Starting phenix.real_space_refine on Thu Jul 2 17:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_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_30938/07_2026/7e1a_30938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1a_30938/07_2026/7e1a_30938.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.77, per 1000 atoms: 0.19 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: 0.80 Conformation dependent library (CDL) restraints added in 311.8 milliseconds 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: 0.31 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: 1.31 Time building geometry restraints manager: 1.06 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: 5021 15.42 - 30.84: 467 30.84 - 46.25: 112 46.25 - 61.67: 4 61.67 - 77.09: 13 Dihedral angle restraints: 5617 sinusoidal: 2206 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 5614 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: 0.640 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.014 0.563 9466 Z= 0.794 Angle : 1.391 25.169 12806 Z= 0.775 Chirality : 0.069 0.314 1462 Planarity : 0.009 0.165 1631 Dihedral : 13.288 77.090 3427 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG U 832 TYR 0.034 0.004 TYR U 178 PHE 0.031 0.004 PHE U 363 TRP 0.035 0.003 TRP U 314 HIS 0.022 0.003 HIS U 72 Details of bonding type rmsd/Z covalent geometry : bond 0.01250 / 0.54 ( 9465) covalent geometry : angle 1.39056 / 0.77 (12806) hydrogen bonds : bond 0.31785 / 19.58 ( 193) hydrogen bonds : angle 11.04683 / 7.82 ( 561) Misc. bond : bond 0.56330 / 35.21 ( 1) *********************** 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 : 0.373 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: 0.8097 (mmm) REVERT: U 205 ASP cc_start: 0.8685 (t0) cc_final: 0.8439 (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: 0.6929 (mt) REVERT: U 442 ASN cc_start: 0.8085 (m-40) cc_final: 0.7851 (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: 0.6892 (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: 0.7953 (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: 0.4309 (m) outliers start: 8 outliers final: 1 residues processed: 216 average time/residue: 0.1095 time to fit residues: 31.6224 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 : 0.328 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 492 GLN U 503 GLN 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 = 0.4242 r_free = 0.4242 target = 0.179757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126555 restraints weight = 13927.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122451 restraints weight = 9563.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122787 restraints weight = 10436.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125367 restraints weight = 7047.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125270 restraints weight = 5221.991| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9466 Z= 0.173 Angle : 0.741 18.983 12806 Z= 0.380 Chirality : 0.044 0.158 1462 Planarity : 0.005 0.047 1631 Dihedral : 7.869 93.108 1290 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.83 % Allowed : 13.87 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.60 (0.18), residues: 1185 helix: -4.00 (0.12), residues: 643 sheet: -3.59 (0.75), residues: 37 loop : -3.15 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U1268 TYR 0.013 0.002 TYR U 274 PHE 0.011 0.001 PHE U 811 TRP 0.012 0.001 TRP U 189 HIS 0.003 0.001 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 9465) covalent geometry : angle 0.74076 / 0.38 (12806) hydrogen bonds : bond 0.04626 / 2.89 ( 193) hydrogen bonds : angle 6.12892 / 4.39 ( 561) Misc. bond : bond 0.00077 / 0.05 ( 1) *********************** 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 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.324 Fit side-chains REVERT: U 132 LEU cc_start: 0.8210 (tp) cc_final: 0.7558 (tp) REVERT: U 174 MET cc_start: 0.8308 (ttm) cc_final: 0.8103 (ttm) REVERT: U 177 PHE cc_start: 0.8052 (t80) cc_final: 0.7730 (t80) REVERT: U 217 MET cc_start: 0.8027 (tpp) cc_final: 0.7648 (tpt) REVERT: U 335 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6902 (mt) REVERT: U 380 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (tt) REVERT: U 413 LEU cc_start: 0.8801 (tt) cc_final: 0.8299 (mp) REVERT: U 443 MET cc_start: 0.8350 (ppp) cc_final: 0.7829 (ppp) REVERT: U 453 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7669 (tt) REVERT: U 492 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7676 (tm-30) REVERT: U 629 PHE cc_start: 0.7141 (p90) cc_final: 0.6492 (p90) REVERT: U 643 LEU cc_start: 0.6363 (tp) cc_final: 0.6121 (tp) REVERT: U 755 MET cc_start: 0.7021 (mtm) cc_final: 0.6794 (mtm) REVERT: U 823 SER cc_start: 0.8905 (t) cc_final: 0.8691 (t) REVERT: U 891 ILE cc_start: 0.8160 (mm) cc_final: 0.7903 (mt) REVERT: U 928 ARG cc_start: 0.7270 (ttt180) cc_final: 0.7006 (ttt180) REVERT: U 1111 PHE cc_start: 0.8519 (m-10) cc_final: 0.7872 (m-10) REVERT: U 1146 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8209 (mmtt) REVERT: U 1202 MET cc_start: 0.5133 (mmm) cc_final: 0.4123 (mtm) REVERT: U 1224 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8168 (mtmm) REVERT: U 1271 ILE cc_start: 0.9218 (mm) cc_final: 0.8898 (mm) REVERT: U 1299 THR cc_start: 0.4023 (OUTLIER) cc_final: 0.3815 (m) REVERT: U 1304 MET cc_start: 0.7431 (mpt) cc_final: 0.7066 (mpp) outliers start: 28 outliers final: 9 residues processed: 160 average time/residue: 0.0927 time to fit residues: 20.8440 Evaluate side-chains 129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 145 TYR 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 453 LEU Chi-restraints excluded: chain U residue 454 VAL 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 1299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.179316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127483 restraints weight = 13896.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121212 restraints weight = 10058.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122269 restraints weight = 10284.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123167 restraints weight = 6943.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124370 restraints weight = 6085.598| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9466 Z= 0.184 Angle : 0.695 19.018 12806 Z= 0.351 Chirality : 0.043 0.138 1462 Planarity : 0.004 0.039 1631 Dihedral : 7.337 93.065 1290 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.15 % Allowed : 14.27 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.13 (0.20), residues: 1185 helix: -3.57 (0.15), residues: 649 sheet: -3.68 (0.72), residues: 41 loop : -2.94 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 743 TYR 0.012 0.002 TYR U 178 PHE 0.012 0.001 PHE U 363 TRP 0.010 0.001 TRP U 60 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 9465) covalent geometry : angle 0.69521 / 0.35 (12806) hydrogen bonds : bond 0.03900 / 2.47 ( 193) hydrogen bonds : angle 5.63065 / 4.01 ( 561) Misc. bond : bond 0.00130 / 0.08 ( 1) *********************** 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 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: U 177 PHE cc_start: 0.7936 (t80) cc_final: 0.7630 (t80) REVERT: U 217 MET cc_start: 0.8049 (tpp) cc_final: 0.7601 (tpt) REVERT: U 335 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6901 (mt) REVERT: U 359 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8859 (tt) REVERT: U 380 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8376 (tt) REVERT: U 413 LEU cc_start: 0.8824 (tt) cc_final: 0.8364 (mp) REVERT: U 453 LEU cc_start: 0.7949 (tm) cc_final: 0.7697 (tt) REVERT: U 629 PHE cc_start: 0.7172 (p90) cc_final: 0.6520 (p90) REVERT: U 743 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7917 (mmm-85) REVERT: U 891 ILE cc_start: 0.8296 (mm) cc_final: 0.8063 (mt) REVERT: U 1111 PHE cc_start: 0.8555 (m-10) cc_final: 0.7847 (m-10) REVERT: U 1175 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6116 (mttm) REVERT: U 1202 MET cc_start: 0.5112 (mmm) cc_final: 0.3920 (mtm) REVERT: U 1224 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8263 (mtmt) REVERT: U 1271 ILE cc_start: 0.9208 (mm) cc_final: 0.8798 (mm) REVERT: U 1304 MET cc_start: 0.7603 (mpt) cc_final: 0.7291 (mpp) outliers start: 41 outliers final: 19 residues processed: 157 average time/residue: 0.0841 time to fit residues: 19.2543 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 145 TYR Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 263 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 454 VAL Chi-restraints excluded: chain U residue 479 VAL 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 Chi-restraints excluded: chain U residue 1175 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 170 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 640 HIS U 842 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124818 restraints weight = 14181.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119788 restraints weight = 9757.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120504 restraints weight = 9270.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121678 restraints weight = 6382.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122562 restraints weight = 5518.934| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9466 Z= 0.189 Angle : 0.693 18.704 12806 Z= 0.344 Chirality : 0.043 0.142 1462 Planarity : 0.004 0.033 1631 Dihedral : 7.032 93.990 1289 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.95 % Allowed : 15.99 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.21), residues: 1185 helix: -3.27 (0.16), residues: 641 sheet: -3.41 (0.93), residues: 31 loop : -2.75 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 928 TYR 0.012 0.001 TYR U 178 PHE 0.012 0.001 PHE U 363 TRP 0.011 0.001 TRP U 314 HIS 0.002 0.001 HIS U 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 9465) covalent geometry : angle 0.69311 / 0.34 (12806) hydrogen bonds : bond 0.03505 / 2.18 ( 193) hydrogen bonds : angle 5.40805 / 3.86 ( 561) Misc. bond : bond 0.00138 / 0.09 ( 1) *********************** 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 156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.395 Fit side-chains REVERT: U 154 ILE cc_start: 0.8251 (tp) cc_final: 0.7949 (tp) REVERT: U 177 PHE cc_start: 0.7919 (t80) cc_final: 0.7621 (t80) REVERT: U 197 GLU cc_start: 0.8099 (tp30) cc_final: 0.7664 (tp30) REVERT: U 217 MET cc_start: 0.8081 (tpp) cc_final: 0.7527 (tpt) REVERT: U 290 THR cc_start: 0.9168 (p) cc_final: 0.8958 (t) REVERT: U 335 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6966 (mt) REVERT: U 359 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8691 (tt) REVERT: U 373 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8321 (tt) REVERT: U 380 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8312 (tt) REVERT: U 413 LEU cc_start: 0.8930 (tt) cc_final: 0.8393 (mp) REVERT: U 453 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7645 (tt) REVERT: U 629 PHE cc_start: 0.7127 (p90) cc_final: 0.6464 (p90) REVERT: U 743 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.6921 (mpp-170) REVERT: U 755 MET cc_start: 0.6916 (mtm) cc_final: 0.6641 (mtm) REVERT: U 891 ILE cc_start: 0.8340 (mm) cc_final: 0.8120 (mt) REVERT: U 1111 PHE cc_start: 0.8597 (m-10) cc_final: 0.8035 (m-10) REVERT: U 1221 ARG cc_start: 0.8359 (ptt-90) cc_final: 0.7581 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8147 (tmtt) REVERT: U 1225 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8336 (tp-100) REVERT: U 1304 MET cc_start: 0.7890 (mpt) cc_final: 0.7534 (mpp) outliers start: 39 outliers final: 18 residues processed: 150 average time/residue: 0.0907 time to fit residues: 19.5854 Evaluate side-chains 125 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 263 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 373 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 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 888 VAL Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 497 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 = 0.4193 r_free = 0.4193 target = 0.178037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114884 restraints weight = 14130.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115427 restraints weight = 9436.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115901 restraints weight = 6553.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116170 restraints weight = 6221.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116483 restraints weight = 5768.864| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9466 Z= 0.159 Angle : 0.669 18.748 12806 Z= 0.328 Chirality : 0.043 0.178 1462 Planarity : 0.004 0.032 1631 Dihedral : 6.729 94.564 1289 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.74 % Allowed : 17.81 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.21), residues: 1185 helix: -3.07 (0.16), residues: 650 sheet: -3.55 (0.92), residues: 30 loop : -2.49 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 517 TYR 0.014 0.001 TYR U 274 PHE 0.012 0.001 PHE U 363 TRP 0.010 0.001 TRP U 314 HIS 0.003 0.001 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9465) covalent geometry : angle 0.66857 / 0.33 (12806) hydrogen bonds : bond 0.03246 / 2.02 ( 193) hydrogen bonds : angle 5.17826 / 3.68 ( 561) Misc. bond : bond 0.00119 / 0.07 ( 1) *********************** 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 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.359 Fit side-chains REVERT: U 154 ILE cc_start: 0.8433 (tp) cc_final: 0.8152 (tp) REVERT: U 177 PHE cc_start: 0.7874 (t80) cc_final: 0.7538 (t80) REVERT: U 197 GLU cc_start: 0.8187 (tp30) cc_final: 0.7683 (tp30) REVERT: U 205 ASP cc_start: 0.8727 (t0) cc_final: 0.8500 (t0) REVERT: U 217 MET cc_start: 0.8229 (tpp) cc_final: 0.7688 (tpt) REVERT: U 290 THR cc_start: 0.9287 (p) cc_final: 0.9064 (t) REVERT: U 335 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6908 (mt) REVERT: U 380 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (tt) REVERT: U 413 LEU cc_start: 0.8914 (tt) cc_final: 0.8284 (mp) REVERT: U 453 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7604 (tt) REVERT: U 629 PHE cc_start: 0.7110 (p90) cc_final: 0.6415 (p90) REVERT: U 891 ILE cc_start: 0.8346 (mm) cc_final: 0.8133 (mt) REVERT: U 1111 PHE cc_start: 0.8690 (m-10) cc_final: 0.7907 (m-10) REVERT: U 1202 MET cc_start: 0.5343 (mmm) cc_final: 0.4336 (mtm) REVERT: U 1224 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8131 (tmtt) REVERT: U 1225 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8262 (tp-100) REVERT: U 1304 MET cc_start: 0.8071 (mpt) cc_final: 0.7727 (mpp) outliers start: 37 outliers final: 23 residues processed: 138 average time/residue: 0.0856 time to fit residues: 17.5533 Evaluate side-chains 131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 145 TYR Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 263 VAL Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 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 567 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 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.0000 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 536 ASN ** 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 = 0.4235 r_free = 0.4235 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128840 restraints weight = 14077.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124514 restraints weight = 9280.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125362 restraints weight = 8693.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126072 restraints weight = 6219.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126610 restraints weight = 5559.231| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9466 Z= 0.097 Angle : 0.633 17.891 12806 Z= 0.303 Chirality : 0.041 0.172 1462 Planarity : 0.003 0.031 1631 Dihedral : 6.146 94.949 1289 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.14 % Allowed : 19.23 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.22), residues: 1185 helix: -2.74 (0.17), residues: 663 sheet: -3.00 (0.89), residues: 34 loop : -2.39 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U1153 TYR 0.017 0.001 TYR U 274 PHE 0.013 0.001 PHE U 363 TRP 0.006 0.001 TRP U 493 HIS 0.004 0.001 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 9465) covalent geometry : angle 0.63341 / 0.30 (12806) hydrogen bonds : bond 0.02696 / 1.66 ( 193) hydrogen bonds : angle 4.74434 / 3.41 ( 561) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** 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 147 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8310 (tp) cc_final: 0.8007 (tp) REVERT: U 177 PHE cc_start: 0.7676 (t80) cc_final: 0.7257 (t80) REVERT: U 197 GLU cc_start: 0.8126 (tp30) cc_final: 0.7641 (tp30) REVERT: U 205 ASP cc_start: 0.8662 (t0) cc_final: 0.8442 (t0) REVERT: U 217 MET cc_start: 0.7629 (tpp) cc_final: 0.7148 (tpt) REVERT: U 232 LEU cc_start: 0.8754 (tt) cc_final: 0.8240 (mm) REVERT: U 290 THR cc_start: 0.9148 (p) cc_final: 0.8921 (t) REVERT: U 362 ILE cc_start: 0.8901 (pp) cc_final: 0.8611 (pt) REVERT: U 413 LEU cc_start: 0.8912 (tt) cc_final: 0.8389 (mp) REVERT: U 443 MET cc_start: 0.8582 (ppp) cc_final: 0.7987 (ppp) REVERT: U 478 MET cc_start: 0.7548 (ppp) cc_final: 0.7304 (ppp) REVERT: U 596 MET cc_start: 0.9090 (mmm) cc_final: 0.8868 (mmm) REVERT: U 629 PHE cc_start: 0.7059 (p90) cc_final: 0.6433 (p90) REVERT: U 910 PHE cc_start: 0.8053 (m-10) cc_final: 0.7848 (m-10) REVERT: U 1202 MET cc_start: 0.5084 (mmm) cc_final: 0.4078 (mtm) REVERT: U 1224 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8011 (tmtt) REVERT: U 1304 MET cc_start: 0.7790 (mpt) cc_final: 0.7498 (mpp) outliers start: 31 outliers final: 18 residues processed: 140 average time/residue: 0.0823 time to fit residues: 17.0481 Evaluate side-chains 119 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 403 ILE 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 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 834 PHE 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 1285 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 0.0040 chunk 115 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4182 r_free = 0.4182 target = 0.177196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125818 restraints weight = 14121.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123006 restraints weight = 9602.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122151 restraints weight = 10629.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123166 restraints weight = 6926.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123576 restraints weight = 5497.603| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9466 Z= 0.196 Angle : 0.695 17.445 12806 Z= 0.336 Chirality : 0.045 0.176 1462 Planarity : 0.004 0.034 1631 Dihedral : 6.429 93.471 1288 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.74 % Allowed : 20.04 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.22), residues: 1185 helix: -2.76 (0.17), residues: 656 sheet: -2.90 (0.91), residues: 34 loop : -2.32 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 299 TYR 0.012 0.001 TYR U 157 PHE 0.010 0.001 PHE U1111 TRP 0.023 0.001 TRP U 493 HIS 0.003 0.001 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 9465) covalent geometry : angle 0.69476 / 0.34 (12806) hydrogen bonds : bond 0.03267 / 2.03 ( 193) hydrogen bonds : angle 5.00658 / 3.55 ( 561) Misc. bond : bond 0.00129 / 0.08 ( 1) *********************** 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 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.358 Fit side-chains REVERT: U 123 MET cc_start: 0.0474 (mmm) cc_final: -0.0403 (mmp) REVERT: U 154 ILE cc_start: 0.8171 (tp) cc_final: 0.7889 (tp) REVERT: U 177 PHE cc_start: 0.7985 (t80) cc_final: 0.7606 (t80) REVERT: U 197 GLU cc_start: 0.8202 (tp30) cc_final: 0.7773 (tp30) REVERT: U 217 MET cc_start: 0.8179 (tpp) cc_final: 0.7889 (tpt) REVERT: U 224 MET cc_start: 0.7670 (tpp) cc_final: 0.7410 (tpt) REVERT: U 413 LEU cc_start: 0.8696 (tt) cc_final: 0.8331 (mp) REVERT: U 443 MET cc_start: 0.8570 (ppp) cc_final: 0.7650 (ppp) REVERT: U 629 PHE cc_start: 0.6950 (p90) cc_final: 0.6344 (p90) REVERT: U 890 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8524 (mmm) REVERT: U 925 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6786 (t80) REVERT: U 1078 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8809 (mm) REVERT: U 1202 MET cc_start: 0.5090 (mmm) cc_final: 0.4079 (mtm) REVERT: U 1221 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7857 (ptt-90) REVERT: U 1224 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8064 (tmtt) REVERT: U 1304 MET cc_start: 0.7805 (mpt) cc_final: 0.7598 (mpp) outliers start: 37 outliers final: 25 residues processed: 134 average time/residue: 0.0826 time to fit residues: 16.3947 Evaluate side-chains 134 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 182 ILE Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 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 580 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 757 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 839 MET 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 925 PHE Chi-restraints excluded: chain U residue 1013 HIS Chi-restraints excluded: chain U residue 1014 PHE Chi-restraints excluded: chain U residue 1078 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 72 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 106 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 996 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.180878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127199 restraints weight = 14003.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122400 restraints weight = 8909.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122950 restraints weight = 9658.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125441 restraints weight = 6777.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125596 restraints weight = 5176.575| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9466 Z= 0.112 Angle : 0.662 17.960 12806 Z= 0.312 Chirality : 0.041 0.168 1462 Planarity : 0.003 0.031 1631 Dihedral : 6.021 95.527 1288 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.24 % Allowed : 21.05 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.23), residues: 1185 helix: -2.52 (0.18), residues: 650 sheet: -2.83 (0.92), residues: 34 loop : -2.19 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U1235 TYR 0.022 0.001 TYR U 274 PHE 0.012 0.001 PHE U 363 TRP 0.017 0.001 TRP U 493 HIS 0.004 0.000 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 9465) covalent geometry : angle 0.66219 / 0.31 (12806) hydrogen bonds : bond 0.02746 / 1.72 ( 193) hydrogen bonds : angle 4.67302 / 3.35 ( 561) Misc. bond : bond 0.00107 / 0.07 ( 1) *********************** 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 142 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.347 Fit side-chains REVERT: U 123 MET cc_start: 0.0647 (mmm) cc_final: 0.0376 (mmp) REVERT: U 154 ILE cc_start: 0.8387 (tp) cc_final: 0.8082 (tp) REVERT: U 177 PHE cc_start: 0.7755 (t80) cc_final: 0.7392 (t80) REVERT: U 197 GLU cc_start: 0.8139 (tp30) cc_final: 0.7605 (tp30) REVERT: U 217 MET cc_start: 0.7745 (tpp) cc_final: 0.7249 (tpt) REVERT: U 232 LEU cc_start: 0.8769 (tt) cc_final: 0.8239 (mm) REVERT: U 290 THR cc_start: 0.9117 (p) cc_final: 0.8890 (t) REVERT: U 362 ILE cc_start: 0.8970 (pp) cc_final: 0.8702 (pt) REVERT: U 413 LEU cc_start: 0.8965 (tt) cc_final: 0.8539 (mp) REVERT: U 443 MET cc_start: 0.8588 (ppp) cc_final: 0.7826 (ppp) REVERT: U 461 LYS cc_start: 0.7684 (ptpp) cc_final: 0.7217 (mmmt) REVERT: U 478 MET cc_start: 0.7529 (ppp) cc_final: 0.7303 (ppp) REVERT: U 559 MET cc_start: 0.6315 (mtt) cc_final: 0.5914 (mtt) REVERT: U 596 MET cc_start: 0.9088 (mmm) cc_final: 0.8833 (mmm) REVERT: U 629 PHE cc_start: 0.6927 (p90) cc_final: 0.6362 (p90) REVERT: U 910 PHE cc_start: 0.8103 (m-10) cc_final: 0.7874 (m-10) REVERT: U 925 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6381 (t80) REVERT: U 1138 MET cc_start: 0.5835 (tpp) cc_final: 0.5097 (tmm) REVERT: U 1202 MET cc_start: 0.5117 (mmm) cc_final: 0.4170 (mtm) REVERT: U 1224 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7943 (tmtt) REVERT: U 1304 MET cc_start: 0.7844 (mpt) cc_final: 0.7631 (mpp) outliers start: 32 outliers final: 25 residues processed: 132 average time/residue: 0.0847 time to fit residues: 16.4083 Evaluate side-chains 125 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 403 ILE 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 580 LEU Chi-restraints excluded: chain U residue 582 LEU Chi-restraints excluded: chain U residue 587 SER Chi-restraints excluded: chain U residue 617 LEU Chi-restraints excluded: chain U residue 757 VAL Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 888 VAL Chi-restraints excluded: chain U residue 925 PHE 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 1123 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 68 optimal weight: 0.0270 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4234 r_free = 0.4234 target = 0.182199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130711 restraints weight = 13964.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127064 restraints weight = 9323.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127895 restraints weight = 10793.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128996 restraints weight = 7027.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129897 restraints weight = 5821.504| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9466 Z= 0.106 Angle : 0.646 17.806 12806 Z= 0.304 Chirality : 0.041 0.162 1462 Planarity : 0.003 0.032 1631 Dihedral : 5.767 94.110 1288 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.73 % Allowed : 21.56 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.23), residues: 1185 helix: -2.32 (0.18), residues: 651 sheet: -2.27 (1.18), residues: 25 loop : -2.25 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U1128 TYR 0.020 0.001 TYR U 274 PHE 0.015 0.001 PHE U 363 TRP 0.006 0.001 TRP U 314 HIS 0.004 0.000 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9465) covalent geometry : angle 0.64592 / 0.30 (12806) hydrogen bonds : bond 0.02658 / 1.66 ( 193) hydrogen bonds : angle 4.51938 / 3.25 ( 561) Misc. bond : bond 0.00093 / 0.06 ( 1) *********************** 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 140 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.405 Fit side-chains REVERT: U 58 ASP cc_start: 0.8452 (t70) cc_final: 0.7894 (t0) REVERT: U 60 TRP cc_start: 0.6857 (m-10) cc_final: 0.6560 (m100) REVERT: U 123 MET cc_start: 0.0366 (mmm) cc_final: 0.0058 (mmp) REVERT: U 154 ILE cc_start: 0.8393 (tp) cc_final: 0.8097 (tp) REVERT: U 177 PHE cc_start: 0.7782 (t80) cc_final: 0.7367 (t80) REVERT: U 183 MET cc_start: 0.8538 (mmm) cc_final: 0.8227 (mmm) REVERT: U 197 GLU cc_start: 0.8177 (tp30) cc_final: 0.7697 (tp30) REVERT: U 217 MET cc_start: 0.7704 (tpp) cc_final: 0.7192 (tpt) REVERT: U 232 LEU cc_start: 0.8736 (tt) cc_final: 0.8227 (mm) REVERT: U 290 THR cc_start: 0.9058 (p) cc_final: 0.8824 (t) REVERT: U 362 ILE cc_start: 0.8953 (pp) cc_final: 0.8633 (pt) REVERT: U 413 LEU cc_start: 0.8924 (tt) cc_final: 0.8390 (mp) REVERT: U 443 MET cc_start: 0.8418 (ppp) cc_final: 0.7847 (ppp) REVERT: U 461 LYS cc_start: 0.7671 (ptpp) cc_final: 0.7219 (mmmt) REVERT: U 559 MET cc_start: 0.6385 (mtt) cc_final: 0.5982 (mtt) REVERT: U 629 PHE cc_start: 0.6948 (p90) cc_final: 0.6485 (p90) REVERT: U 878 MET cc_start: 0.8244 (tpp) cc_final: 0.7214 (tmm) REVERT: U 910 PHE cc_start: 0.8113 (m-10) cc_final: 0.7877 (m-10) REVERT: U 1043 LYS cc_start: 0.8547 (ptmt) cc_final: 0.7928 (pttp) REVERT: U 1146 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8088 (mmtm) REVERT: U 1202 MET cc_start: 0.5726 (mmm) cc_final: 0.4760 (mtm) REVERT: U 1224 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7732 (mtmt) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.0932 time to fit residues: 17.4198 Evaluate side-chains 125 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 252 ILE 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 757 VAL Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET 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 1123 ILE 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 5 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 536 ASN U 598 GLN ** U 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115925 restraints weight = 14032.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119394 restraints weight = 7824.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121658 restraints weight = 5390.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123012 restraints weight = 4344.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123712 restraints weight = 3838.201| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9466 Z= 0.114 Angle : 0.666 17.378 12806 Z= 0.311 Chirality : 0.041 0.158 1462 Planarity : 0.003 0.032 1631 Dihedral : 5.684 93.538 1288 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.73 % Allowed : 21.86 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.23), residues: 1185 helix: -2.14 (0.18), residues: 657 sheet: -2.26 (1.17), residues: 25 loop : -2.27 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 487 TYR 0.026 0.001 TYR U 274 PHE 0.013 0.001 PHE U 363 TRP 0.005 0.001 TRP U 314 HIS 0.004 0.001 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 9465) covalent geometry : angle 0.66589 / 0.31 (12806) hydrogen bonds : bond 0.02646 / 1.65 ( 193) hydrogen bonds : angle 4.48654 / 3.22 ( 561) Misc. bond : bond 0.00107 / 0.07 ( 1) ********************** 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 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.290 Fit side-chains REVERT: U 58 ASP cc_start: 0.8364 (t70) cc_final: 0.7862 (t0) REVERT: U 60 TRP cc_start: 0.6885 (m-10) cc_final: 0.6645 (m100) REVERT: U 123 MET cc_start: 0.0651 (mmm) cc_final: 0.0365 (mmp) REVERT: U 154 ILE cc_start: 0.8772 (tp) cc_final: 0.8441 (tp) REVERT: U 177 PHE cc_start: 0.7731 (t80) cc_final: 0.7320 (t80) REVERT: U 197 GLU cc_start: 0.8230 (tp30) cc_final: 0.7737 (tp30) REVERT: U 217 MET cc_start: 0.8013 (tpp) cc_final: 0.7564 (tpt) REVERT: U 232 LEU cc_start: 0.8797 (tt) cc_final: 0.8277 (mm) REVERT: U 290 THR cc_start: 0.9243 (p) cc_final: 0.9016 (t) REVERT: U 362 ILE cc_start: 0.8952 (pp) cc_final: 0.8643 (pt) REVERT: U 413 LEU cc_start: 0.8880 (tt) cc_final: 0.8310 (mp) REVERT: U 443 MET cc_start: 0.8478 (ppp) cc_final: 0.7987 (ppp) REVERT: U 461 LYS cc_start: 0.7671 (ptpp) cc_final: 0.7205 (mmmt) REVERT: U 478 MET cc_start: 0.7131 (ppp) cc_final: 0.6653 (ppp) REVERT: U 559 MET cc_start: 0.6258 (mtt) cc_final: 0.5852 (mtt) REVERT: U 629 PHE cc_start: 0.7172 (p90) cc_final: 0.6598 (p90) REVERT: U 878 MET cc_start: 0.8143 (tpp) cc_final: 0.7031 (tmm) REVERT: U 910 PHE cc_start: 0.8131 (m-10) cc_final: 0.7879 (m-10) REVERT: U 925 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6148 (t80) REVERT: U 1043 LYS cc_start: 0.8492 (ptmt) cc_final: 0.7970 (pttp) REVERT: U 1138 MET cc_start: 0.5766 (tpp) cc_final: 0.5484 (tmm) REVERT: U 1146 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7991 (mmtm) REVERT: U 1202 MET cc_start: 0.5832 (mmm) cc_final: 0.4900 (mtm) REVERT: U 1224 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7813 (mtmt) outliers start: 27 outliers final: 22 residues processed: 124 average time/residue: 0.0840 time to fit residues: 15.4428 Evaluate side-chains 125 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 176 LYS Chi-restraints excluded: chain U residue 182 ILE Chi-restraints excluded: chain U residue 244 VAL Chi-restraints excluded: chain U residue 252 ILE 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 757 VAL Chi-restraints excluded: chain U residue 823 SER Chi-restraints excluded: chain U residue 834 PHE Chi-restraints excluded: chain U residue 839 MET 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 1014 PHE Chi-restraints excluded: chain U residue 1121 THR 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 22 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 50.0000 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4282 r_free = 0.4282 target = 0.184007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120691 restraints weight = 14045.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123600 restraints weight = 8525.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124482 restraints weight = 5985.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124518 restraints weight = 5254.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124648 restraints weight = 5212.992| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9466 Z= 0.107 Angle : 0.654 17.158 12806 Z= 0.305 Chirality : 0.041 0.155 1462 Planarity : 0.003 0.033 1631 Dihedral : 5.555 93.319 1288 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.73 % Allowed : 22.06 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.23), residues: 1185 helix: -1.99 (0.19), residues: 648 sheet: -2.58 (0.91), residues: 34 loop : -2.18 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 487 TYR 0.025 0.001 TYR U 274 PHE 0.014 0.001 PHE U 363 TRP 0.005 0.001 TRP U 314 HIS 0.004 0.000 HIS U1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9465) covalent geometry : angle 0.65418 / 0.30 (12806) hydrogen bonds : bond 0.02601 / 1.63 ( 193) hydrogen bonds : angle 4.40606 / 3.16 ( 561) Misc. bond : bond 0.00101 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1638.04 seconds wall clock time: 29 minutes 4.78 seconds (1744.78 seconds total)