.2262 (OUTLIER) cc_final: 0.1806 (t80) REVERT: E 97 GLU cc_start: 0.1134 (OUTLIER) cc_final: 0.0439 (mm-30) REVERT: E 124 MET cc_start: -0.1826 (tmm) cc_final: -0.3983 (mtp) REVERT: E 205 LYS cc_start: 0.1419 (OUTLIER) cc_final: 0.0144 (mmtp) REVERT: E 373 LEU cc_start: 0.1151 (OUTLIER) cc_final: 0.0931 (mm) REVERT: E 677 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.3960 (ttp80) REVERT: E 866 MET cc_start: 0.0481 (tmm) cc_final: -0.0685 (mmt) REVERT: E 940 TYR cc_start: 0.3889 (OUTLIER) cc_final: 0.3564 (t80) REVERT: E 948 ASN cc_start: 0.4067 (OUTLIER) cc_final: 0.3454 (t0) REVERT: E 976 MET cc_start: 0.1937 (ppp) cc_final: 0.1734 (ppp) REVERT: F 172 GLU cc_start: 0.6419 (tt0) cc_final: 0.6164 (pm20) REVERT: F 219 LYS cc_start: 0.1680 (OUTLIER) cc_final: 0.1163 (mttt) outliers start: 174 outliers final: 109 residues processed: 456 average time/residue: 0.2044 time to fit residues: 150.9911 Evaluate side-chains 423 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 294 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 743 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 677 ARG Chi-restraints excluded: chain E residue 684 ILE Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 948 ASN Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 234 optimal weight: 0.7980 chunk 266 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 231 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.163712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.138398 restraints weight = 126598.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.140500 restraints weight = 78457.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.140633 restraints weight = 49554.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.140912 restraints weight = 43005.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.141190 restraints weight = 40858.192| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2675 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33348 Z= 0.141 Angle : 0.667 12.323 44901 Z= 0.342 Chirality : 0.043 0.270 4796 Planarity : 0.004 0.073 5697 Dihedral : 5.068 55.545 4281 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.15 % Allowed : 27.84 % Favored : 68.01 % 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: -0.49 (0.13), residues: 3808 helix: 0.27 (0.11), residues: 2341 sheet: -1.65 (0.39), residues: 157 loop : -1.07 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 285 TYR 0.031 0.002 TYR D 625 PHE 0.034 0.002 PHE E 45 TRP 0.034 0.002 TRP D 757 HIS 0.010 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00312 (33348) covalent geometry : angle 0.66714 (44901) hydrogen bonds : bond 0.03878 ( 1689) hydrogen bonds : angle 4.83535 ( 4902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 308 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.0784 (OUTLIER) cc_final: -0.1223 (t80) REVERT: A 475 GLN cc_start: -0.2093 (OUTLIER) cc_final: -0.2723 (tt0) REVERT: A 665 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8521 (tptp) REVERT: A 735 LYS cc_start: 0.6120 (tptt) cc_final: 0.5447 (tptt) REVERT: A 765 ASN cc_start: 0.5450 (t0) cc_final: 0.4991 (t0) REVERT: A 930 MET cc_start: 0.5269 (mpt) cc_final: 0.2484 (ptm) REVERT: A 936 MET cc_start: 0.2858 (mmm) cc_final: 0.2321 (mtt) REVERT: B 98 MET cc_start: 0.0560 (OUTLIER) cc_final: 0.0257 (tpp) REVERT: B 160 ASN cc_start: 0.1810 (OUTLIER) cc_final: 0.1542 (m110) REVERT: B 174 PHE cc_start: 0.3146 (OUTLIER) cc_final: 0.2235 (p90) REVERT: B 447 ARG cc_start: 0.5908 (mmp-170) cc_final: 0.5645 (mmp80) REVERT: B 585 LEU cc_start: 0.1401 (mt) cc_final: 0.0945 (tp) REVERT: B 704 MET cc_start: 0.0441 (pmm) cc_final: 0.0105 (pmm) REVERT: B 923 GLU cc_start: 0.6716 (tp30) cc_final: 0.6238 (mp0) REVERT: B 930 MET cc_start: 0.1627 (ppp) cc_final: 0.0139 (ptp) REVERT: C 206 MET cc_start: 0.3441 (pmm) cc_final: 0.3165 (mpp) REVERT: C 231 MET cc_start: 0.2458 (tpt) cc_final: -0.0460 (mtm) REVERT: D 71 TYR cc_start: -0.1677 (OUTLIER) cc_final: -0.2824 (m-80) REVERT: D 204 MET cc_start: -0.1576 (tpp) cc_final: -0.2135 (mmm) REVERT: D 361 PHE cc_start: -0.2632 (OUTLIER) cc_final: -0.3515 (m-80) REVERT: D 837 PHE cc_start: 0.3173 (t80) cc_final: 0.2641 (t80) REVERT: D 920 TYR cc_start: 0.5971 (t80) cc_final: 0.5618 (t80) REVERT: D 930 MET cc_start: 0.0124 (tpt) cc_final: -0.0400 (tpp) REVERT: E 124 MET cc_start: -0.2349 (tmm) cc_final: -0.4002 (mtp) REVERT: E 205 LYS cc_start: 0.1912 (OUTLIER) cc_final: 0.0687 (mmtp) REVERT: E 721 TYR cc_start: -0.2536 (OUTLIER) cc_final: -0.2953 (t80) REVERT: E 866 MET cc_start: 0.0775 (tmm) cc_final: -0.0411 (mmt) REVERT: E 976 MET cc_start: 0.1857 (ppp) cc_final: 0.1654 (ppp) REVERT: E 1003 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5697 (t80) REVERT: F 172 GLU cc_start: 0.6433 (tt0) cc_final: 0.6168 (pm20) REVERT: F 219 LYS cc_start: 0.1734 (OUTLIER) cc_final: 0.1135 (mttt) outliers start: 149 outliers final: 105 residues processed: 428 average time/residue: 0.2052 time to fit residues: 142.8186 Evaluate side-chains 406 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 290 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 743 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 721 TYR Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 1003 TYR Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 182 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 385 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN ** D 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.160172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.130015 restraints weight = 110430.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.132833 restraints weight = 56893.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.134431 restraints weight = 35114.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.135661 restraints weight = 25191.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.136290 restraints weight = 20000.900| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2768 moved from start: 0.7679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33348 Z= 0.155 Angle : 0.687 12.211 44901 Z= 0.355 Chirality : 0.043 0.252 4796 Planarity : 0.004 0.070 5697 Dihedral : 5.237 59.633 4280 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.15 % Allowed : 28.29 % Favored : 67.57 % 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: -0.56 (0.13), residues: 3808 helix: 0.20 (0.11), residues: 2359 sheet: -1.72 (0.41), residues: 147 loop : -1.11 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 478 TYR 0.044 0.002 TYR A 649 PHE 0.030 0.002 PHE B 381 TRP 0.031 0.002 TRP E 919 HIS 0.011 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00346 (33348) covalent geometry : angle 0.68652 (44901) hydrogen bonds : bond 0.03987 ( 1689) hydrogen bonds : angle 4.92578 ( 4902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 315 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.1151 (tp) cc_final: 0.0803 (pt) REVERT: A 202 ASN cc_start: 0.3774 (OUTLIER) cc_final: 0.2625 (m-40) REVERT: A 223 TYR cc_start: 0.0094 (OUTLIER) cc_final: -0.1808 (t80) REVERT: A 475 GLN cc_start: -0.2204 (OUTLIER) cc_final: -0.3402 (tt0) REVERT: A 665 LYS cc_start: 0.8725 (ptpp) cc_final: 0.8405 (tptp) REVERT: A 735 LYS cc_start: 0.6055 (tptt) cc_final: 0.5387 (tptt) REVERT: A 883 GLU cc_start: 0.4804 (mm-30) cc_final: 0.4541 (mm-30) REVERT: A 930 MET cc_start: 0.5090 (mpt) cc_final: 0.2354 (ptm) REVERT: A 936 MET cc_start: 0.2472 (mmm) cc_final: 0.1725 (mtt) REVERT: B 32 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7207 (pp20) REVERT: B 98 MET cc_start: 0.0371 (tpp) cc_final: 0.0123 (tpp) REVERT: B 174 PHE cc_start: 0.3267 (OUTLIER) cc_final: 0.2378 (p90) REVERT: B 388 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.5807 (m-80) REVERT: B 447 ARG cc_start: 0.6039 (mmp-170) cc_final: 0.5796 (mmp80) REVERT: B 491 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7147 (tm-30) REVERT: B 543 GLU cc_start: 0.7681 (pm20) cc_final: 0.7113 (pt0) REVERT: B 704 MET cc_start: 0.1327 (pmm) cc_final: 0.1101 (pmm) REVERT: B 923 GLU cc_start: 0.6228 (tp30) cc_final: 0.5828 (mp0) REVERT: B 930 MET cc_start: 0.1136 (ppp) cc_final: -0.0293 (ptp) REVERT: C 206 MET cc_start: 0.3243 (pmm) cc_final: 0.2998 (mpp) REVERT: C 231 MET cc_start: 0.1354 (tpt) cc_final: -0.0891 (mtm) REVERT: D 204 MET cc_start: -0.1127 (tpp) cc_final: -0.2513 (tpp) REVERT: D 241 HIS cc_start: 0.0033 (OUTLIER) cc_final: -0.0398 (p-80) REVERT: D 361 PHE cc_start: -0.2512 (OUTLIER) cc_final: -0.3594 (m-80) REVERT: D 837 PHE cc_start: 0.3158 (t80) cc_final: 0.2647 (t80) REVERT: D 920 TYR cc_start: 0.5984 (t80) cc_final: 0.5701 (t80) REVERT: D 930 MET cc_start: 0.1175 (tpt) cc_final: 0.0368 (tpp) REVERT: D 976 MET cc_start: -0.5242 (tmm) cc_final: -0.5589 (ttt) REVERT: E 124 MET cc_start: -0.2593 (tmm) cc_final: -0.3764 (mtp) REVERT: E 202 ASN cc_start: -0.3533 (OUTLIER) cc_final: -0.4310 (m-40) REVERT: E 215 PHE cc_start: 0.2876 (m-80) cc_final: 0.2386 (m-80) REVERT: E 396 MET cc_start: -0.4986 (mmt) cc_final: -0.5618 (tpp) REVERT: E 677 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.4243 (ttp80) REVERT: E 721 TYR cc_start: -0.2499 (OUTLIER) cc_final: -0.2999 (t80) REVERT: E 866 MET cc_start: 0.0878 (tmm) cc_final: -0.0215 (mmt) REVERT: F 172 GLU cc_start: 0.6433 (tt0) cc_final: 0.6173 (pm20) REVERT: F 219 LYS cc_start: 0.1716 (OUTLIER) cc_final: 0.1138 (ptpt) outliers start: 149 outliers final: 113 residues processed: 431 average time/residue: 0.2102 time to fit residues: 148.0003 Evaluate side-chains 420 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 295 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 743 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 943 PHE Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 677 ARG Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 721 TYR Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 127 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN D 196 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 609 HIS D1002 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN E 483 GLN E 536 GLN ** E 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 948 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.160554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.132099 restraints weight = 115320.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.134837 restraints weight = 61212.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.136415 restraints weight = 38776.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.137477 restraints weight = 27618.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.137988 restraints weight = 22007.934| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3218 moved from start: 0.9192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 33348 Z= 0.252 Angle : 0.909 19.481 44901 Z= 0.473 Chirality : 0.050 0.486 4796 Planarity : 0.006 0.069 5697 Dihedral : 6.120 52.991 4280 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.54 % Allowed : 28.17 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.40 (0.13), residues: 3808 helix: -0.46 (0.10), residues: 2327 sheet: -1.78 (0.43), residues: 138 loop : -1.46 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 478 TYR 0.043 0.003 TYR A 649 PHE 0.052 0.003 PHE E 45 TRP 0.039 0.004 TRP D 757 HIS 0.015 0.002 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00556 (33348) covalent geometry : angle 0.90885 (44901) hydrogen bonds : bond 0.05338 ( 1689) hydrogen bonds : angle 5.78201 ( 4902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 342 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.1448 (OUTLIER) cc_final: 0.1174 (t0) REVERT: A 185 LEU cc_start: 0.1213 (tp) cc_final: 0.0711 (pt) REVERT: A 223 TYR cc_start: 0.0165 (OUTLIER) cc_final: -0.2096 (t80) REVERT: A 619 LEU cc_start: 0.7477 (mm) cc_final: 0.7071 (tp) REVERT: A 665 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8473 (tptp) REVERT: A 712 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.5973 (t80) REVERT: A 735 LYS cc_start: 0.6353 (tptt) cc_final: 0.5880 (tptt) REVERT: A 930 MET cc_start: 0.5716 (mpt) cc_final: 0.2823 (ptm) REVERT: A 936 MET cc_start: 0.2782 (mmm) cc_final: 0.2090 (mtt) REVERT: B 37 SER cc_start: 0.7282 (OUTLIER) cc_final: 0.6557 (t) REVERT: B 174 PHE cc_start: 0.3522 (OUTLIER) cc_final: 0.3282 (m-80) REVERT: B 388 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: B 447 ARG cc_start: 0.6125 (mmp-170) cc_final: 0.5879 (mmp80) REVERT: B 480 ARG cc_start: 0.8507 (mmp80) cc_final: 0.8145 (mmp80) REVERT: B 543 GLU cc_start: 0.7668 (pm20) cc_final: 0.7049 (pt0) REVERT: B 784 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7313 (mm-30) REVERT: B 923 GLU cc_start: 0.6150 (tp30) cc_final: 0.5949 (tp30) REVERT: B 930 MET cc_start: 0.1221 (ppp) cc_final: -0.0325 (ptp) REVERT: C 39 GLU cc_start: 0.5099 (tp30) cc_final: 0.4060 (tm-30) REVERT: C 206 MET cc_start: 0.3491 (pmm) cc_final: 0.3211 (mpp) REVERT: D 71 TYR cc_start: -0.0657 (OUTLIER) cc_final: -0.2841 (m-80) REVERT: D 79 TYR cc_start: 0.3409 (OUTLIER) cc_final: 0.2243 (m-80) REVERT: D 204 MET cc_start: -0.1411 (tpp) cc_final: -0.2721 (tpp) REVERT: D 361 PHE cc_start: -0.1498 (OUTLIER) cc_final: -0.2727 (m-80) REVERT: D 930 MET cc_start: 0.2484 (tpt) cc_final: 0.1823 (tpp) REVERT: E 124 MET cc_start: -0.2334 (tmm) cc_final: -0.3383 (mtp) REVERT: E 185 LEU cc_start: 0.3720 (mt) cc_final: 0.2747 (tt) REVERT: E 202 ASN cc_start: -0.4022 (OUTLIER) cc_final: -0.4488 (m-40) REVERT: E 396 MET cc_start: -0.4645 (mmt) cc_final: -0.5277 (tpp) REVERT: E 647 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.3017 (ppp) REVERT: E 677 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.4423 (ttp80) REVERT: E 721 TYR cc_start: -0.1918 (OUTLIER) cc_final: -0.2504 (t80) REVERT: E 866 MET cc_start: 0.0625 (tmm) cc_final: -0.0297 (mmt) REVERT: F 172 GLU cc_start: 0.6419 (tt0) cc_final: 0.6047 (pp20) REVERT: F 219 LYS cc_start: 0.1754 (OUTLIER) cc_final: 0.1219 (ptpt) outliers start: 163 outliers final: 116 residues processed: 471 average time/residue: 0.2162 time to fit residues: 164.7476 Evaluate side-chains 439 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 309 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 743 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 829 GLN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 677 ARG Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 721 TYR Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 253 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN A 786 HIS ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.161516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.132684 restraints weight = 116702.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.135272 restraints weight = 62117.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.137073 restraints weight = 38742.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.138151 restraints weight = 27563.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.138769 restraints weight = 21869.588| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3062 moved from start: 0.9262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 33348 Z= 0.160 Angle : 0.748 16.253 44901 Z= 0.386 Chirality : 0.045 0.241 4796 Planarity : 0.005 0.081 5697 Dihedral : 5.660 58.406 4280 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.31 % Allowed : 29.90 % Favored : 66.79 % 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: -1.13 (0.13), residues: 3808 helix: -0.29 (0.10), residues: 2361 sheet: -1.77 (0.42), residues: 155 loop : -1.26 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 38 TYR 0.042 0.002 TYR A 649 PHE 0.035 0.002 PHE E 45 TRP 0.036 0.003 TRP E 448 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00361 (33348) covalent geometry : angle 0.74800 (44901) hydrogen bonds : bond 0.04380 ( 1689) hydrogen bonds : angle 5.33010 ( 4902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 315 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.0772 (OUTLIER) cc_final: -0.2513 (p90) REVERT: A 185 LEU cc_start: 0.1167 (tp) cc_final: 0.0707 (pt) REVERT: A 202 ASN cc_start: 0.4380 (OUTLIER) cc_final: 0.4135 (t0) REVERT: A 223 TYR cc_start: -0.0242 (OUTLIER) cc_final: -0.2100 (t80) REVERT: A 585 LEU cc_start: 0.4865 (tp) cc_final: 0.4352 (pp) REVERT: A 619 LEU cc_start: 0.7438 (mm) cc_final: 0.7041 (tp) REVERT: A 665 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8459 (tptp) REVERT: A 735 LYS cc_start: 0.6443 (tptt) cc_final: 0.5922 (tptt) REVERT: A 883 GLU cc_start: 0.4758 (mm-30) cc_final: 0.4489 (mm-30) REVERT: A 930 MET cc_start: 0.5600 (mpt) cc_final: 0.2957 (ppp) REVERT: A 936 MET cc_start: 0.2556 (mmm) cc_final: 0.2018 (mtt) REVERT: B 388 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6135 (m-80) REVERT: B 447 ARG cc_start: 0.6280 (mmp-170) cc_final: 0.5926 (mmp80) REVERT: B 491 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7614 (tm-30) REVERT: B 543 GLU cc_start: 0.7642 (pm20) cc_final: 0.7084 (pt0) REVERT: B 923 GLU cc_start: 0.5990 (tp30) cc_final: 0.5711 (tp30) REVERT: B 930 MET cc_start: 0.1100 (ppp) cc_final: -0.0385 (ptp) REVERT: C 39 GLU cc_start: 0.5115 (tp30) cc_final: 0.4281 (tm-30) REVERT: D 71 TYR cc_start: -0.1123 (OUTLIER) cc_final: -0.3005 (m-80) REVERT: D 79 TYR cc_start: 0.2950 (OUTLIER) cc_final: 0.1929 (m-80) REVERT: D 204 MET cc_start: -0.1022 (tpp) cc_final: -0.2184 (tpp) REVERT: D 361 PHE cc_start: -0.1665 (OUTLIER) cc_final: -0.2792 (m-80) REVERT: D 659 PHE cc_start: 0.2752 (m-10) cc_final: 0.2552 (m-10) REVERT: D 930 MET cc_start: 0.1582 (tpt) cc_final: 0.0791 (tpp) REVERT: E 124 MET cc_start: -0.2675 (tmm) cc_final: -0.3584 (mtp) REVERT: E 185 LEU cc_start: 0.3646 (mt) cc_final: 0.2961 (tt) REVERT: E 202 ASN cc_start: -0.4095 (OUTLIER) cc_final: -0.4855 (m-40) REVERT: E 396 MET cc_start: -0.4791 (mmt) cc_final: -0.5396 (tpp) REVERT: E 647 MET cc_start: 0.4142 (OUTLIER) cc_final: 0.3021 (ppp) REVERT: E 786 HIS cc_start: -0.2713 (OUTLIER) cc_final: -0.3060 (t-170) REVERT: E 866 MET cc_start: 0.0836 (tmm) cc_final: -0.0161 (mmt) REVERT: F 172 GLU cc_start: 0.6417 (tt0) cc_final: 0.6009 (pp20) REVERT: F 219 LYS cc_start: 0.1791 (OUTLIER) cc_final: 0.1263 (ptpt) outliers start: 119 outliers final: 98 residues processed: 405 average time/residue: 0.2094 time to fit residues: 137.5862 Evaluate side-chains 409 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 300 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 218 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 996 TYR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 743 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 859 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 79 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 361 PHE Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 776 ASP Chi-restraints excluded: chain D residue 979 HIS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 139 ASP Chi-restraints excluded: chain E residue 142 CYS Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 378 TYR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 647 MET Chi-restraints excluded: chain E residue 672 SER Chi-restraints excluded: chain E residue 677 ARG Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain E residue 713 ILE Chi-restraints excluded: chain E residue 730 GLU Chi-restraints excluded: chain E residue 740 LEU Chi-restraints excluded: chain E residue 778 PHE Chi-restraints excluded: chain E residue 786 HIS Chi-restraints excluded: chain E residue 940 TYR Chi-restraints excluded: chain E residue 1005 ILE Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain F residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 81 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 359 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 377 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 881 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.135438 restraints weight = 119289.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.139038 restraints weight = 64777.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.139150 restraints weight = 38502.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.140262 restraints weight = 28217.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.140287 restraints weight = 23869.474| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3148 moved from start: 0.9765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 33348 Z= 0.173 Angle : 0.768 16.420 44901 Z= 0.397 Chirality : 0.046 0.315 4796 Planarity : 0.005 0.072 5697 Dihedral : 5.631 57.052 4278 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.62 % Allowed : 29.70 % Favored : 66.68 % 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: -1.18 (0.13), residues: 3808 helix: -0.31 (0.10), residues: 2351 sheet: -1.57 (0.42), residues: 162 loop : -1.33 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 380 TYR 0.038 0.002 TYR A 649 PHE 0.040 0.002 PHE B 381 TRP 0.034 0.003 TRP B 601 HIS 0.033 0.002 HIS A 810 Details of bonding type rmsd covalent geometry : bond 0.00391 (33348) covalent geometry : angle 0.76809 (44901) hydrogen bonds : bond 0.04477 ( 1689) hydrogen bonds : angle 5.34453 ( 4902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8000.50 seconds wall clock time: 138 minutes 45.86 seconds (8325.86 seconds total)