Starting phenix.real_space_refine on Tue Jun 17 17:33:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.map" model { file = "/net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wy9_37920/06_2025/8wy9_37920.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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 75 5.16 5 C 13028 2.51 5 N 3257 2.21 5 O 3769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20129 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7786 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 19, 'TRANS': 912} Chain breaks: 7 Chain: "B" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7869 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 19, 'TRANS': 920} Chain breaks: 7 Chain: "C" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2225 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "D" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2249 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 10, 'TRANS': 264} Time building chain proxies: 14.13, per 1000 atoms: 0.70 Number of scatterers: 20129 At special positions: 0 Unit cell: (100.067, 126.531, 180.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 3769 8.00 N 3257 7.00 C 13028 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: 4.69 Conformation dependent library (CDL) restraints added in 2.6 seconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 7 sheets defined 70.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.031A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.707A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.597A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.745A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.522A pdb=" N ASN A 182 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.591A 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 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.793A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.553A 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 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 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 removed outlier: 4.035A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 469 through 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 540 through 547 removed outlier: 3.773A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.856A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.837A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.288A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.521A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.724A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.905A pdb=" N HIS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 removed outlier: 3.670A pdb=" N ILE A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 4.020A pdb=" N PHE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 removed outlier: 4.058A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.866A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 954 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 954' Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 3.955A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 974 removed outlier: 4.321A 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 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.947A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.784A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 3.569A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.910A 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 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.592A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.901A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.566A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 281 through 298 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.604A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.579A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 493 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.420A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 559 through 563 removed outlier: 3.634A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 700 Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.862A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.040A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.599A pdb=" N ILE B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.530A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 878 through 895 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.564A pdb=" N GLU B 932 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.535A pdb=" N ASP B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) 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: 4.054A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 991 Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.930A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.791A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.706A pdb=" N LEU C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.769A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.596A pdb=" N VAL C 183 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.707A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.525A pdb=" N TYR C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 297 removed outlier: 3.851A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 39 removed outlier: 3.936A pdb=" N GLU D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.993A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.769A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.898A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.873A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 158 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 233 Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.065A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.332A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.205A 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 'B' and resid 150 through 152 removed outlier: 3.808A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.045A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.125A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3171 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: 7.58 Time building geometry restraints manager: 5.60 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: 6376 1.34 - 1.46: 5165 1.46 - 1.58: 8927 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 20594 Sorted by residual: bond pdb=" CB PRO B 506 " pdb=" CG PRO B 506 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.70e+00 bond pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CG PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.503 1.463 0.040 3.40e-02 8.65e+02 1.36e+00 bond pdb=" CB PRO A 74 " pdb=" CG PRO A 74 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.21e+00 bond pdb=" CB ASN B 797 " pdb=" CG ASN B 797 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 20589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 27543 2.23 - 4.46: 190 4.46 - 6.69: 23 6.69 - 8.92: 5 8.92 - 11.15: 4 Bond angle restraints: 27765 Sorted by residual: angle pdb=" N PRO A 74 " pdb=" CD PRO A 74 " pdb=" CG PRO A 74 " ideal model delta sigma weight residual 103.20 97.54 5.66 1.50e+00 4.44e-01 1.43e+01 angle pdb=" CA PRO A 74 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 112.00 107.00 5.00 1.40e+00 5.10e-01 1.27e+01 angle pdb=" CA LEU B 838 " pdb=" CB LEU B 838 " pdb=" CG LEU B 838 " ideal model delta sigma weight residual 116.30 127.45 -11.15 3.50e+00 8.16e-02 1.02e+01 angle pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " pdb=" CD GLU A 510 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.70e+00 3.46e-01 8.55e+00 angle pdb=" CA GLU A 510 " pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.26e+00 ... (remaining 27760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10325 17.83 - 35.66: 1445 35.66 - 53.49: 399 53.49 - 71.31: 79 71.31 - 89.14: 21 Dihedral angle restraints: 12269 sinusoidal: 5093 harmonic: 7176 Sorted by residual: dihedral pdb=" CA GLU A 923 " pdb=" C GLU A 923 " pdb=" N GLU A 924 " pdb=" CA GLU A 924 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR D 166 " pdb=" C TYR D 166 " pdb=" N LEU D 167 " pdb=" CA LEU D 167 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 12266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2451 0.049 - 0.099: 437 0.099 - 0.148: 67 0.148 - 0.197: 0 0.197 - 0.246: 2 Chirality restraints: 2957 Sorted by residual: chirality pdb=" CG LEU A 966 " pdb=" CB LEU A 966 " pdb=" CD1 LEU A 966 " pdb=" CD2 LEU A 966 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU B 363 " pdb=" CB LEU B 363 " pdb=" CD1 LEU B 363 " pdb=" CD2 LEU B 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CG LEU D 228 " pdb=" CB LEU D 228 " pdb=" CD1 LEU D 228 " pdb=" CD2 LEU D 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 2954 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " -0.041 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 744 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO B 745 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 510 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" CD GLU A 510 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 510 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 510 " 0.011 2.00e-02 2.50e+03 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 307 2.65 - 3.21: 18648 3.21 - 3.77: 33334 3.77 - 4.34: 47436 4.34 - 4.90: 75015 Nonbonded interactions: 174740 Sorted by model distance: nonbonded pdb=" O VAL A 470 " pdb=" OG SER A 474 " model vdw 2.086 3.040 nonbonded pdb=" O TYR B 313 " pdb=" OG SER B 317 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 590 " model vdw 2.185 3.040 nonbonded pdb=" O TYR C 197 " pdb=" OG SER C 201 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 37 " pdb=" O MET A 124 " model vdw 2.190 3.040 ... (remaining 174735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 399 or resid 406 through 493 or resid 504 throu \ gh 565 or resid 579 through 786 or resid 793 through 1005)) selection = (chain 'B' and (resid 22 through 462 or resid 468 through 629 or resid 645 throu \ gh 700 or resid 703 through 1005)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 26 through 297) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 347.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 48.810 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 412.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.002 0.065 20594 Z= 0.108 Angle : 0.508 11.154 27765 Z= 0.268 Chirality : 0.038 0.246 2957 Planarity : 0.003 0.060 3536 Dihedral : 17.958 89.142 7655 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.47 % Allowed : 26.86 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2383 helix: 0.91 (0.13), residues: 1496 sheet: -0.82 (0.67), residues: 40 loop : -0.09 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 757 HIS 0.003 0.001 HIS B 978 PHE 0.016 0.001 PHE A 943 TYR 0.021 0.001 TYR A 709 ARG 0.008 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.16799 ( 1092) hydrogen bonds : angle 6.03114 ( 3171) covalent geometry : bond 0.00242 (20594) covalent geometry : angle 0.50833 (27765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 989 LYS cc_start: 0.8244 (mptt) cc_final: 0.7871 (mptt) REVERT: B 776 ASP cc_start: 0.8208 (t70) cc_final: 0.7930 (t0) REVERT: B 913 MET cc_start: 0.7842 (ptm) cc_final: 0.7476 (pmm) REVERT: D 216 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (pp) outliers start: 77 outliers final: 57 residues processed: 298 average time/residue: 1.3567 time to fit residues: 460.3155 Evaluate side-chains 253 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 370 ARG Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 391 ASN A 475 GLN A 711 GLN A 797 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097700 restraints weight = 31402.656| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.14 r_work: 0.3243 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20594 Z= 0.139 Angle : 0.525 9.949 27765 Z= 0.279 Chirality : 0.040 0.178 2957 Planarity : 0.004 0.054 3536 Dihedral : 6.623 63.648 2755 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.28 % Allowed : 25.06 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2383 helix: 1.15 (0.13), residues: 1506 sheet: -1.16 (0.64), residues: 32 loop : 0.03 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 757 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 856 TYR 0.012 0.001 TYR A 755 ARG 0.007 0.001 ARG B 587 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1092) hydrogen bonds : angle 4.71770 ( 3171) covalent geometry : bond 0.00317 (20594) covalent geometry : angle 0.52524 (27765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 223 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 348 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8001 (ttt180) REVERT: A 377 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: A 525 ASP cc_start: 0.8630 (m-30) cc_final: 0.8409 (m-30) REVERT: A 714 SER cc_start: 0.8998 (t) cc_final: 0.8772 (p) REVERT: A 965 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8507 (tptt) REVERT: A 975 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: A 989 LYS cc_start: 0.8247 (mptt) cc_final: 0.8014 (mmmm) REVERT: A 995 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8098 (tpm170) REVERT: B 181 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: B 491 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 526 ASP cc_start: 0.8374 (t0) cc_final: 0.8146 (t70) REVERT: B 634 LEU cc_start: 0.8056 (mm) cc_final: 0.7816 (mt) REVERT: B 776 ASP cc_start: 0.8529 (t70) cc_final: 0.8291 (t0) REVERT: B 913 MET cc_start: 0.8159 (ptm) cc_final: 0.7711 (pmm) REVERT: D 81 SER cc_start: 0.8891 (m) cc_final: 0.8533 (p) REVERT: D 227 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8010 (mtm) REVERT: D 237 LYS cc_start: 0.8524 (tptp) cc_final: 0.8253 (tptp) REVERT: D 238 ASP cc_start: 0.8812 (m-30) cc_final: 0.8555 (m-30) outliers start: 95 outliers final: 31 residues processed: 299 average time/residue: 1.2465 time to fit residues: 425.9550 Evaluate side-chains 243 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 26 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098270 restraints weight = 31154.571| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.15 r_work: 0.3238 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20594 Z= 0.134 Angle : 0.503 10.110 27765 Z= 0.265 Chirality : 0.040 0.157 2957 Planarity : 0.003 0.045 3536 Dihedral : 5.207 57.416 2684 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.51 % Allowed : 24.34 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2383 helix: 1.21 (0.13), residues: 1520 sheet: -1.52 (0.64), residues: 32 loop : -0.03 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 856 TYR 0.017 0.001 TYR A 804 ARG 0.008 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1092) hydrogen bonds : angle 4.52249 ( 3171) covalent geometry : bond 0.00309 (20594) covalent geometry : angle 0.50322 (27765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 225 time to evaluate : 2.391 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: A 202 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (t0) REVERT: A 377 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 525 ASP cc_start: 0.8677 (m-30) cc_final: 0.8380 (m-30) REVERT: A 714 SER cc_start: 0.8993 (t) cc_final: 0.8764 (p) REVERT: A 915 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 965 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8430 (tptp) REVERT: A 989 LYS cc_start: 0.8283 (mptt) cc_final: 0.7759 (mptt) REVERT: A 995 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8036 (tpm170) REVERT: B 181 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: B 491 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 526 ASP cc_start: 0.8361 (t0) cc_final: 0.8158 (t70) REVERT: B 557 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8345 (tmmm) REVERT: B 776 ASP cc_start: 0.8515 (t70) cc_final: 0.8272 (t0) REVERT: B 913 MET cc_start: 0.8192 (ptm) cc_final: 0.7790 (pmm) REVERT: B 936 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3494 (mpp) REVERT: C 32 GLU cc_start: 0.7973 (tp30) cc_final: 0.7686 (tp30) REVERT: D 81 SER cc_start: 0.8798 (m) cc_final: 0.8465 (p) REVERT: D 105 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8204 (ttpt) REVERT: D 147 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.6992 (ptpt) REVERT: D 181 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: D 227 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: D 233 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7760 (ptp90) REVERT: D 237 LYS cc_start: 0.8480 (tptp) cc_final: 0.8177 (tptp) REVERT: D 238 ASP cc_start: 0.8795 (m-30) cc_final: 0.8512 (m-30) REVERT: D 278 ASN cc_start: 0.7972 (t0) cc_final: 0.7259 (m110) outliers start: 100 outliers final: 32 residues processed: 299 average time/residue: 1.2275 time to fit residues: 419.7978 Evaluate side-chains 250 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 233 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098363 restraints weight = 31459.259| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.14 r_work: 0.3240 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20594 Z= 0.139 Angle : 0.499 10.389 27765 Z= 0.261 Chirality : 0.040 0.144 2957 Planarity : 0.003 0.045 3536 Dihedral : 5.053 58.647 2677 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.33 % Allowed : 24.16 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2383 helix: 1.24 (0.13), residues: 1528 sheet: -1.76 (0.63), residues: 32 loop : -0.02 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 958 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 856 TYR 0.015 0.001 TYR A 951 ARG 0.009 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1092) hydrogen bonds : angle 4.44064 ( 3171) covalent geometry : bond 0.00325 (20594) covalent geometry : angle 0.49898 (27765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 223 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8338 (pttp) REVERT: A 377 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: A 525 ASP cc_start: 0.8728 (m-30) cc_final: 0.8387 (m-30) REVERT: A 714 SER cc_start: 0.9011 (t) cc_final: 0.8778 (p) REVERT: A 740 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7966 (tp) REVERT: A 915 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7803 (p) REVERT: A 936 MET cc_start: 0.6425 (mmm) cc_final: 0.6213 (mmm) REVERT: A 965 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8415 (tptp) REVERT: A 975 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: A 989 LYS cc_start: 0.8382 (mptt) cc_final: 0.7808 (mptt) REVERT: A 995 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8137 (tpm170) REVERT: A 998 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: B 181 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: B 557 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8392 (tmmm) REVERT: B 626 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 776 ASP cc_start: 0.8547 (t70) cc_final: 0.8315 (t0) REVERT: B 913 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7800 (pmm) REVERT: B 936 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3450 (mpp) REVERT: C 145 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6977 (mpp80) REVERT: D 81 SER cc_start: 0.8819 (m) cc_final: 0.8498 (p) REVERT: D 147 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7131 (ptpt) REVERT: D 181 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: D 227 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: D 233 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7749 (ptp90) REVERT: D 237 LYS cc_start: 0.8509 (tptp) cc_final: 0.8200 (tptp) REVERT: D 238 ASP cc_start: 0.8790 (m-30) cc_final: 0.8529 (m-30) REVERT: D 267 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8450 (mtp85) outliers start: 96 outliers final: 38 residues processed: 293 average time/residue: 1.2206 time to fit residues: 408.2862 Evaluate side-chains 261 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 230 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 829 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098539 restraints weight = 31390.114| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.16 r_work: 0.3250 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20594 Z= 0.130 Angle : 0.494 10.579 27765 Z= 0.259 Chirality : 0.039 0.146 2957 Planarity : 0.003 0.044 3536 Dihedral : 4.865 59.897 2673 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.73 % Allowed : 23.66 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2383 helix: 1.30 (0.13), residues: 1529 sheet: -1.74 (0.64), residues: 32 loop : -0.02 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 958 HIS 0.015 0.001 HIS A 979 PHE 0.013 0.001 PHE A 856 TYR 0.019 0.001 TYR A 709 ARG 0.010 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1092) hydrogen bonds : angle 4.36792 ( 3171) covalent geometry : bond 0.00302 (20594) covalent geometry : angle 0.49387 (27765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 221 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8798 (t0) REVERT: A 304 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8316 (pttp) REVERT: A 377 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: A 525 ASP cc_start: 0.8757 (m-30) cc_final: 0.8428 (m-30) REVERT: A 714 SER cc_start: 0.9015 (t) cc_final: 0.8785 (p) REVERT: A 740 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 784 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: A 915 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 965 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8428 (tptp) REVERT: A 989 LYS cc_start: 0.8438 (mptt) cc_final: 0.7838 (mptt) REVERT: A 995 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8030 (tpm170) REVERT: A 999 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7277 (mt) REVERT: B 181 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: B 315 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (mmtm) REVERT: B 491 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: B 557 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8425 (tmmm) REVERT: B 626 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 744 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8814 (t80) REVERT: B 776 ASP cc_start: 0.8545 (t70) cc_final: 0.8317 (t0) REVERT: B 913 MET cc_start: 0.8190 (ptm) cc_final: 0.7783 (pmm) REVERT: B 936 MET cc_start: 0.3913 (OUTLIER) cc_final: 0.3338 (mpp) REVERT: B 1001 MET cc_start: 0.8601 (mtm) cc_final: 0.8219 (ttp) REVERT: C 145 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7036 (mpp80) REVERT: C 165 ARG cc_start: 0.7415 (ptm160) cc_final: 0.7198 (ptm160) REVERT: D 81 SER cc_start: 0.8788 (m) cc_final: 0.8466 (p) REVERT: D 147 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7112 (ptpt) REVERT: D 181 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: D 227 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8044 (mtm) REVERT: D 233 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7756 (ptp90) REVERT: D 237 LYS cc_start: 0.8554 (tptp) cc_final: 0.8238 (tptp) REVERT: D 238 ASP cc_start: 0.8815 (m-30) cc_final: 0.8548 (m-30) REVERT: D 267 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8458 (mtp85) outliers start: 105 outliers final: 40 residues processed: 304 average time/residue: 1.2674 time to fit residues: 439.4190 Evaluate side-chains 267 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 122 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 832 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097007 restraints weight = 31444.995| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.15 r_work: 0.3233 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20594 Z= 0.145 Angle : 0.507 10.783 27765 Z= 0.263 Chirality : 0.040 0.148 2957 Planarity : 0.003 0.048 3536 Dihedral : 4.824 59.106 2672 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.15 % Allowed : 24.25 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2383 helix: 1.30 (0.13), residues: 1529 sheet: -1.68 (0.65), residues: 32 loop : -0.01 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 958 HIS 0.014 0.001 HIS A 979 PHE 0.013 0.001 PHE A 856 TYR 0.021 0.001 TYR A 709 ARG 0.011 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1092) hydrogen bonds : angle 4.35924 ( 3171) covalent geometry : bond 0.00340 (20594) covalent geometry : angle 0.50743 (27765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 217 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8828 (t0) REVERT: A 304 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8285 (pttp) REVERT: A 377 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: A 525 ASP cc_start: 0.8789 (m-30) cc_final: 0.8438 (m-30) REVERT: A 740 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 784 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 839 PHE cc_start: 0.8537 (t80) cc_final: 0.8233 (t80) REVERT: A 915 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 939 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7027 (mm110) REVERT: A 965 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8484 (tptt) REVERT: A 975 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6897 (t-90) REVERT: A 989 LYS cc_start: 0.8470 (mptt) cc_final: 0.7883 (mptt) REVERT: A 995 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (tpm170) REVERT: B 181 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: B 491 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: B 626 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 744 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8833 (t80) REVERT: B 776 ASP cc_start: 0.8575 (t70) cc_final: 0.8345 (t0) REVERT: B 913 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7771 (pmm) REVERT: B 936 MET cc_start: 0.3931 (OUTLIER) cc_final: 0.3296 (mpp) REVERT: B 1001 MET cc_start: 0.8631 (mtm) cc_final: 0.8204 (ttp) REVERT: C 145 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.7030 (mpp80) REVERT: D 81 SER cc_start: 0.8800 (m) cc_final: 0.8479 (p) REVERT: D 147 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7154 (ptpt) REVERT: D 181 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: D 227 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: D 233 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7736 (ptp90) outliers start: 92 outliers final: 39 residues processed: 287 average time/residue: 1.2493 time to fit residues: 408.7313 Evaluate side-chains 261 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 113 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 183 optimal weight: 0.0670 chunk 140 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 240 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN D 202 ASN D 278 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098555 restraints weight = 31409.865| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.17 r_work: 0.3243 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20594 Z= 0.119 Angle : 0.500 11.229 27765 Z= 0.259 Chirality : 0.039 0.160 2957 Planarity : 0.003 0.050 3536 Dihedral : 4.762 60.587 2672 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.15 % Allowed : 24.47 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2383 helix: 1.36 (0.13), residues: 1530 sheet: -1.69 (0.65), residues: 32 loop : 0.00 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 958 HIS 0.016 0.001 HIS A 979 PHE 0.011 0.001 PHE A 856 TYR 0.023 0.001 TYR A 709 ARG 0.012 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 1092) hydrogen bonds : angle 4.30039 ( 3171) covalent geometry : bond 0.00275 (20594) covalent geometry : angle 0.49983 (27765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 214 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8255 (pttp) REVERT: A 377 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: A 525 ASP cc_start: 0.8797 (m-30) cc_final: 0.8431 (m-30) REVERT: A 740 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 784 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: A 939 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6998 (mm110) REVERT: A 965 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8538 (tptt) REVERT: A 975 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6879 (t-90) REVERT: A 989 LYS cc_start: 0.8510 (mptt) cc_final: 0.7927 (mptt) REVERT: A 995 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8041 (tpm170) REVERT: B 181 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: B 315 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8805 (mmtm) REVERT: B 491 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: B 626 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 744 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8856 (t80) REVERT: B 776 ASP cc_start: 0.8531 (t70) cc_final: 0.8310 (t0) REVERT: B 913 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7760 (pmm) REVERT: B 936 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.3275 (mpp) REVERT: B 1001 MET cc_start: 0.8627 (mtm) cc_final: 0.8390 (ttp) REVERT: C 145 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.7025 (mpp80) REVERT: D 81 SER cc_start: 0.8781 (m) cc_final: 0.8445 (p) REVERT: D 227 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: D 233 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7741 (ptp90) REVERT: D 278 ASN cc_start: 0.7942 (t0) cc_final: 0.7261 (m110) outliers start: 92 outliers final: 38 residues processed: 285 average time/residue: 1.2535 time to fit residues: 408.4640 Evaluate side-chains 262 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.141413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098538 restraints weight = 31550.386| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.19 r_work: 0.3239 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20594 Z= 0.124 Angle : 0.508 11.968 27765 Z= 0.263 Chirality : 0.039 0.166 2957 Planarity : 0.003 0.055 3536 Dihedral : 4.750 61.090 2672 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.20 % Allowed : 25.10 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2383 helix: 1.37 (0.13), residues: 1532 sheet: -1.69 (0.66), residues: 32 loop : 0.01 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 958 HIS 0.015 0.001 HIS A 979 PHE 0.011 0.001 PHE A 856 TYR 0.015 0.001 TYR B 709 ARG 0.012 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1092) hydrogen bonds : angle 4.29711 ( 3171) covalent geometry : bond 0.00289 (20594) covalent geometry : angle 0.50843 (27765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (pttp) REVERT: A 377 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: A 525 ASP cc_start: 0.8798 (m-30) cc_final: 0.8449 (m-30) REVERT: A 740 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 784 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: A 939 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6957 (mm110) REVERT: A 965 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8579 (tptt) REVERT: A 976 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6289 (ptp) REVERT: A 995 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (tpm170) REVERT: B 181 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: B 315 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8814 (mmtm) REVERT: B 491 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: B 626 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 744 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 776 ASP cc_start: 0.8549 (t70) cc_final: 0.8340 (t0) REVERT: B 913 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7796 (pmm) REVERT: B 936 MET cc_start: 0.3866 (OUTLIER) cc_final: 0.3403 (mpp) REVERT: C 145 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7062 (mpp80) REVERT: D 81 SER cc_start: 0.8781 (m) cc_final: 0.8448 (p) REVERT: D 227 MET cc_start: 0.8332 (tpt) cc_final: 0.8064 (mtm) REVERT: D 233 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7734 (ptp90) REVERT: D 278 ASN cc_start: 0.7958 (t0) cc_final: 0.7276 (m110) outliers start: 71 outliers final: 39 residues processed: 265 average time/residue: 1.2728 time to fit residues: 386.3567 Evaluate side-chains 252 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 491 GLN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 999 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 164 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 230 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 475 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094567 restraints weight = 30863.827| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.25 r_work: 0.3145 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20594 Z= 0.122 Angle : 0.515 12.208 27765 Z= 0.267 Chirality : 0.039 0.189 2957 Planarity : 0.003 0.041 3536 Dihedral : 4.653 61.845 2670 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.92 % Allowed : 24.43 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2383 helix: 1.37 (0.13), residues: 1531 sheet: -1.68 (0.65), residues: 32 loop : -0.00 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 958 HIS 0.024 0.001 HIS A 979 PHE 0.015 0.001 PHE B 699 TYR 0.027 0.001 TYR A 951 ARG 0.007 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1092) hydrogen bonds : angle 4.29181 ( 3171) covalent geometry : bond 0.00284 (20594) covalent geometry : angle 0.51470 (27765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 209 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8144 (pttp) REVERT: A 377 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7240 (mt0) REVERT: A 525 ASP cc_start: 0.8799 (m-30) cc_final: 0.8436 (m-30) REVERT: A 740 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7743 (tp) REVERT: A 784 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: A 939 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6963 (mm110) REVERT: A 965 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8521 (tptt) REVERT: A 975 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.7099 (t-90) REVERT: A 995 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8048 (tpm170) REVERT: B 175 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8458 (mtm180) REVERT: B 315 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (mmtm) REVERT: B 626 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 744 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8772 (t80) REVERT: B 776 ASP cc_start: 0.8509 (t70) cc_final: 0.8294 (t0) REVERT: B 913 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7806 (pmm) REVERT: B 936 MET cc_start: 0.3907 (OUTLIER) cc_final: 0.3410 (mpp) REVERT: B 1004 PHE cc_start: 0.8403 (m-10) cc_final: 0.8199 (m-10) REVERT: C 145 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6967 (mpp80) REVERT: C 289 VAL cc_start: 0.7964 (m) cc_final: 0.7746 (p) REVERT: D 81 SER cc_start: 0.8753 (m) cc_final: 0.8418 (p) REVERT: D 223 TYR cc_start: 0.8530 (t80) cc_final: 0.8161 (t80) REVERT: D 227 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: D 233 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7826 (ptp90) REVERT: D 278 ASN cc_start: 0.7969 (t0) cc_final: 0.7245 (m110) outliers start: 87 outliers final: 45 residues processed: 273 average time/residue: 1.3234 time to fit residues: 410.2459 Evaluate side-chains 265 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 939 GLN Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1003 TYR Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 39 ASN D 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093301 restraints weight = 30978.290| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.27 r_work: 0.3131 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20594 Z= 0.143 Angle : 0.538 12.301 27765 Z= 0.278 Chirality : 0.040 0.201 2957 Planarity : 0.003 0.062 3536 Dihedral : 4.669 61.687 2670 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.11 % Allowed : 25.42 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2383 helix: 1.36 (0.13), residues: 1531 sheet: -1.67 (0.66), residues: 32 loop : 0.00 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 958 HIS 0.022 0.001 HIS A 979 PHE 0.015 0.001 PHE B 699 TYR 0.022 0.001 TYR A 951 ARG 0.015 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 1092) hydrogen bonds : angle 4.32077 ( 3171) covalent geometry : bond 0.00336 (20594) covalent geometry : angle 0.53826 (27765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (pttp) REVERT: A 377 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: A 525 ASP cc_start: 0.8798 (m-30) cc_final: 0.8459 (m-30) REVERT: A 695 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 740 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7807 (tp) REVERT: A 784 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 965 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8557 (tptt) REVERT: A 975 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.7113 (t-90) REVERT: A 995 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8063 (tpm170) REVERT: B 626 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 744 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8788 (t80) REVERT: B 776 ASP cc_start: 0.8527 (t70) cc_final: 0.8305 (t0) REVERT: B 813 LYS cc_start: 0.7942 (tttm) cc_final: 0.7530 (pttp) REVERT: B 913 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7797 (pmm) REVERT: B 936 MET cc_start: 0.3968 (OUTLIER) cc_final: 0.3441 (mpp) REVERT: B 976 MET cc_start: 0.4607 (mpm) cc_final: 0.3872 (mtm) REVERT: C 145 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6961 (mpp80) REVERT: D 227 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7962 (mtm) REVERT: D 233 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7821 (ptp90) REVERT: D 278 ASN cc_start: 0.7990 (t0) cc_final: 0.7234 (m110) outliers start: 69 outliers final: 43 residues processed: 256 average time/residue: 1.3144 time to fit residues: 384.6893 Evaluate side-chains 255 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 826 CYS Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 234 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 391 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 236 GLN D 202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092866 restraints weight = 31018.471| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.25 r_work: 0.3117 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20594 Z= 0.162 Angle : 0.548 12.315 27765 Z= 0.284 Chirality : 0.041 0.287 2957 Planarity : 0.003 0.043 3536 Dihedral : 4.702 61.616 2670 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.93 % Allowed : 25.64 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2383 helix: 1.32 (0.13), residues: 1530 sheet: -1.66 (0.66), residues: 32 loop : -0.02 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 958 HIS 0.021 0.001 HIS A 979 PHE 0.016 0.001 PHE B 699 TYR 0.021 0.001 TYR A 951 ARG 0.009 0.001 ARG B 587 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1092) hydrogen bonds : angle 4.36969 ( 3171) covalent geometry : bond 0.00383 (20594) covalent geometry : angle 0.54801 (27765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20677.80 seconds wall clock time: 357 minutes 11.79 seconds (21431.79 seconds total)