Starting phenix.real_space_refine on Thu Jul 2 17:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dv5_30870/07_2026/7dv5_30870.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 56 5.16 5 C 5977 2.51 5 N 1567 2.21 5 O 1719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 9319 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'TCH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9319 At special positions: 0 Unit cell: (91.91, 157.56, 96.96, 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 56 16.00 O 1719 8.00 N 1567 7.00 C 5977 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: 0.97 Conformation dependent library (CDL) restraints added in 288.9 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: 63 helices and 3 sheets defined 44.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'U' and resid 55 through 59 removed outlier: 3.992A pdb=" N ILE U 59 " --> pdb=" O SER U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 87 removed outlier: 4.652A pdb=" N LEU U 80 " --> pdb=" O GLN U 76 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU U 81 " --> pdb=" O PRO U 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE U 82 " --> pdb=" O GLY U 78 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR U 87 " --> pdb=" O PHE U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 99 removed outlier: 4.158A pdb=" N GLU U 96 " --> pdb=" O ASP U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 149 removed outlier: 3.701A pdb=" N ILE U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER U 143 " --> pdb=" O ILE U 139 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR U 144 " --> pdb=" O LYS U 140 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA U 146 " --> pdb=" O ALA U 142 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY U 147 " --> pdb=" O SER U 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 154 Processing helix chain 'U' and resid 157 through 162 Processing helix chain 'U' and resid 164 through 168 removed outlier: 3.656A pdb=" N ALA U 167 " --> pdb=" O VAL U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 182 removed outlier: 3.914A pdb=" N LYS U 176 " --> pdb=" O GLN U 172 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE U 179 " --> pdb=" O ARG U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 192 removed outlier: 3.609A pdb=" N ASP U 191 " --> pdb=" O ILE U 187 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS U 192 " --> pdb=" O GLY U 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 187 through 192' Processing helix chain 'U' and resid 214 through 222 removed outlier: 4.600A pdb=" N ALA U 218 " --> pdb=" O ALA U 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU U 219 " --> pdb=" O ASP U 215 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE U 220 " --> pdb=" O GLN U 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 236 removed outlier: 3.835A pdb=" N GLY U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 243 removed outlier: 3.716A pdb=" N THR U 242 " --> pdb=" O GLY U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 244 through 248 Processing helix chain 'U' and resid 250 through 255 removed outlier: 3.777A pdb=" N GLY U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 275 removed outlier: 3.984A pdb=" N TYR U 269 " --> pdb=" O LYS U 265 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU U 271 " --> pdb=" O THR U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 294 removed outlier: 3.902A pdb=" N VAL U 291 " --> pdb=" O SER U 287 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA U 292 " --> pdb=" O MET U 288 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA U 293 " --> pdb=" O ARG U 289 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE U 294 " --> pdb=" O THR U 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 287 through 294' Processing helix chain 'U' and resid 296 through 301 removed outlier: 4.044A pdb=" N VAL U 301 " --> pdb=" O GLU U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 306 Processing helix chain 'U' and resid 320 through 335 removed outlier: 3.834A pdb=" N THR U 326 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY U 327 " --> pdb=" O GLY U 323 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU U 332 " --> pdb=" O PHE U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 341 Processing helix chain 'U' and resid 342 through 350 removed outlier: 3.935A pdb=" N THR U 346 " --> pdb=" O TRP U 342 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU U 347 " --> pdb=" O TYR U 343 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL U 348 " --> pdb=" O GLY U 344 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 375 removed outlier: 3.609A pdb=" N VAL U 366 " --> pdb=" O ILE U 362 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN U 372 " --> pdb=" O VAL U 368 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU U 373 " --> pdb=" O GLY U 369 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY U 374 " --> pdb=" O ALA U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 390 Processing helix chain 'U' and resid 392 through 397 removed outlier: 3.501A pdb=" N THR U 396 " --> pdb=" O SER U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 497 removed outlier: 3.924A pdb=" N ASP U 496 " --> pdb=" O GLN U 492 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN U 497 " --> pdb=" O TRP U 493 " (cutoff:3.500A) Processing helix chain 'U' and resid 524 through 535 removed outlier: 3.962A pdb=" N VAL U 529 " --> pdb=" O MET U 525 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN U 530 " --> pdb=" O GLU U 526 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU U 534 " --> pdb=" O GLN U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 537 through 543 removed outlier: 3.862A pdb=" N ASP U 543 " --> pdb=" O ASN U 539 " (cutoff:3.500A) Processing helix chain 'U' and resid 560 through 563 Processing helix chain 'U' and resid 564 through 574 removed outlier: 3.687A pdb=" N ALA U 568 " --> pdb=" O LYS U 564 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE U 569 " --> pdb=" O GLN U 565 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA U 570 " --> pdb=" O ARG U 566 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 603 removed outlier: 3.682A pdb=" N VAL U 600 " --> pdb=" O MET U 596 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU U 601 " --> pdb=" O VAL U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 652 through 656 removed outlier: 3.811A pdb=" N THR U 655 " --> 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: 3.908A 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 753 through 761 Processing helix chain 'U' and resid 767 through 780 removed outlier: 3.519A pdb=" N TYR U 772 " --> pdb=" O VAL U 768 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA U 773 " --> pdb=" O THR U 769 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE U 774 " --> pdb=" O PRO U 770 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER U 777 " --> pdb=" O ALA U 773 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN U 778 " --> pdb=" O PHE U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 789 through 794 removed outlier: 3.741A pdb=" N SER U 793 " --> pdb=" O GLU U 789 " (cutoff:3.500A) Processing helix chain 'U' and resid 802 through 810 removed outlier: 3.884A pdb=" N VAL U 808 " --> pdb=" O ALA U 804 " (cutoff:3.500A) Processing helix chain 'U' and resid 811 through 819 Processing helix chain 'U' and resid 819 through 841 removed outlier: 3.828A pdb=" N GLY U 824 " --> pdb=" O PHE U 820 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU U 825 " --> pdb=" O ALA U 821 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR U 828 " --> pdb=" O GLY U 824 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG U 830 " --> pdb=" O LEU U 826 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG U 832 " --> pdb=" O THR U 828 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS U 833 " --> pdb=" O LYS U 829 " (cutoff:3.500A) Processing helix chain 'U' and resid 868 through 880 removed outlier: 3.920A pdb=" N ALA U 872 " --> pdb=" O VAL U 868 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER U 874 " --> pdb=" O GLY U 870 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN U 875 " --> pdb=" O ALA U 871 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE U 876 " --> pdb=" O ALA U 872 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY U 877 " --> pdb=" O GLY U 873 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET U 878 " --> pdb=" O SER U 874 " (cutoff:3.500A) Processing helix chain 'U' and resid 887 through 897 removed outlier: 3.910A pdb=" N PHE U 896 " --> pdb=" O ILE U 892 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER U 897 " --> pdb=" O ALA U 893 " (cutoff:3.500A) Processing helix chain 'U' and resid 900 through 905 removed outlier: 3.881A pdb=" N ILE U 904 " --> pdb=" O LEU U 900 " (cutoff:3.500A) Processing helix chain 'U' and resid 908 through 917 removed outlier: 3.593A pdb=" N ALA U 912 " --> pdb=" O PHE U 908 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU U 913 " --> pdb=" O PRO U 909 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER U 914 " --> pdb=" O PHE U 910 " (cutoff:3.500A) Processing helix chain 'U' and resid 922 through 926 Processing helix chain 'U' and resid 929 through 933 Processing helix chain 'U' and resid 935 through 940 Processing helix chain 'U' and resid 947 through 952 removed outlier: 3.518A pdb=" N ALA U 951 " --> pdb=" O ILE U 947 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY U 952 " --> pdb=" O ARG U 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 947 through 952' Processing helix chain 'U' and resid 965 through 967 No H-bonds generated for 'chain 'U' and resid 965 through 967' Processing helix chain 'U' and resid 968 through 973 removed outlier: 3.682A pdb=" N THR U 973 " --> pdb=" O LYS U 969 " (cutoff:3.500A) Processing helix chain 'U' and resid 991 through 996 Processing helix chain 'U' and resid 996 through 1009 removed outlier: 3.733A pdb=" N ARG U1001 " --> pdb=" O SER U 997 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR U1002 " --> pdb=" O ALA U 998 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU U1006 " --> pdb=" O TYR U1002 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER U1008 " --> pdb=" O GLY U1004 " (cutoff:3.500A) Processing helix chain 'U' and resid 1014 through 1019 removed outlier: 3.921A pdb=" N PHE U1018 " --> pdb=" O PHE U1014 " (cutoff:3.500A) Processing helix chain 'U' and resid 1029 through 1034 removed outlier: 3.612A pdb=" N ALA U1034 " --> pdb=" O ALA U1030 " (cutoff:3.500A) Processing helix chain 'U' and resid 1047 through 1056 removed outlier: 3.771A pdb=" N PHE U1051 " --> pdb=" O SER U1047 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE U1052 " --> pdb=" O ALA U1048 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN U1053 " --> pdb=" O ALA U1049 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP U1056 " --> pdb=" O PHE U1052 " (cutoff:3.500A) Processing helix chain 'U' and resid 1119 through 1125 removed outlier: 3.570A pdb=" N ILE U1123 " --> pdb=" O LYS U1119 " (cutoff:3.500A) Processing helix chain 'U' and resid 1148 through 1154 removed outlier: 3.514A pdb=" N LEU U1152 " --> pdb=" O ASN U1148 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER U1154 " --> pdb=" O GLN U1150 " (cutoff:3.500A) Processing helix chain 'U' and resid 1170 through 1176 Processing helix chain 'U' and resid 1185 through 1191 removed outlier: 4.029A pdb=" N ILE U1189 " --> pdb=" O MET U1185 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA U1190 " --> pdb=" O GLU U1186 " (cutoff:3.500A) Processing helix chain 'U' and resid 1220 through 1223 Processing helix chain 'U' and resid 1224 through 1234 removed outlier: 3.604A pdb=" N ALA U1230 " --> pdb=" O ARG U1226 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA U1232 " --> pdb=" O ALA U1228 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U1233 " --> pdb=" O ILE U1229 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL U1234 " --> pdb=" O ALA U1230 " (cutoff:3.500A) Processing helix chain 'U' and resid 1250 through 1264 removed outlier: 3.717A pdb=" N THR U1256 " --> pdb=" O GLU U1252 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA U1260 " --> pdb=" O THR U1256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP U1262 " --> pdb=" O GLN U1258 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS U1263 " --> pdb=" O VAL U1259 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA U1264 " --> pdb=" O ALA U1260 " (cutoff:3.500A) Processing helix chain 'U' and resid 1299 through 1303 removed outlier: 3.734A pdb=" N LEU U1303 " --> pdb=" O HIS U1300 " (cutoff:3.500A) Processing helix chain 'U' and resid 1308 through 1315 removed outlier: 3.644A pdb=" N LYS U1312 " --> pdb=" O GLY U1308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU U1313 " --> pdb=" O ALA U1309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 420 through 426 removed outlier: 3.627A pdb=" N ILE U 420 " --> pdb=" O ILE U 445 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET U 443 " --> pdb=" O PHE U 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN U 424 " --> pdb=" O LEU U 441 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU U 441 " --> pdb=" O ASN U 424 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR U 426 " --> pdb=" O ASN U 439 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN U 439 " --> pdb=" O THR U 426 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 498 through 501 removed outlier: 6.236A pdb=" N LEU U 580 " --> pdb=" O ILE U 611 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 1156 through 1159 removed outlier: 6.775A pdb=" N GLY U1157 " --> pdb=" O LEU U1241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 183 hydrogen bonds defined for protein. 513 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: 1.27 Time building geometry restraints manager: 1.22 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: 2531 1.33 - 1.45: 1907 1.45 - 1.57: 4975 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9503 Sorted by residual: bond pdb=" CG1 ILE U 171 " pdb=" CD1 ILE U 171 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.43e+01 bond pdb=" O3S TCH U1401 " pdb=" S26 TCH U1401 " ideal model delta sigma weight residual 1.475 1.548 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O3S TCH U1402 " pdb=" S26 TCH U1402 " ideal model delta sigma weight residual 1.475 1.547 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N VAL U 348 " pdb=" CA VAL U 348 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 9.19e+00 bond pdb=" N ILE U1280 " pdb=" CA ILE U1280 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 9498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.13: 12820 8.13 - 16.26: 39 16.26 - 24.39: 4 24.39 - 32.52: 1 32.52 - 40.65: 2 Bond angle restraints: 12866 Sorted by residual: angle pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" C ARG U 920 " ideal model delta sigma weight residual 110.80 151.45 -40.65 2.13e+00 2.20e-01 3.64e+02 angle pdb=" N ILE U 112 " pdb=" CA ILE U 112 " pdb=" C ILE U 112 " ideal model delta sigma weight residual 110.62 132.26 -21.64 1.14e+00 7.69e-01 3.60e+02 angle pdb=" C ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta sigma weight residual 110.42 75.84 34.58 1.99e+00 2.53e-01 3.02e+02 angle pdb=" N THR U 111 " pdb=" CA THR U 111 " pdb=" C THR U 111 " ideal model delta sigma weight residual 108.00 82.83 25.17 1.48e+00 4.57e-01 2.89e+02 angle pdb=" C THR U 111 " pdb=" CA THR U 111 " pdb=" CB THR U 111 " ideal model delta sigma weight residual 116.34 137.97 -21.63 1.40e+00 5.10e-01 2.39e+02 ... (remaining 12861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.22: 5254 20.22 - 40.44: 315 40.44 - 60.66: 37 60.66 - 80.88: 16 80.88 - 101.10: 2 Dihedral angle restraints: 5624 sinusoidal: 2213 harmonic: 3411 Sorted by residual: dihedral pdb=" C THR U1279 " pdb=" N THR U1279 " pdb=" CA THR U1279 " pdb=" CB THR U1279 " ideal model delta harmonic sigma weight residual -122.00 -98.92 -23.08 0 2.50e+00 1.60e-01 8.52e+01 dihedral pdb=" C ARG U 920 " pdb=" N ARG U 920 " pdb=" CA ARG U 920 " pdb=" CB ARG U 920 " ideal model delta harmonic sigma weight residual -122.60 -100.02 -22.58 0 2.50e+00 1.60e-01 8.16e+01 dihedral pdb=" N MET U 921 " pdb=" C MET U 921 " pdb=" CA MET U 921 " pdb=" CB MET U 921 " ideal model delta harmonic sigma weight residual 122.80 102.72 20.08 0 2.50e+00 1.60e-01 6.45e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 1441 0.194 - 0.388: 27 0.388 - 0.581: 1 0.581 - 0.775: 3 0.775 - 0.969: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CA ARG U 920 " pdb=" N ARG U 920 " pdb=" C ARG U 920 " pdb=" CB ARG U 920 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA THR U1279 " pdb=" N THR U1279 " pdb=" C THR U1279 " pdb=" CB THR U1279 " both_signs ideal model delta sigma weight residual False 2.53 3.22 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA ILE U 112 " pdb=" N ILE U 112 " pdb=" C ILE U 112 " pdb=" CB ILE U 112 " both_signs ideal model delta sigma weight residual False 2.43 1.76 0.67 2.00e-01 2.50e+01 1.14e+01 ... (remaining 1470 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 TCH U1401 " -0.113 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C24 TCH U1401 " 0.043 2.00e-02 2.50e+03 pdb=" C25 TCH U1401 " -0.153 2.00e-02 2.50e+03 pdb=" N24 TCH U1401 " 0.203 2.00e-02 2.50e+03 pdb=" O24 TCH U1401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR U 769 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO U 770 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 770 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO U 770 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS U 969 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO U 970 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO U 970 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO U 970 " -0.041 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 56 2.53 - 3.12: 6619 3.12 - 3.71: 13728 3.71 - 4.31: 18822 4.31 - 4.90: 30814 Nonbonded interactions: 70039 Sorted by model distance: nonbonded pdb=" O ARG U 920 " pdb=" CB ARG U 920 " model vdw 1.936 2.752 nonbonded pdb=" OD1 ASP U 350 " pdb=" N GLU U 351 " model vdw 2.014 3.120 nonbonded pdb=" N THR U 111 " pdb=" O THR U 111 " model vdw 2.079 2.496 nonbonded pdb=" N THR U1279 " pdb=" O THR U1279 " model vdw 2.257 2.496 nonbonded pdb=" C SER U1278 " pdb=" O THR U1279 " model vdw 2.272 3.270 ... (remaining 70034 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: 0.520 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 0.843 9504 Z= 0.989 Angle : 1.462 40.646 12866 Z= 0.824 Chirality : 0.083 0.969 1473 Planarity : 0.008 0.126 1632 Dihedral : 13.902 101.104 3434 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.73 % Favored : 88.19 % Rotamer: Outliers : 2.23 % Allowed : 8.81 % Favored : 88.97 % Cbeta Deviations : 0.55 % 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: -6.60 (0.15), residues: 1185 helix: -4.90 (0.07), residues: 634 sheet: -4.65 (0.54), residues: 26 loop : -3.52 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG U1001 TYR 0.028 0.003 TYR U 981 PHE 0.026 0.003 PHE U 629 TRP 0.023 0.003 TRP U 163 HIS 0.009 0.002 HIS U 72 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.48 ( 9503) covalent geometry : angle 1.46224 / 0.82 (12866) hydrogen bonds : bond 0.33037 / 21.43 ( 183) hydrogen bonds : angle 11.16376 / 7.66 ( 513) Misc. bond : bond 0.84260 / 52.66 ( 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 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: U 268 ASP cc_start: 0.7978 (m-30) cc_final: 0.7694 (t0) REVERT: U 424 ASN cc_start: 0.5405 (p0) cc_final: 0.4737 (p0) REVERT: U 426 THR cc_start: 0.7168 (t) cc_final: 0.6866 (p) REVERT: U 478 MET cc_start: 0.6556 (ppp) cc_final: 0.5940 (mmt) REVERT: U 516 ILE cc_start: 0.9009 (mt) cc_final: 0.8713 (mm) REVERT: U 533 LYS cc_start: 0.7873 (tttm) cc_final: 0.7368 (pttt) REVERT: U 913 LEU cc_start: 0.8529 (tm) cc_final: 0.8062 (mt) REVERT: U 918 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.5911 (tp-100) REVERT: U 925 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.3421 (p90) REVERT: U 946 ASN cc_start: 0.8606 (p0) cc_final: 0.8400 (p0) REVERT: U 1033 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (ttp80) REVERT: U 1037 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: U 1145 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7573 (ptmt) REVERT: U 1161 GLN cc_start: 0.6938 (tt0) cc_final: 0.6567 (tp40) REVERT: U 1221 ARG cc_start: 0.6777 (ttp-170) cc_final: 0.6565 (ttp-170) REVERT: U 1261 LEU cc_start: 0.8459 (mp) cc_final: 0.8225 (mt) outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.1136 time to fit residues: 31.0168 Evaluate side-chains 129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 343 TYR Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 651 PHE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 921 MET Chi-restraints excluded: chain U residue 925 PHE Chi-restraints excluded: chain U residue 1029 THR Chi-restraints excluded: chain U residue 1033 ARG Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 72 HIS U 110 ASN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 867 GLN U1107 GLN U1124 GLN U1258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125466 restraints weight = 13590.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125062 restraints weight = 8362.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125884 restraints weight = 7136.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126225 restraints weight = 5748.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126587 restraints weight = 4907.696| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9504 Z= 0.137 Angle : 0.689 8.289 12866 Z= 0.355 Chirality : 0.043 0.153 1473 Planarity : 0.005 0.053 1632 Dihedral : 9.069 81.703 1326 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.34 % Allowed : 13.77 % Favored : 82.89 % 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: -5.79 (0.17), residues: 1185 helix: -4.16 (0.12), residues: 640 sheet: -3.77 (0.72), residues: 26 loop : -3.25 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U1128 TYR 0.018 0.002 TYR U1176 PHE 0.013 0.001 PHE U1085 TRP 0.014 0.001 TRP U 330 HIS 0.004 0.001 HIS U 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9503) covalent geometry : angle 0.68867 / 0.35 (12866) hydrogen bonds : bond 0.04011 / 2.63 ( 183) hydrogen bonds : angle 5.56883 / 3.84 ( 513) Misc. bond : bond 0.00049 / 0.03 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8251 (m-10) cc_final: 0.7965 (m-80) REVERT: U 154 ILE cc_start: 0.8821 (tp) cc_final: 0.8257 (tp) REVERT: U 173 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: U 191 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: U 424 ASN cc_start: 0.5346 (p0) cc_final: 0.4999 (p0) REVERT: U 478 MET cc_start: 0.6499 (ppp) cc_final: 0.5757 (mmt) REVERT: U 533 LYS cc_start: 0.7625 (tttm) cc_final: 0.7250 (pttt) REVERT: U 576 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7312 (t0) REVERT: U 610 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7892 (mp) REVERT: U 913 LEU cc_start: 0.8460 (tm) cc_final: 0.7948 (mt) REVERT: U 918 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5473 (tp-100) REVERT: U 920 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.4976 (mtt90) REVERT: U 921 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4481 (ttp) REVERT: U 928 ARG cc_start: 0.7161 (tpt170) cc_final: 0.5994 (ptp90) REVERT: U 946 ASN cc_start: 0.8427 (p0) cc_final: 0.8214 (p0) REVERT: U 966 GLU cc_start: 0.7684 (tp30) cc_final: 0.7442 (tp30) REVERT: U 1037 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: U 1145 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7482 (ptmt) REVERT: U 1161 GLN cc_start: 0.6933 (tt0) cc_final: 0.6486 (tp40) REVERT: U 1171 MET cc_start: 0.8192 (tmm) cc_final: 0.7825 (tmm) REVERT: U 1270 CYS cc_start: 0.7571 (t) cc_final: 0.6830 (m) outliers start: 33 outliers final: 8 residues processed: 164 average time/residue: 0.0982 time to fit residues: 22.0958 Evaluate side-chains 131 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 921 MET Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.168548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128025 restraints weight = 13581.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125544 restraints weight = 10911.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126504 restraints weight = 9909.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127034 restraints weight = 7511.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127752 restraints weight = 6310.848| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9504 Z= 0.142 Angle : 0.636 7.994 12866 Z= 0.326 Chirality : 0.043 0.145 1473 Planarity : 0.004 0.046 1632 Dihedral : 8.075 81.663 1313 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.15 % Allowed : 14.37 % Favored : 81.48 % 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: -5.20 (0.19), residues: 1185 helix: -3.56 (0.15), residues: 645 sheet: -3.39 (0.73), residues: 26 loop : -3.16 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 792 TYR 0.015 0.001 TYR U 274 PHE 0.012 0.001 PHE U 811 TRP 0.016 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9503) covalent geometry : angle 0.63599 / 0.33 (12866) hydrogen bonds : bond 0.03392 / 2.18 ( 183) hydrogen bonds : angle 4.82387 / 3.30 ( 513) Misc. bond : bond 0.00015 / 0.01 ( 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 172 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8148 (m-10) cc_final: 0.7929 (m-80) REVERT: U 154 ILE cc_start: 0.8849 (tp) cc_final: 0.8325 (tp) REVERT: U 173 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: U 191 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: U 424 ASN cc_start: 0.5363 (p0) cc_final: 0.5051 (p0) REVERT: U 472 TYR cc_start: 0.8565 (m-80) cc_final: 0.8352 (m-80) REVERT: U 478 MET cc_start: 0.6443 (ppp) cc_final: 0.5799 (mmt) REVERT: U 533 LYS cc_start: 0.7595 (tttm) cc_final: 0.7259 (pttt) REVERT: U 576 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7162 (t0) REVERT: U 578 LYS cc_start: 0.8016 (mppt) cc_final: 0.7531 (mmtt) REVERT: U 878 MET cc_start: 0.8204 (tmm) cc_final: 0.7951 (tmm) REVERT: U 913 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7992 (mt) REVERT: U 918 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.5457 (tp-100) REVERT: U 920 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5100 (mtt90) REVERT: U 921 MET cc_start: 0.5580 (tpt) cc_final: 0.4430 (ttp) REVERT: U 928 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6257 (ptp90) REVERT: U 966 GLU cc_start: 0.7609 (tp30) cc_final: 0.7401 (tp30) REVERT: U 1031 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8491 (tt) REVERT: U 1037 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7187 (m-10) REVERT: U 1145 LYS cc_start: 0.7963 (mmmm) cc_final: 0.7334 (ptmt) REVERT: U 1161 GLN cc_start: 0.6971 (tt0) cc_final: 0.6538 (tp40) REVERT: U 1270 CYS cc_start: 0.7488 (t) cc_final: 0.6895 (m) outliers start: 41 outliers final: 19 residues processed: 162 average time/residue: 0.0938 time to fit residues: 20.8058 Evaluate side-chains 137 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 191 ASP Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 347 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 98 GLN ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129156 restraints weight = 13393.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126447 restraints weight = 11754.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127701 restraints weight = 10114.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128243 restraints weight = 7390.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128354 restraints weight = 6366.144| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9504 Z= 0.119 Angle : 0.610 9.973 12866 Z= 0.308 Chirality : 0.041 0.140 1473 Planarity : 0.003 0.041 1632 Dihedral : 7.578 81.183 1310 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.06 % Allowed : 15.18 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.20), residues: 1185 helix: -3.17 (0.16), residues: 645 sheet: -3.03 (0.73), residues: 26 loop : -3.00 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 792 TYR 0.014 0.001 TYR U 538 PHE 0.025 0.001 PHE U 427 TRP 0.014 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9503) covalent geometry : angle 0.61046 / 0.31 (12866) hydrogen bonds : bond 0.02897 / 1.90 ( 183) hydrogen bonds : angle 4.50474 / 3.07 ( 513) Misc. bond : bond 0.00031 / 0.02 ( 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 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 123 MET cc_start: -0.0105 (mmt) cc_final: -0.0485 (mmt) REVERT: U 144 TYR cc_start: 0.8068 (m-10) cc_final: 0.7843 (m-80) REVERT: U 154 ILE cc_start: 0.8853 (tp) cc_final: 0.8318 (tp) REVERT: U 173 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8384 (mtmm) REVERT: U 183 MET cc_start: 0.8881 (mmm) cc_final: 0.8420 (mmm) REVERT: U 373 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8678 (tp) REVERT: U 424 ASN cc_start: 0.5268 (p0) cc_final: 0.4908 (p0) REVERT: U 472 TYR cc_start: 0.8603 (m-80) cc_final: 0.8375 (m-80) REVERT: U 478 MET cc_start: 0.6516 (ppp) cc_final: 0.5879 (mmt) REVERT: U 533 LYS cc_start: 0.7555 (tttm) cc_final: 0.7230 (pttt) REVERT: U 576 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7183 (t0) REVERT: U 578 LYS cc_start: 0.8100 (mppt) cc_final: 0.7594 (mmtt) REVERT: U 610 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8064 (mp) REVERT: U 878 MET cc_start: 0.8207 (tmm) cc_final: 0.7918 (tmm) REVERT: U 913 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7968 (mt) REVERT: U 918 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.5460 (tp-100) REVERT: U 920 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5045 (mtt90) REVERT: U 921 MET cc_start: 0.5503 (tpt) cc_final: 0.4504 (ttp) REVERT: U 933 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7599 (tt) REVERT: U 946 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (p0) REVERT: U 1031 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8464 (tt) REVERT: U 1037 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: U 1145 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7310 (ptmt) REVERT: U 1161 GLN cc_start: 0.7012 (tt0) cc_final: 0.6359 (tp40) REVERT: U 1221 ARG cc_start: 0.7398 (tmm160) cc_final: 0.6950 (ppt170) REVERT: U 1270 CYS cc_start: 0.7366 (t) cc_final: 0.6844 (m) outliers start: 50 outliers final: 23 residues processed: 163 average time/residue: 0.0869 time to fit residues: 19.6000 Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL 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 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1265 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 85 optimal weight: 0.0570 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS ** U 946 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.169627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127808 restraints weight = 13455.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124980 restraints weight = 11607.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126186 restraints weight = 10127.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126763 restraints weight = 7359.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126877 restraints weight = 6302.734| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9504 Z= 0.154 Angle : 0.622 9.608 12866 Z= 0.313 Chirality : 0.042 0.142 1473 Planarity : 0.004 0.039 1632 Dihedral : 7.461 81.689 1308 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.86 % Allowed : 17.31 % Favored : 77.83 % 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: -4.61 (0.20), residues: 1185 helix: -2.99 (0.17), residues: 649 sheet: -2.82 (0.75), residues: 26 loop : -3.04 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 299 TYR 0.013 0.001 TYR U 274 PHE 0.018 0.001 PHE U 427 TRP 0.012 0.001 TRP U 846 HIS 0.005 0.001 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9503) covalent geometry : angle 0.62231 / 0.31 (12866) hydrogen bonds : bond 0.02972 / 1.93 ( 183) hydrogen bonds : angle 4.51066 / 3.07 ( 513) Misc. bond : bond 0.00049 / 0.03 ( 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 169 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.340 Fit side-chains REVERT: U 128 ARG cc_start: 0.7636 (mpt180) cc_final: 0.7237 (mpt180) REVERT: U 144 TYR cc_start: 0.8094 (m-10) cc_final: 0.7874 (m-80) REVERT: U 154 ILE cc_start: 0.8880 (tp) cc_final: 0.8322 (tp) REVERT: U 173 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: U 183 MET cc_start: 0.8924 (mmm) cc_final: 0.8467 (mmm) REVERT: U 299 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7866 (tmm-80) REVERT: U 373 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8752 (tp) REVERT: U 424 ASN cc_start: 0.5287 (p0) cc_final: 0.4971 (p0) REVERT: U 478 MET cc_start: 0.6519 (ppp) cc_final: 0.5903 (mmt) REVERT: U 533 LYS cc_start: 0.7621 (tttm) cc_final: 0.7253 (pttt) REVERT: U 576 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7173 (t0) REVERT: U 578 LYS cc_start: 0.8087 (mppt) cc_final: 0.7587 (mmtt) REVERT: U 596 MET cc_start: 0.6626 (tpt) cc_final: 0.5880 (ptt) REVERT: U 610 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8051 (mp) REVERT: U 878 MET cc_start: 0.8217 (tmm) cc_final: 0.7867 (tmm) REVERT: U 913 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7963 (mt) REVERT: U 918 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5478 (tp-100) REVERT: U 920 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5023 (mtt90) REVERT: U 921 MET cc_start: 0.5652 (tpt) cc_final: 0.4454 (ttp) REVERT: U 933 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7807 (tt) REVERT: U 1031 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8504 (tt) REVERT: U 1037 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: U 1145 LYS cc_start: 0.7802 (mmmm) cc_final: 0.7289 (ptmt) REVERT: U 1161 GLN cc_start: 0.7120 (tt0) cc_final: 0.6327 (tp40) REVERT: U 1185 MET cc_start: 0.5037 (tpp) cc_final: 0.4485 (tpt) REVERT: U 1221 ARG cc_start: 0.7353 (tmm160) cc_final: 0.6859 (ppt170) REVERT: U 1270 CYS cc_start: 0.7517 (t) cc_final: 0.6917 (m) outliers start: 48 outliers final: 26 residues processed: 156 average time/residue: 0.0898 time to fit residues: 19.5295 Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL 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 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 795 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1265 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.170773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128397 restraints weight = 13374.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127819 restraints weight = 9867.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128902 restraints weight = 8010.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129511 restraints weight = 6149.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129536 restraints weight = 6037.426| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9504 Z= 0.149 Angle : 0.604 8.423 12866 Z= 0.307 Chirality : 0.043 0.134 1473 Planarity : 0.004 0.038 1632 Dihedral : 7.346 82.003 1308 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.57 % Allowed : 16.60 % Favored : 77.83 % 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: -4.37 (0.21), residues: 1185 helix: -2.81 (0.17), residues: 643 sheet: -2.73 (0.74), residues: 26 loop : -2.90 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 299 TYR 0.013 0.001 TYR U 274 PHE 0.019 0.001 PHE U1014 TRP 0.012 0.001 TRP U 846 HIS 0.002 0.001 HIS U1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9503) covalent geometry : angle 0.60445 / 0.31 (12866) hydrogen bonds : bond 0.02930 / 1.89 ( 183) hydrogen bonds : angle 4.42761 / 3.01 ( 513) Misc. bond : bond 0.00034 / 0.02 ( 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 173 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8447 (mm) REVERT: U 123 MET cc_start: -0.0469 (mmt) cc_final: -0.0902 (mmt) REVERT: U 154 ILE cc_start: 0.8862 (tp) cc_final: 0.8289 (tp) REVERT: U 173 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8355 (mtmm) REVERT: U 183 MET cc_start: 0.8956 (mmm) cc_final: 0.8461 (mmm) REVERT: U 299 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7763 (tmm-80) REVERT: U 373 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8777 (tp) REVERT: U 424 ASN cc_start: 0.5258 (p0) cc_final: 0.4856 (p0) REVERT: U 478 MET cc_start: 0.6462 (ppp) cc_final: 0.5878 (mmt) REVERT: U 533 LYS cc_start: 0.7602 (tttm) cc_final: 0.7264 (pttt) REVERT: U 576 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7252 (t0) REVERT: U 596 MET cc_start: 0.6567 (tpt) cc_final: 0.5974 (ptt) REVERT: U 610 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8025 (mp) REVERT: U 878 MET cc_start: 0.8188 (tmm) cc_final: 0.7815 (tmm) REVERT: U 913 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8000 (mt) REVERT: U 918 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5380 (tp-100) REVERT: U 920 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.5025 (mtt90) REVERT: U 921 MET cc_start: 0.5610 (tpt) cc_final: 0.4487 (ttp) REVERT: U 933 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7833 (tt) REVERT: U 946 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8278 (p0) REVERT: U 1031 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8510 (tt) REVERT: U 1037 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7285 (m-10) REVERT: U 1145 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7278 (ptmt) REVERT: U 1161 GLN cc_start: 0.7136 (tt0) cc_final: 0.6414 (tp40) REVERT: U 1270 CYS cc_start: 0.7640 (t) cc_final: 0.6940 (m) outliers start: 55 outliers final: 30 residues processed: 158 average time/residue: 0.0837 time to fit residues: 18.5250 Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL 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 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 863 THR Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 91 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126730 restraints weight = 13206.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125141 restraints weight = 12850.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126300 restraints weight = 11770.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126833 restraints weight = 8202.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126931 restraints weight = 7144.181| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9504 Z= 0.116 Angle : 0.592 8.284 12866 Z= 0.298 Chirality : 0.041 0.134 1473 Planarity : 0.003 0.036 1632 Dihedral : 7.137 81.668 1308 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.86 % Allowed : 18.32 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.21), residues: 1185 helix: -2.59 (0.18), residues: 641 sheet: -2.62 (0.76), residues: 26 loop : -2.81 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 299 TYR 0.033 0.001 TYR U 538 PHE 0.020 0.001 PHE U1014 TRP 0.013 0.001 TRP U 846 HIS 0.006 0.001 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9503) covalent geometry : angle 0.59240 / 0.30 (12866) hydrogen bonds : bond 0.02758 / 1.82 ( 183) hydrogen bonds : angle 4.32145 / 2.92 ( 513) Misc. bond : bond 0.00026 / 0.02 ( 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 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8498 (mm) REVERT: U 154 ILE cc_start: 0.8808 (tp) cc_final: 0.8263 (tp) REVERT: U 173 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8411 (mtmm) REVERT: U 183 MET cc_start: 0.8843 (mmm) cc_final: 0.8356 (mmm) REVERT: U 299 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7771 (tmm-80) REVERT: U 373 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8779 (tp) REVERT: U 424 ASN cc_start: 0.5140 (p0) cc_final: 0.4718 (p0) REVERT: U 478 MET cc_start: 0.6415 (ppp) cc_final: 0.5822 (mmt) REVERT: U 533 LYS cc_start: 0.7586 (tttm) cc_final: 0.7298 (pttt) REVERT: U 576 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7318 (t0) REVERT: U 596 MET cc_start: 0.6470 (tpt) cc_final: 0.5884 (ptm) REVERT: U 610 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8161 (mp) REVERT: U 631 HIS cc_start: 0.5168 (OUTLIER) cc_final: 0.4954 (m-70) REVERT: U 878 MET cc_start: 0.8180 (tmm) cc_final: 0.7826 (tmm) REVERT: U 913 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7962 (mt) REVERT: U 918 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5281 (tp-100) REVERT: U 920 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.4926 (mtt90) REVERT: U 921 MET cc_start: 0.5548 (tpt) cc_final: 0.4425 (ttp) REVERT: U 933 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7845 (tt) REVERT: U 1031 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8488 (tt) REVERT: U 1037 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7273 (m-10) REVERT: U 1145 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7287 (ptmt) REVERT: U 1161 GLN cc_start: 0.7141 (tt0) cc_final: 0.6444 (tp40) REVERT: U 1270 CYS cc_start: 0.7536 (t) cc_final: 0.6902 (m) outliers start: 48 outliers final: 28 residues processed: 154 average time/residue: 0.1047 time to fit residues: 22.2820 Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL 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 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 631 HIS Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125215 restraints weight = 13165.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123388 restraints weight = 13494.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124493 restraints weight = 12772.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125160 restraints weight = 8820.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125112 restraints weight = 8318.310| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9504 Z= 0.164 Angle : 0.621 8.229 12866 Z= 0.314 Chirality : 0.043 0.201 1473 Planarity : 0.004 0.038 1632 Dihedral : 7.129 82.125 1308 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.26 % Allowed : 19.23 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.05 (0.21), residues: 1185 helix: -2.53 (0.18), residues: 645 sheet: -2.74 (0.75), residues: 26 loop : -2.77 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U1128 TYR 0.012 0.001 TYR U 274 PHE 0.022 0.001 PHE U1014 TRP 0.013 0.001 TRP U 846 HIS 0.013 0.001 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 9503) covalent geometry : angle 0.62115 / 0.31 (12866) hydrogen bonds : bond 0.02915 / 1.89 ( 183) hydrogen bonds : angle 4.41418 / 2.98 ( 513) Misc. bond : bond 0.00023 / 0.01 ( 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 171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8529 (mm) REVERT: U 123 MET cc_start: -0.0316 (mmt) cc_final: -0.0840 (mmt) REVERT: U 154 ILE cc_start: 0.8856 (tp) cc_final: 0.8300 (tp) REVERT: U 173 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: U 183 MET cc_start: 0.8852 (mmm) cc_final: 0.8359 (mmm) REVERT: U 224 MET cc_start: 0.8283 (tpt) cc_final: 0.7850 (tpt) REVERT: U 373 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8640 (tp) REVERT: U 424 ASN cc_start: 0.5139 (p0) cc_final: 0.4710 (p0) REVERT: U 478 MET cc_start: 0.6499 (ppp) cc_final: 0.5853 (mmt) REVERT: U 533 LYS cc_start: 0.7570 (tttm) cc_final: 0.7293 (pttt) REVERT: U 576 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7327 (t0) REVERT: U 596 MET cc_start: 0.6490 (tpt) cc_final: 0.5939 (ptm) REVERT: U 610 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8158 (mp) REVERT: U 631 HIS cc_start: 0.5350 (OUTLIER) cc_final: 0.5090 (m-70) REVERT: U 878 MET cc_start: 0.8202 (tmm) cc_final: 0.7822 (tmm) REVERT: U 913 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7978 (mt) REVERT: U 918 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5228 (tp-100) REVERT: U 920 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.4908 (mtt90) REVERT: U 933 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7861 (tt) REVERT: U 1031 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8520 (tt) REVERT: U 1037 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: U 1145 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7321 (ptmt) outliers start: 52 outliers final: 31 residues processed: 155 average time/residue: 0.0848 time to fit residues: 18.2813 Evaluate side-chains 155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL 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 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 487 ARG Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 631 HIS Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN U1198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130220 restraints weight = 13087.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130140 restraints weight = 9622.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130913 restraints weight = 7204.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131004 restraints weight = 6087.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132428 restraints weight = 5292.040| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 9504 Z= 0.103 Angle : 0.585 8.915 12866 Z= 0.295 Chirality : 0.041 0.185 1473 Planarity : 0.003 0.034 1632 Dihedral : 6.827 81.344 1308 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.35 % Allowed : 20.34 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.22), residues: 1185 helix: -2.25 (0.19), residues: 631 sheet: -2.65 (0.77), residues: 26 loop : -2.65 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 299 TYR 0.014 0.001 TYR U1005 PHE 0.022 0.001 PHE U1014 TRP 0.013 0.001 TRP U 846 HIS 0.020 0.001 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.10 ( 9503) covalent geometry : angle 0.58507 / 0.30 (12866) hydrogen bonds : bond 0.02540 / 1.67 ( 183) hydrogen bonds : angle 4.20407 / 2.82 ( 513) Misc. bond : bond 0.00011 / 0.01 ( 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 166 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8454 (mm) REVERT: U 154 ILE cc_start: 0.8808 (tp) cc_final: 0.8274 (tp) REVERT: U 173 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8398 (mtmm) REVERT: U 299 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7768 (tmm-80) REVERT: U 373 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8731 (tp) REVERT: U 424 ASN cc_start: 0.5117 (p0) cc_final: 0.4678 (p0) REVERT: U 478 MET cc_start: 0.6393 (ppp) cc_final: 0.5909 (mmt) REVERT: U 533 LYS cc_start: 0.7647 (tttm) cc_final: 0.7324 (pttt) REVERT: U 576 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7297 (t0) REVERT: U 596 MET cc_start: 0.6559 (tpt) cc_final: 0.6034 (ptm) REVERT: U 610 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8006 (mp) REVERT: U 631 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.5039 (m-70) REVERT: U 878 MET cc_start: 0.8170 (tmm) cc_final: 0.7821 (tmm) REVERT: U 913 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7966 (mt) REVERT: U 918 GLN cc_start: 0.6290 (OUTLIER) cc_final: 0.5315 (tp-100) REVERT: U 920 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.4864 (mtt90) REVERT: U 921 MET cc_start: 0.5537 (tpt) cc_final: 0.4601 (ttm) REVERT: U 933 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7575 (tt) REVERT: U 1037 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: U 1145 LYS cc_start: 0.7729 (mmmm) cc_final: 0.7229 (ptmt) REVERT: U 1151 PHE cc_start: 0.7533 (t80) cc_final: 0.7055 (t80) REVERT: U 1161 GLN cc_start: 0.7154 (tp40) cc_final: 0.6821 (tp40) outliers start: 43 outliers final: 26 residues processed: 153 average time/residue: 0.0977 time to fit residues: 20.6171 Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 486 ILE Chi-restraints excluded: chain U residue 487 ARG Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 631 HIS Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 94 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.173555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129295 restraints weight = 13172.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129041 restraints weight = 9647.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129976 restraints weight = 7608.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130380 restraints weight = 5823.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130594 restraints weight = 5148.686| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 9504 Z= 0.126 Angle : 0.604 9.205 12866 Z= 0.304 Chirality : 0.042 0.187 1473 Planarity : 0.003 0.035 1632 Dihedral : 6.779 81.402 1308 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.35 % Allowed : 20.85 % Favored : 74.80 % 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: -3.66 (0.22), residues: 1185 helix: -2.16 (0.19), residues: 639 sheet: -2.60 (0.76), residues: 39 loop : -2.65 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 299 TYR 0.011 0.001 TYR U 274 PHE 0.027 0.001 PHE U 90 TRP 0.012 0.001 TRP U 846 HIS 0.013 0.001 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 9503) covalent geometry : angle 0.60404 / 0.30 (12866) hydrogen bonds : bond 0.02594 / 1.69 ( 183) hydrogen bonds : angle 4.21631 / 2.83 ( 513) Misc. bond : bond 0.00007 / 0.00 ( 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 160 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8489 (mm) REVERT: U 123 MET cc_start: -0.0533 (mmt) cc_final: -0.1309 (mmt) REVERT: U 154 ILE cc_start: 0.8823 (tp) cc_final: 0.8297 (tp) REVERT: U 173 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8432 (mtmm) REVERT: U 183 MET cc_start: 0.8883 (mmm) cc_final: 0.8298 (mmm) REVERT: U 299 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7793 (tmm-80) REVERT: U 373 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8746 (tp) REVERT: U 424 ASN cc_start: 0.5104 (p0) cc_final: 0.4653 (p0) REVERT: U 478 MET cc_start: 0.6493 (ppp) cc_final: 0.5768 (mmt) REVERT: U 533 LYS cc_start: 0.7616 (tttm) cc_final: 0.7297 (pttt) REVERT: U 576 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7322 (t0) REVERT: U 596 MET cc_start: 0.6695 (tpt) cc_final: 0.6009 (ptm) REVERT: U 610 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8067 (mp) REVERT: U 631 HIS cc_start: 0.5170 (OUTLIER) cc_final: 0.4774 (m-70) REVERT: U 878 MET cc_start: 0.8199 (tmm) cc_final: 0.7831 (tmm) REVERT: U 913 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7975 (mt) REVERT: U 918 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5282 (tp-100) REVERT: U 920 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.4750 (mtt90) REVERT: U 933 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7564 (tt) REVERT: U 1031 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8519 (tt) REVERT: U 1037 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7256 (m-10) REVERT: U 1145 LYS cc_start: 0.7738 (mmmm) cc_final: 0.7251 (ptmt) REVERT: U 1151 PHE cc_start: 0.7582 (t80) cc_final: 0.7064 (t80) REVERT: U 1161 GLN cc_start: 0.7215 (tp40) cc_final: 0.6885 (tp40) outliers start: 43 outliers final: 26 residues processed: 148 average time/residue: 0.0920 time to fit residues: 18.6110 Evaluate side-chains 152 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 487 ARG Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 631 HIS Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1021 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1152 LEU Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 484 HIS ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130373 restraints weight = 13130.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131404 restraints weight = 9838.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131837 restraints weight = 7272.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132440 restraints weight = 5372.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132445 restraints weight = 4863.293| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 9504 Z= 0.216 Angle : 0.667 9.123 12866 Z= 0.340 Chirality : 0.045 0.192 1473 Planarity : 0.004 0.041 1632 Dihedral : 7.021 82.817 1308 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.15 % Allowed : 20.95 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.22), residues: 1185 helix: -2.33 (0.18), residues: 649 sheet: -2.96 (0.71), residues: 40 loop : -2.70 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 792 TYR 0.028 0.002 TYR U 538 PHE 0.024 0.002 PHE U1014 TRP 0.013 0.002 TRP U 846 HIS 0.019 0.002 HIS U 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 ( 9503) covalent geometry : angle 0.66677 / 0.34 (12866) hydrogen bonds : bond 0.03204 / 2.09 ( 183) hydrogen bonds : angle 4.54669 / 3.05 ( 513) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.87 seconds wall clock time: 24 minutes 5.97 seconds (1445.97 seconds total)