Starting phenix.real_space_refine on Fri Mar 14 02:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1a_30938/03_2025/7e1a_30938.cif" } resolution = 3.66 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= 0.006 sd= 0.079 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 55 5.16 5 C 5951 2.51 5 N 1566 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9284 Number of models: 1 Model: "" Number of chains: 2 Chain: "U" Number of atoms: 9249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9249 Classifications: {'peptide': 1189} Link IDs: {'PTRANS': 32, 'TRANS': 1156} Chain breaks: 1 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'TCH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.79, per 1000 atoms: 0.62 Number of scatterers: 9284 At special positions: 0 Unit cell: (93.28, 94.34, 161.12, 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 55 16.00 O 1712 8.00 N 1566 7.00 C 5951 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 48.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'U' and resid 63 through 74 removed outlier: 3.778A pdb=" N CYS U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA U 69 " --> pdb=" O GLY U 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 84 Processing helix chain 'U' and resid 88 through 102 removed outlier: 3.506A pdb=" N TYR U 93 " --> pdb=" O VAL U 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN U 101 " --> pdb=" O LEU U 97 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE U 102 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 139 removed outlier: 3.831A pdb=" N ILE U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 removed outlier: 3.717A pdb=" N ALA U 168 " --> pdb=" O VAL U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 181 removed outlier: 3.544A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 191 removed outlier: 3.926A pdb=" N PHE U 190 " --> pdb=" O GLU U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 199 removed outlier: 3.777A pdb=" N LEU U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 236 removed outlier: 3.805A pdb=" N LEU U 232 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU U 233 " --> pdb=" O CYS U 229 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 249 through 254 Processing helix chain 'U' and resid 256 through 264 removed outlier: 4.143A pdb=" N GLY U 260 " --> pdb=" O ALA U 256 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER U 262 " --> pdb=" O THR U 258 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL U 263 " --> pdb=" O ILE U 259 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER U 264 " --> pdb=" O GLY U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 275 removed outlier: 3.902A pdb=" N LYS U 272 " --> pdb=" O ASP U 268 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA U 273 " --> pdb=" O TYR U 269 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR U 274 " --> pdb=" O GLU U 270 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA U 275 " --> pdb=" O LEU U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 276 through 285 removed outlier: 4.284A pdb=" N VAL U 280 " --> pdb=" O LYS U 276 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP U 282 " --> pdb=" O GLY U 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL U 284 " --> pdb=" O VAL U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 295 removed outlier: 3.645A pdb=" N VAL U 291 " --> pdb=" O SER U 287 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 306 removed outlier: 3.748A pdb=" N LYS U 306 " --> pdb=" O GLU U 302 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 309 No H-bonds generated for 'chain 'U' and resid 307 through 309' Processing helix chain 'U' and resid 315 through 324 removed outlier: 3.504A pdb=" N GLY U 319 " --> pdb=" O GLY U 315 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL U 321 " --> pdb=" O ARG U 317 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 351 removed outlier: 3.981A pdb=" N PHE U 334 " --> pdb=" O TRP U 330 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU U 335 " --> pdb=" O CYS U 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR U 343 " --> pdb=" O LEU U 339 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU U 347 " --> pdb=" O TYR U 343 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU U 349 " --> pdb=" O SER U 345 " (cutoff:3.500A) Processing helix chain 'U' and resid 366 through 372 removed outlier: 4.175A pdb=" N ASN U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 373 through 375 No H-bonds generated for 'chain 'U' and resid 373 through 375' Processing helix chain 'U' and resid 380 through 389 removed outlier: 4.065A pdb=" N ALA U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY U 386 " --> pdb=" O ALA U 382 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 397 Processing helix chain 'U' and resid 462 through 467 removed outlier: 4.006A pdb=" N LEU U 467 " --> pdb=" O THR U 463 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 470 No H-bonds generated for 'chain 'U' and resid 468 through 470' Processing helix chain 'U' and resid 490 through 498 removed outlier: 4.568A pdb=" N ASP U 496 " --> pdb=" O GLN U 492 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN U 497 " --> pdb=" O TRP U 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE U 498 " --> pdb=" O LEU U 494 " (cutoff:3.500A) Processing helix chain 'U' and resid 511 through 516 removed outlier: 3.635A pdb=" N ILE U 516 " --> pdb=" O ILE U 512 " (cutoff:3.500A) Processing helix chain 'U' and resid 517 through 519 No H-bonds generated for 'chain 'U' and resid 517 through 519' Processing helix chain 'U' and resid 524 through 535 removed outlier: 4.588A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA U 532 " --> pdb=" O ILE U 528 " (cutoff:3.500A) Processing helix chain 'U' and resid 538 through 543 removed outlier: 4.105A pdb=" N MET U 542 " --> pdb=" O TYR U 538 " (cutoff:3.500A) Processing helix chain 'U' and resid 550 through 554 removed outlier: 4.204A pdb=" N GLY U 553 " --> pdb=" O THR U 550 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU U 554 " --> pdb=" O LEU U 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 550 through 554' Processing helix chain 'U' and resid 563 through 574 removed outlier: 3.691A pdb=" N VAL U 567 " --> pdb=" O GLN U 563 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) Processing helix chain 'U' and resid 590 through 602 removed outlier: 3.980A pdb=" N ALA U 595 " --> pdb=" O ASN U 591 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET U 596 " --> pdb=" O GLU U 592 " (cutoff:3.500A) Processing helix chain 'U' and resid 650 through 658 removed outlier: 3.518A pdb=" N THR U 655 " --> pdb=" O PHE U 651 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU U 656 " --> pdb=" O THR U 652 " (cutoff:3.500A) Processing helix chain 'U' and resid 742 through 748 Processing helix chain 'U' and resid 749 through 752 removed outlier: 3.761A pdb=" N TRP U 752 " --> pdb=" O ALA U 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 749 through 752' Processing helix chain 'U' and resid 756 through 764 removed outlier: 3.730A pdb=" N GLY U 761 " --> pdb=" O VAL U 757 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA U 762 " --> pdb=" O GLY U 758 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL U 764 " --> pdb=" O VAL U 760 " (cutoff:3.500A) Processing helix chain 'U' and resid 768 through 780 removed outlier: 3.692A pdb=" N PHE U 774 " --> pdb=" O PRO U 770 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU U 780 " --> pdb=" O PHE U 776 " (cutoff:3.500A) Processing helix chain 'U' and resid 787 through 819 removed outlier: 3.807A pdb=" N GLN U 791 " --> pdb=" O ASP U 787 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG U 792 " --> pdb=" O LYS U 788 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN U 796 " --> pdb=" O ARG U 792 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU U 800 " --> pdb=" O ASN U 796 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU U 801 " --> pdb=" O GLY U 797 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 802 " --> pdb=" O VAL U 798 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL U 803 " --> pdb=" O CYS U 799 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA U 804 " --> pdb=" O LEU U 800 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER U 809 " --> pdb=" O MET U 805 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU U 810 " --> pdb=" O GLY U 806 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE U 811 " --> pdb=" O CYS U 807 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN U 813 " --> pdb=" O SER U 809 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU U 815 " --> pdb=" O PHE U 811 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN U 816 " --> pdb=" O THR U 812 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY U 817 " --> pdb=" O GLN U 813 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA U 819 " --> pdb=" O LEU U 815 " (cutoff:3.500A) Processing helix chain 'U' and resid 829 through 839 Processing helix chain 'U' and resid 843 through 847 removed outlier: 3.589A pdb=" N TRP U 846 " --> pdb=" O ASP U 843 " (cutoff:3.500A) Processing helix chain 'U' and resid 859 through 864 removed outlier: 3.849A pdb=" N THR U 863 " --> pdb=" O THR U 859 " (cutoff:3.500A) Processing helix chain 'U' and resid 872 through 877 removed outlier: 3.739A pdb=" N ILE U 876 " --> pdb=" O ALA U 872 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY U 877 " --> pdb=" O GLY U 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 872 through 877' Processing helix chain 'U' and resid 880 through 888 removed outlier: 3.624A pdb=" N THR U 884 " --> pdb=" O VAL U 880 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL U 886 " --> pdb=" O SER U 882 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL U 888 " --> pdb=" O THR U 884 " (cutoff:3.500A) Processing helix chain 'U' and resid 888 through 896 removed outlier: 3.562A pdb=" N ILE U 892 " --> pdb=" O VAL U 888 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) Processing helix chain 'U' and resid 900 through 906 removed outlier: 4.020A pdb=" N ILE U 904 " --> pdb=" O LEU U 900 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU U 905 " --> pdb=" O SER U 901 " (cutoff:3.500A) Processing helix chain 'U' and resid 907 through 913 removed outlier: 3.529A pdb=" N ALA U 912 " --> pdb=" O PHE U 908 " (cutoff:3.500A) Processing helix chain 'U' and resid 918 through 923 Processing helix chain 'U' and resid 929 through 934 Processing helix chain 'U' and resid 935 through 940 removed outlier: 3.921A pdb=" N ILE U 939 " --> pdb=" O MET U 935 " (cutoff:3.500A) Processing helix chain 'U' and resid 946 through 951 removed outlier: 3.603A pdb=" N VAL U 950 " --> pdb=" O ASN U 946 " (cutoff:3.500A) Processing helix chain 'U' and resid 957 through 965 removed outlier: 4.539A pdb=" N LEU U 963 " --> pdb=" O PHE U 959 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU U 964 " --> pdb=" O ILE U 960 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR U 965 " --> pdb=" O GLU U 961 " (cutoff:3.500A) Processing helix chain 'U' and resid 982 through 987 removed outlier: 3.679A pdb=" N PHE U 987 " --> pdb=" O PHE U 983 " (cutoff:3.500A) Processing helix chain 'U' and resid 994 through 1010 removed outlier: 3.659A pdb=" N SER U 999 " --> pdb=" O ALA U 995 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR U1000 " --> pdb=" O ASN U 996 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR U1002 " --> pdb=" O ALA U 998 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER U1008 " --> pdb=" O GLY U1004 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN U1009 " --> pdb=" O TYR U1005 " (cutoff:3.500A) Processing helix chain 'U' and resid 1013 through 1015 No H-bonds generated for 'chain 'U' and resid 1013 through 1015' Processing helix chain 'U' and resid 1016 through 1022 removed outlier: 3.728A pdb=" N VAL U1020 " --> pdb=" O TYR U1016 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE U1021 " --> pdb=" O VAL U1017 " (cutoff:3.500A) Processing helix chain 'U' and resid 1025 through 1036 removed outlier: 3.622A pdb=" N ALA U1030 " --> pdb=" O LEU U1026 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU U1031 " --> pdb=" O SER U1027 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA U1034 " --> pdb=" O ALA U1030 " (cutoff:3.500A) Processing helix chain 'U' and resid 1041 through 1056 removed outlier: 3.735A pdb=" N ILE U1046 " --> pdb=" O ALA U1042 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER U1047 " --> pdb=" O LYS U1043 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG U1050 " --> pdb=" O ILE U1046 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE U1051 " --> pdb=" O SER U1047 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN U1053 " --> pdb=" O ALA U1049 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU U1054 " --> pdb=" O ARG U1050 " (cutoff:3.500A) Processing helix chain 'U' and resid 1120 through 1125 Processing helix chain 'U' and resid 1143 through 1147 Processing helix chain 'U' and resid 1148 through 1153 Processing helix chain 'U' and resid 1170 through 1175 removed outlier: 3.564A pdb=" N ILE U1174 " --> pdb=" O ILE U1170 " (cutoff:3.500A) Processing helix chain 'U' and resid 1176 through 1178 No H-bonds generated for 'chain 'U' and resid 1176 through 1178' Processing helix chain 'U' and resid 1185 through 1195 removed outlier: 4.143A pdb=" N ILE U1189 " --> pdb=" O MET U1185 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA U1192 " --> pdb=" O VAL U1188 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS U1193 " --> pdb=" O ILE U1189 " (cutoff:3.500A) Processing helix chain 'U' and resid 1199 through 1204 removed outlier: 3.757A pdb=" N LEU U1204 " --> pdb=" O PHE U1200 " (cutoff:3.500A) Processing helix chain 'U' and resid 1220 through 1234 removed outlier: 4.231A pdb=" N ARG U1226 " --> pdb=" O GLY U1222 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE U1227 " --> pdb=" O GLU U1223 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA U1228 " --> pdb=" O LYS U1224 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA U1230 " --> pdb=" O ARG U1226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA U1232 " --> pdb=" O ALA U1228 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U1234 " --> pdb=" O ALA U1230 " (cutoff:3.500A) Processing helix chain 'U' and resid 1252 through 1264 removed outlier: 3.559A pdb=" N GLN U1258 " --> pdb=" O GLU U1254 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL U1259 " --> pdb=" O LYS U1255 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) Processing helix chain 'U' and resid 1299 through 1303 removed outlier: 3.608A pdb=" N LEU U1303 " --> pdb=" O HIS U1300 " (cutoff:3.500A) Processing helix chain 'U' and resid 1308 through 1314 Processing sheet with id=AA1, first strand: chain 'U' and resid 420 through 422 Processing sheet with id=AA2, first strand: chain 'U' and resid 426 through 427 removed outlier: 3.618A pdb=" N PHE U 427 " --> pdb=" O LEU U 438 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU U 438 " --> pdb=" O PHE U 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'U' and resid 500 through 501 removed outlier: 5.843A pdb=" N LEU U 580 " --> pdb=" O ILE U 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 7.111A pdb=" N GLY U1157 " --> pdb=" O LEU U1241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 193 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2349 1.33 - 1.45: 1944 1.45 - 1.57: 5082 1.57 - 1.69: 1 1.69 - 1.81: 89 Bond restraints: 9465 Sorted by residual: bond pdb=" C ALA U 214 " pdb=" N ASP U 215 " ideal model delta sigma weight residual 1.335 1.269 0.065 1.42e-02 4.96e+03 2.12e+01 bond pdb=" O3S TCH U1401 " pdb=" S26 TCH U1401 " ideal model delta sigma weight residual 1.475 1.549 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.376 0.137 3.90e-02 6.57e+02 1.23e+01 bond pdb=" CG1 ILE U 245 " pdb=" CD1 ILE U 245 " ideal model delta sigma weight residual 1.513 1.382 0.131 3.90e-02 6.57e+02 1.13e+01 bond pdb=" CB VAL U1024 " pdb=" CG2 VAL U1024 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 ... (remaining 9460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 12690 5.03 - 10.07: 102 10.07 - 15.10: 13 15.10 - 20.14: 0 20.14 - 25.17: 1 Bond angle restraints: 12806 Sorted by residual: angle pdb=" N VAL U 152 " pdb=" CA VAL U 152 " pdb=" C VAL U 152 " ideal model delta sigma weight residual 113.20 104.66 8.54 9.60e-01 1.09e+00 7.91e+01 angle pdb=" C HIS U1013 " pdb=" N PHE U1014 " pdb=" CA PHE U1014 " ideal model delta sigma weight residual 120.82 131.96 -11.14 1.50e+00 4.44e-01 5.52e+01 angle pdb=" N ILE U 158 " pdb=" CA ILE U 158 " pdb=" C ILE U 158 " ideal model delta sigma weight residual 113.53 106.72 6.81 9.80e-01 1.04e+00 4.83e+01 angle pdb=" N ILE U 221 " pdb=" CA ILE U 221 " pdb=" C ILE U 221 " ideal model delta sigma weight residual 111.91 105.90 6.01 8.90e-01 1.26e+00 4.56e+01 angle pdb=" N VAL U1017 " pdb=" CA VAL U1017 " pdb=" C VAL U1017 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 ... (remaining 12801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5084 15.42 - 30.84: 471 30.84 - 46.25: 112 46.25 - 61.67: 4 61.67 - 77.09: 15 Dihedral angle restraints: 5686 sinusoidal: 2275 harmonic: 3411 Sorted by residual: dihedral pdb=" CA PRO U1039 " pdb=" C PRO U1039 " pdb=" N SER U1040 " pdb=" CA SER U1040 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA ARG U 181 " pdb=" C ARG U 181 " pdb=" N ILE U 182 " pdb=" CA ILE U 182 " ideal model delta harmonic sigma weight residual 180.00 149.73 30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA ILE U 362 " pdb=" C ILE U 362 " pdb=" N PHE U 363 " pdb=" CA PHE U 363 " ideal model delta harmonic sigma weight residual 180.00 150.24 29.76 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 5683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 989 0.063 - 0.126: 380 0.126 - 0.189: 66 0.189 - 0.251: 20 0.251 - 0.314: 7 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB VAL U 764 " pdb=" CA VAL U 764 " pdb=" CG1 VAL U 764 " pdb=" CG2 VAL U 764 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE U 221 " pdb=" CA ILE U 221 " pdb=" CG1 ILE U 221 " pdb=" CG2 ILE U 221 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL U 248 " pdb=" CA VAL U 248 " pdb=" CG1 VAL U 248 " pdb=" CG2 VAL U 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1459 not shown) Planarity restraints: 1631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 TCH U1401 " 0.142 2.00e-02 2.50e+03 1.65e-01 3.39e+02 pdb=" C24 TCH U1401 " -0.054 2.00e-02 2.50e+03 pdb=" C25 TCH U1401 " 0.198 2.00e-02 2.50e+03 pdb=" N24 TCH U1401 " -0.270 2.00e-02 2.50e+03 pdb=" O24 TCH U1401 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " 0.051 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO U 970 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN U 76 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO U 77 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO U 77 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO U 77 " 0.042 5.00e-02 4.00e+02 ... (remaining 1628 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2053 2.77 - 3.30: 8542 3.30 - 3.83: 14514 3.83 - 4.37: 16969 4.37 - 4.90: 28369 Nonbonded interactions: 70447 Sorted by model distance: nonbonded pdb=" OD1 ASP U 864 " pdb=" OG SER U1047 " model vdw 2.233 3.040 nonbonded pdb=" O SER U 809 " pdb=" OG SER U 809 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR U 145 " pdb=" O2S TCH U1401 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR U 355 " pdb=" OG1 THR U 358 " model vdw 2.260 3.040 nonbonded pdb=" O THR U 155 " pdb=" OG1 THR U 155 " model vdw 2.262 3.040 ... (remaining 70442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.012 0.137 9465 Z= 0.812 Angle : 1.391 25.169 12806 Z= 0.775 Chirality : 0.069 0.314 1462 Planarity : 0.009 0.165 1631 Dihedral : 13.322 77.090 3496 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.65 % Favored : 88.27 % Rotamer: Outliers : 0.81 % Allowed : 8.91 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -6.43 (0.15), residues: 1185 helix: -4.74 (0.08), residues: 637 sheet: -4.05 (0.64), residues: 37 loop : -3.46 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP U 314 HIS 0.022 0.003 HIS U 72 PHE 0.031 0.004 PHE U 363 TYR 0.034 0.004 TYR U 178 ARG 0.009 0.001 ARG U 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: U 123 MET cc_start: 0.3728 (mtp) cc_final: 0.2894 (ttm) REVERT: U 183 MET cc_start: 0.8632 (mmm) cc_final: 0.8096 (mmm) REVERT: U 205 ASP cc_start: 0.8685 (t0) cc_final: 0.8440 (t0) REVERT: U 217 MET cc_start: 0.8143 (tpp) cc_final: 0.7781 (tpt) REVERT: U 252 ILE cc_start: 0.7727 (tt) cc_final: 0.6928 (mt) REVERT: U 442 ASN cc_start: 0.8085 (m-40) cc_final: 0.7852 (m-40) REVERT: U 453 LEU cc_start: 0.7903 (tm) cc_final: 0.7688 (tt) REVERT: U 478 MET cc_start: 0.7594 (ppp) cc_final: 0.6893 (ppp) REVERT: U 492 GLN cc_start: 0.8508 (mm110) cc_final: 0.7674 (tm-30) REVERT: U 600 VAL cc_start: 0.8954 (t) cc_final: 0.8745 (t) REVERT: U 863 THR cc_start: 0.8222 (m) cc_final: 0.7954 (t) REVERT: U 891 ILE cc_start: 0.8531 (mm) cc_final: 0.8174 (mt) REVERT: U 921 MET cc_start: 0.7516 (tmt) cc_final: 0.6862 (tmt) REVERT: U 1111 PHE cc_start: 0.8693 (m-10) cc_final: 0.8158 (m-10) REVERT: U 1299 THR cc_start: 0.4668 (OUTLIER) cc_final: 0.4310 (m) outliers start: 8 outliers final: 1 residues processed: 216 average time/residue: 0.2602 time to fit residues: 74.1874 Evaluate side-chains 123 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 170 GLN U 492 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 ASN U 605 GLN U 640 HIS U 842 GLN U1142 HIS U1196 GLN U1258 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125299 restraints weight = 13959.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120325 restraints weight = 9099.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121327 restraints weight = 11454.136| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9465 Z= 0.320 Angle : 0.773 19.070 12806 Z= 0.397 Chirality : 0.045 0.167 1462 Planarity : 0.005 0.049 1631 Dihedral : 8.482 84.671 1359 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.14 % Allowed : 13.77 % Favored : 83.10 % 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: -5.65 (0.18), residues: 1185 helix: -4.02 (0.12), residues: 647 sheet: -3.99 (0.68), residues: 42 loop : -3.11 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 314 HIS 0.003 0.001 HIS U1013 PHE 0.012 0.002 PHE U 783 TYR 0.015 0.002 TYR U 178 ARG 0.004 0.001 ARG U 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.965 Fit side-chains REVERT: U 123 MET cc_start: 0.3764 (mtp) cc_final: 0.3345 (mtp) REVERT: U 132 LEU cc_start: 0.8284 (tp) cc_final: 0.7710 (tp) REVERT: U 177 PHE cc_start: 0.8042 (t80) cc_final: 0.7737 (t80) REVERT: U 217 MET cc_start: 0.8064 (tpp) cc_final: 0.7673 (tpt) REVERT: U 297 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: U 335 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6933 (mt) REVERT: U 380 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8445 (tt) REVERT: U 413 LEU cc_start: 0.8806 (tt) cc_final: 0.8333 (mp) REVERT: U 414 ASP cc_start: 0.7863 (p0) cc_final: 0.7544 (p0) REVERT: U 443 MET cc_start: 0.8538 (ppp) cc_final: 0.8036 (ppp) REVERT: U 453 LEU cc_start: 0.7999 (tm) cc_final: 0.7646 (tt) REVERT: U 492 GLN cc_start: 0.8423 (mm-40) cc_final: 0.7714 (tm-30) REVERT: U 629 PHE cc_start: 0.7104 (p90) cc_final: 0.6434 (p90) REVERT: U 643 LEU cc_start: 0.6430 (tp) cc_final: 0.6154 (tp) REVERT: U 755 MET cc_start: 0.7054 (mtm) cc_final: 0.6827 (mtm) REVERT: U 823 SER cc_start: 0.8878 (t) cc_final: 0.8670 (t) REVERT: U 879 ILE cc_start: 0.8700 (tp) cc_final: 0.8336 (pt) REVERT: U 891 ILE cc_start: 0.8202 (mm) cc_final: 0.7929 (mt) REVERT: U 928 ARG cc_start: 0.7376 (ttt180) cc_final: 0.7114 (ttt180) REVERT: U 1111 PHE cc_start: 0.8538 (m-10) cc_final: 0.7896 (m-10) REVERT: U 1146 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8181 (mmtt) REVERT: U 1202 MET cc_start: 0.5174 (mmm) cc_final: 0.4145 (mtm) REVERT: U 1221 ARG cc_start: 0.8268 (ptt180) cc_final: 0.8003 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8206 (mtmm) REVERT: U 1271 ILE cc_start: 0.9299 (mm) cc_final: 0.8966 (mm) REVERT: U 1299 THR cc_start: 0.4111 (OUTLIER) cc_final: 0.3894 (m) REVERT: U 1304 MET cc_start: 0.7404 (mpt) cc_final: 0.7064 (mpp) outliers start: 31 outliers final: 11 residues processed: 160 average time/residue: 0.2397 time to fit residues: 55.2225 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 619 THR Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126834 restraints weight = 14028.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122592 restraints weight = 9763.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123111 restraints weight = 11604.417| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9465 Z= 0.292 Angle : 0.696 19.277 12806 Z= 0.353 Chirality : 0.043 0.142 1462 Planarity : 0.004 0.038 1631 Dihedral : 7.862 83.066 1359 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.25 % Allowed : 13.77 % Favored : 81.98 % 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: -5.16 (0.20), residues: 1185 helix: -3.58 (0.15), residues: 648 sheet: -3.88 (0.70), residues: 42 loop : -2.95 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 60 HIS 0.003 0.001 HIS U1142 PHE 0.012 0.001 PHE U 363 TYR 0.013 0.002 TYR U 178 ARG 0.003 0.000 ARG U 928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 177 PHE cc_start: 0.7999 (t80) cc_final: 0.7692 (t80) REVERT: U 197 GLU cc_start: 0.8172 (tp30) cc_final: 0.7626 (tp30) REVERT: U 217 MET cc_start: 0.8040 (tpp) cc_final: 0.7616 (tpt) REVERT: U 335 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6942 (mt) REVERT: U 359 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8930 (tt) REVERT: U 380 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (tt) REVERT: U 413 LEU cc_start: 0.8820 (tt) cc_final: 0.8419 (mp) REVERT: U 453 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7708 (tt) REVERT: U 629 PHE cc_start: 0.7044 (p90) cc_final: 0.6405 (p90) REVERT: U 743 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: U 891 ILE cc_start: 0.8295 (mm) cc_final: 0.8061 (mt) REVERT: U 1111 PHE cc_start: 0.8495 (m-10) cc_final: 0.7878 (m-10) REVERT: U 1224 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8232 (mtmt) REVERT: U 1271 ILE cc_start: 0.9226 (mm) cc_final: 0.8858 (mm) REVERT: U 1304 MET cc_start: 0.7454 (mpt) cc_final: 0.7155 (mpp) outliers start: 42 outliers final: 22 residues processed: 160 average time/residue: 0.2022 time to fit residues: 46.3517 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 192 CYS Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 524 THR Chi-restraints excluded: chain U residue 540 PHE Chi-restraints excluded: chain U residue 548 PHE Chi-restraints excluded: chain U residue 567 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1079 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 640 HIS U 842 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.180439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127434 restraints weight = 13960.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123468 restraints weight = 8079.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123982 restraints weight = 8955.614| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9465 Z= 0.162 Angle : 0.652 19.095 12806 Z= 0.318 Chirality : 0.040 0.136 1462 Planarity : 0.004 0.035 1631 Dihedral : 7.114 82.928 1358 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.73 % Allowed : 16.80 % Favored : 80.47 % 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: -4.66 (0.21), residues: 1185 helix: -3.21 (0.16), residues: 659 sheet: -3.36 (0.76), residues: 41 loop : -2.67 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 189 HIS 0.003 0.001 HIS U1013 PHE 0.014 0.001 PHE U 363 TYR 0.013 0.001 TYR U 157 ARG 0.003 0.000 ARG U 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8328 (tp) cc_final: 0.8034 (tp) REVERT: U 177 PHE cc_start: 0.7809 (t80) cc_final: 0.7498 (t80) REVERT: U 197 GLU cc_start: 0.8110 (tp30) cc_final: 0.7557 (tp30) REVERT: U 217 MET cc_start: 0.7638 (tpp) cc_final: 0.7271 (tpt) REVERT: U 232 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8236 (mm) REVERT: U 290 THR cc_start: 0.9119 (p) cc_final: 0.8909 (t) REVERT: U 413 LEU cc_start: 0.8855 (tt) cc_final: 0.8415 (mp) REVERT: U 450 MET cc_start: 0.7557 (pmm) cc_final: 0.6987 (ppp) REVERT: U 453 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7703 (tt) REVERT: U 478 MET cc_start: 0.7502 (ppp) cc_final: 0.7246 (ppp) REVERT: U 629 PHE cc_start: 0.7082 (p90) cc_final: 0.6498 (p90) REVERT: U 910 PHE cc_start: 0.8077 (m-10) cc_final: 0.7813 (m-10) REVERT: U 1111 PHE cc_start: 0.8560 (m-10) cc_final: 0.8030 (m-10) REVERT: U 1202 MET cc_start: 0.5157 (mmm) cc_final: 0.4181 (mtm) REVERT: U 1224 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8035 (tmtt) REVERT: U 1304 MET cc_start: 0.7731 (mpt) cc_final: 0.7391 (mpp) outliers start: 27 outliers final: 12 residues processed: 142 average time/residue: 0.2396 time to fit residues: 51.3143 Evaluate side-chains 117 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 232 LEU Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 1013 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 0.0040 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 842 GLN U 996 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.184419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131205 restraints weight = 13854.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127485 restraints weight = 9875.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128046 restraints weight = 8903.399| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9465 Z= 0.148 Angle : 0.629 18.073 12806 Z= 0.303 Chirality : 0.041 0.198 1462 Planarity : 0.003 0.032 1631 Dihedral : 6.647 79.027 1358 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.73 % Allowed : 18.93 % Favored : 78.34 % 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: -4.16 (0.22), residues: 1185 helix: -2.87 (0.17), residues: 667 sheet: -2.85 (1.11), residues: 24 loop : -2.39 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 493 HIS 0.003 0.001 HIS U1013 PHE 0.011 0.001 PHE U 363 TYR 0.017 0.001 TYR U 157 ARG 0.003 0.000 ARG U1153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.200 Fit side-chains REVERT: U 154 ILE cc_start: 0.8457 (tp) cc_final: 0.8146 (tp) REVERT: U 157 TYR cc_start: 0.7973 (t80) cc_final: 0.7768 (t80) REVERT: U 177 PHE cc_start: 0.7764 (t80) cc_final: 0.7449 (t80) REVERT: U 183 MET cc_start: 0.8540 (mmm) cc_final: 0.8221 (mmm) REVERT: U 197 GLU cc_start: 0.8104 (tp30) cc_final: 0.7601 (tp30) REVERT: U 217 MET cc_start: 0.7530 (tpp) cc_final: 0.7130 (tpt) REVERT: U 232 LEU cc_start: 0.8731 (tt) cc_final: 0.8230 (mm) REVERT: U 290 THR cc_start: 0.8939 (p) cc_final: 0.8735 (t) REVERT: U 362 ILE cc_start: 0.9002 (pp) cc_final: 0.8737 (pt) REVERT: U 380 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7943 (tt) REVERT: U 413 LEU cc_start: 0.8643 (tt) cc_final: 0.8407 (mp) REVERT: U 450 MET cc_start: 0.7629 (pmm) cc_final: 0.7164 (ppp) REVERT: U 453 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7739 (mp) REVERT: U 629 PHE cc_start: 0.7077 (p90) cc_final: 0.6458 (p90) REVERT: U 910 PHE cc_start: 0.8069 (m-10) cc_final: 0.7858 (m-10) REVERT: U 1111 PHE cc_start: 0.8601 (m-10) cc_final: 0.8096 (m-10) REVERT: U 1202 MET cc_start: 0.4965 (mmm) cc_final: 0.3973 (mtm) REVERT: U 1221 ARG cc_start: 0.8174 (ptt-90) cc_final: 0.7208 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8532 (mtmm) cc_final: 0.7970 (tmtt) REVERT: U 1304 MET cc_start: 0.7577 (mpt) cc_final: 0.7262 (mpp) outliers start: 27 outliers final: 12 residues processed: 137 average time/residue: 0.2372 time to fit residues: 46.3724 Evaluate side-chains 119 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 453 LEU Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 844 ILE Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.187089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120184 restraints weight = 14024.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123037 restraints weight = 8522.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124873 restraints weight = 6214.282| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9465 Z= 0.351 Angle : 0.720 16.836 12806 Z= 0.350 Chirality : 0.045 0.181 1462 Planarity : 0.004 0.080 1631 Dihedral : 6.969 77.081 1357 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.15 % Allowed : 18.72 % Favored : 77.13 % 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: -4.15 (0.22), residues: 1185 helix: -2.85 (0.17), residues: 649 sheet: -3.13 (0.86), residues: 34 loop : -2.39 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 493 HIS 0.003 0.001 HIS U1013 PHE 0.010 0.002 PHE U 70 TYR 0.012 0.002 TYR U 178 ARG 0.003 0.000 ARG U 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8838 (tp) cc_final: 0.8531 (tp) REVERT: U 177 PHE cc_start: 0.7956 (t80) cc_final: 0.7722 (t80) REVERT: U 197 GLU cc_start: 0.8281 (tp30) cc_final: 0.7884 (tp30) REVERT: U 217 MET cc_start: 0.8138 (tpp) cc_final: 0.7712 (tpt) REVERT: U 290 THR cc_start: 0.9096 (p) cc_final: 0.8875 (t) REVERT: U 371 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8426 (mp) REVERT: U 380 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8533 (tt) REVERT: U 443 MET cc_start: 0.8403 (ppp) cc_final: 0.7786 (ppp) REVERT: U 450 MET cc_start: 0.7621 (pmm) cc_final: 0.7239 (ppp) REVERT: U 629 PHE cc_start: 0.7038 (p90) cc_final: 0.6484 (p90) REVERT: U 1111 PHE cc_start: 0.8571 (m-10) cc_final: 0.8082 (m-10) REVERT: U 1202 MET cc_start: 0.5230 (mmm) cc_final: 0.4005 (mtm) REVERT: U 1221 ARG cc_start: 0.8173 (ptt-90) cc_final: 0.7784 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8067 (tmtt) REVERT: U 1304 MET cc_start: 0.7958 (mpt) cc_final: 0.7605 (mpp) outliers start: 41 outliers final: 26 residues processed: 141 average time/residue: 0.2483 time to fit residues: 52.9690 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 263 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 422 PHE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 548 PHE Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 775 LEU Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1121 THR Chi-restraints excluded: chain U residue 1139 ILE Chi-restraints excluded: chain U residue 1285 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 63 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 598 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 842 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.189371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123570 restraints weight = 14072.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126545 restraints weight = 8370.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128550 restraints weight = 6049.299| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9465 Z= 0.219 Angle : 0.662 16.733 12806 Z= 0.318 Chirality : 0.043 0.172 1462 Planarity : 0.004 0.062 1631 Dihedral : 6.785 80.790 1357 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.25 % Allowed : 19.13 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.00 (0.22), residues: 1185 helix: -2.72 (0.17), residues: 651 sheet: -2.99 (0.89), residues: 34 loop : -2.33 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 493 HIS 0.003 0.001 HIS U1013 PHE 0.011 0.001 PHE U 363 TYR 0.010 0.001 TYR U 178 ARG 0.002 0.000 ARG U1235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: U 153 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8397 (tp) REVERT: U 154 ILE cc_start: 0.8796 (tp) cc_final: 0.8476 (tp) REVERT: U 177 PHE cc_start: 0.7791 (t80) cc_final: 0.7508 (t80) REVERT: U 197 GLU cc_start: 0.8212 (tp30) cc_final: 0.7820 (tp30) REVERT: U 217 MET cc_start: 0.7919 (tpp) cc_final: 0.7595 (tpt) REVERT: U 232 LEU cc_start: 0.8708 (tt) cc_final: 0.8326 (mm) REVERT: U 290 THR cc_start: 0.9105 (p) cc_final: 0.8883 (t) REVERT: U 362 ILE cc_start: 0.9005 (pp) cc_final: 0.8721 (pt) REVERT: U 371 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8351 (mp) REVERT: U 380 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8425 (tt) REVERT: U 450 MET cc_start: 0.7574 (pmm) cc_final: 0.7241 (ppp) REVERT: U 453 LEU cc_start: 0.7770 (tt) cc_final: 0.7552 (mp) REVERT: U 629 PHE cc_start: 0.6869 (p90) cc_final: 0.6403 (p90) REVERT: U 890 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8462 (mmm) REVERT: U 1035 PHE cc_start: 0.6888 (t80) cc_final: 0.6621 (t80) REVERT: U 1111 PHE cc_start: 0.8597 (m-10) cc_final: 0.8197 (m-10) REVERT: U 1202 MET cc_start: 0.5317 (mmm) cc_final: 0.4100 (mtm) REVERT: U 1221 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7842 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8008 (tmtt) REVERT: U 1304 MET cc_start: 0.7969 (mpt) cc_final: 0.7717 (mpp) outliers start: 42 outliers final: 27 residues processed: 143 average time/residue: 0.1853 time to fit residues: 39.1795 Evaluate side-chains 135 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 153 LEU Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 263 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 380 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 548 PHE Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 775 LEU Chi-restraints excluded: chain U residue 794 GLN Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 890 MET Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 546 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.194325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130214 restraints weight = 14233.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133999 restraints weight = 9221.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133434 restraints weight = 6094.777| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9465 Z= 0.160 Angle : 0.649 16.519 12806 Z= 0.306 Chirality : 0.041 0.175 1462 Planarity : 0.003 0.050 1631 Dihedral : 6.405 79.166 1357 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.74 % Allowed : 20.24 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.69 (0.22), residues: 1185 helix: -2.42 (0.18), residues: 661 sheet: -2.30 (1.13), residues: 25 loop : -2.31 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 PHE 0.016 0.001 PHE U 363 TYR 0.009 0.001 TYR U 178 ARG 0.004 0.000 ARG U 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: U 74 ILE cc_start: 0.8960 (tt) cc_final: 0.8711 (tt) REVERT: U 154 ILE cc_start: 0.8835 (tp) cc_final: 0.8550 (tp) REVERT: U 177 PHE cc_start: 0.7698 (t80) cc_final: 0.7369 (t80) REVERT: U 197 GLU cc_start: 0.8145 (tp30) cc_final: 0.7684 (tp30) REVERT: U 217 MET cc_start: 0.7860 (tpp) cc_final: 0.7477 (tpt) REVERT: U 232 LEU cc_start: 0.8741 (tt) cc_final: 0.8351 (mm) REVERT: U 290 THR cc_start: 0.9136 (p) cc_final: 0.8917 (t) REVERT: U 362 ILE cc_start: 0.9006 (pp) cc_final: 0.8722 (pt) REVERT: U 443 MET cc_start: 0.8703 (ppp) cc_final: 0.7964 (ppp) REVERT: U 450 MET cc_start: 0.7519 (pmm) cc_final: 0.7154 (ppp) REVERT: U 461 LYS cc_start: 0.7649 (ptpp) cc_final: 0.7137 (mmmt) REVERT: U 478 MET cc_start: 0.7308 (ppp) cc_final: 0.6822 (ppp) REVERT: U 559 MET cc_start: 0.6184 (mtt) cc_final: 0.5765 (mtt) REVERT: U 629 PHE cc_start: 0.6938 (p90) cc_final: 0.6493 (p90) REVERT: U 878 MET cc_start: 0.7981 (tpp) cc_final: 0.7364 (tmm) REVERT: U 910 PHE cc_start: 0.8060 (m-10) cc_final: 0.7826 (m-10) REVERT: U 925 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6201 (t80) REVERT: U 964 GLU cc_start: 0.8430 (mp0) cc_final: 0.8191 (mp0) REVERT: U 1056 ASP cc_start: 0.7897 (t70) cc_final: 0.7643 (p0) REVERT: U 1111 PHE cc_start: 0.8541 (m-10) cc_final: 0.8190 (m-10) REVERT: U 1138 MET cc_start: 0.5686 (tpp) cc_final: 0.4989 (tmm) REVERT: U 1202 MET cc_start: 0.5959 (mmm) cc_final: 0.4782 (mtm) REVERT: U 1221 ARG cc_start: 0.8216 (ptt-90) cc_final: 0.7830 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8001 (tmtt) REVERT: U 1304 MET cc_start: 0.7935 (mpt) cc_final: 0.7686 (mpp) outliers start: 37 outliers final: 25 residues processed: 140 average time/residue: 0.2138 time to fit residues: 44.6122 Evaluate side-chains 138 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 174 MET Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 363 PHE Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1139 ILE Chi-restraints excluded: chain U residue 1285 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 22 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.8092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.194499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128359 restraints weight = 13889.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131280 restraints weight = 8221.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133378 restraints weight = 5943.697| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9465 Z= 0.166 Angle : 0.637 16.099 12806 Z= 0.301 Chirality : 0.041 0.164 1462 Planarity : 0.003 0.046 1631 Dihedral : 6.240 76.777 1357 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.73 % Allowed : 21.76 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.55 (0.23), residues: 1185 helix: -2.26 (0.18), residues: 672 sheet: -2.24 (1.16), residues: 25 loop : -2.30 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 PHE 0.014 0.001 PHE U 363 TYR 0.009 0.001 TYR U 650 ARG 0.003 0.000 ARG U1235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: U 58 ASP cc_start: 0.8234 (t70) cc_final: 0.7789 (t0) REVERT: U 74 ILE cc_start: 0.8980 (tt) cc_final: 0.8752 (tt) REVERT: U 154 ILE cc_start: 0.8833 (tp) cc_final: 0.8538 (tp) REVERT: U 177 PHE cc_start: 0.7672 (t80) cc_final: 0.7335 (t80) REVERT: U 197 GLU cc_start: 0.8192 (tp30) cc_final: 0.7737 (tp30) REVERT: U 217 MET cc_start: 0.7854 (tpp) cc_final: 0.7516 (tpt) REVERT: U 232 LEU cc_start: 0.8747 (tt) cc_final: 0.8374 (mm) REVERT: U 290 THR cc_start: 0.9153 (p) cc_final: 0.8921 (t) REVERT: U 362 ILE cc_start: 0.8978 (pp) cc_final: 0.8694 (pt) REVERT: U 443 MET cc_start: 0.8320 (ppp) cc_final: 0.7536 (ppp) REVERT: U 450 MET cc_start: 0.7565 (pmm) cc_final: 0.7268 (ppp) REVERT: U 461 LYS cc_start: 0.7555 (ptpp) cc_final: 0.7182 (mmmt) REVERT: U 559 MET cc_start: 0.6331 (mtt) cc_final: 0.5952 (mtt) REVERT: U 629 PHE cc_start: 0.7176 (p90) cc_final: 0.6701 (p90) REVERT: U 878 MET cc_start: 0.8203 (tpp) cc_final: 0.7315 (tmm) REVERT: U 910 PHE cc_start: 0.8051 (m-10) cc_final: 0.7806 (m-10) REVERT: U 925 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6140 (t80) REVERT: U 964 GLU cc_start: 0.8421 (mp0) cc_final: 0.8173 (mp0) REVERT: U 1056 ASP cc_start: 0.7859 (t70) cc_final: 0.7599 (p0) REVERT: U 1138 MET cc_start: 0.5540 (tpp) cc_final: 0.5184 (tmm) REVERT: U 1202 MET cc_start: 0.5895 (mmm) cc_final: 0.4727 (mtm) REVERT: U 1224 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7831 (mtmt) REVERT: U 1304 MET cc_start: 0.7949 (mpt) cc_final: 0.7691 (mpp) outliers start: 27 outliers final: 22 residues processed: 133 average time/residue: 0.2153 time to fit residues: 41.0909 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 363 PHE Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 479 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1285 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 842 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.194605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129757 restraints weight = 14125.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132140 restraints weight = 9399.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132910 restraints weight = 6433.545| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9465 Z= 0.156 Angle : 0.646 16.111 12806 Z= 0.304 Chirality : 0.041 0.162 1462 Planarity : 0.003 0.042 1631 Dihedral : 6.051 75.727 1357 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.83 % Allowed : 21.86 % Favored : 75.30 % 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: -3.35 (0.23), residues: 1185 helix: -2.05 (0.18), residues: 678 sheet: -2.65 (0.90), residues: 34 loop : -2.25 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 493 HIS 0.004 0.000 HIS U1013 PHE 0.014 0.001 PHE U 363 TYR 0.008 0.001 TYR U 178 ARG 0.003 0.000 ARG U 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: U 58 ASP cc_start: 0.8363 (t70) cc_final: 0.7952 (t0) REVERT: U 154 ILE cc_start: 0.8776 (tp) cc_final: 0.8462 (tp) REVERT: U 177 PHE cc_start: 0.7624 (t80) cc_final: 0.7263 (t80) REVERT: U 197 GLU cc_start: 0.8167 (tp30) cc_final: 0.7800 (tp30) REVERT: U 217 MET cc_start: 0.7780 (tpp) cc_final: 0.7484 (tpt) REVERT: U 232 LEU cc_start: 0.8724 (tt) cc_final: 0.8336 (mm) REVERT: U 290 THR cc_start: 0.9129 (p) cc_final: 0.8896 (t) REVERT: U 362 ILE cc_start: 0.8970 (pp) cc_final: 0.8691 (pt) REVERT: U 443 MET cc_start: 0.8643 (ppp) cc_final: 0.7900 (ppp) REVERT: U 450 MET cc_start: 0.7528 (pmm) cc_final: 0.7185 (ppp) REVERT: U 461 LYS cc_start: 0.7475 (ptpp) cc_final: 0.7051 (mmmt) REVERT: U 559 MET cc_start: 0.6222 (mtt) cc_final: 0.5815 (mtt) REVERT: U 596 MET cc_start: 0.9080 (mmm) cc_final: 0.8860 (mmm) REVERT: U 878 MET cc_start: 0.8146 (tpp) cc_final: 0.7558 (tmm) REVERT: U 910 PHE cc_start: 0.8038 (m-10) cc_final: 0.7792 (m-10) REVERT: U 925 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5934 (t80) REVERT: U 964 GLU cc_start: 0.8403 (mp0) cc_final: 0.8131 (mp0) REVERT: U 1056 ASP cc_start: 0.7858 (t70) cc_final: 0.7540 (p0) REVERT: U 1146 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8205 (mmtm) REVERT: U 1202 MET cc_start: 0.5937 (mmm) cc_final: 0.4826 (mtm) REVERT: U 1224 LYS cc_start: 0.8251 (mtmm) cc_final: 0.8049 (tmtt) REVERT: U 1304 MET cc_start: 0.7865 (mpt) cc_final: 0.7625 (mpp) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.2029 time to fit residues: 38.4010 Evaluate side-chains 124 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 171 ILE Chi-restraints excluded: chain U residue 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 246 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 363 PHE Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 454 VAL Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 768 VAL Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1285 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.192881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126678 restraints weight = 14129.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129702 restraints weight = 8427.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131647 restraints weight = 6117.303| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9465 Z= 0.199 Angle : 0.667 16.150 12806 Z= 0.314 Chirality : 0.042 0.161 1462 Planarity : 0.003 0.044 1631 Dihedral : 6.090 74.653 1357 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.53 % Allowed : 22.37 % Favored : 75.10 % 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: -3.23 (0.23), residues: 1185 helix: -1.96 (0.19), residues: 671 sheet: -2.42 (0.88), residues: 34 loop : -2.19 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 PHE 0.014 0.001 PHE U 363 TYR 0.009 0.001 TYR U 178 ARG 0.008 0.000 ARG U 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.03 seconds wall clock time: 59 minutes 37.26 seconds (3577.26 seconds total)