Starting phenix.real_space_refine on Wed Mar 4 00:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dv5_30870/03_2026/7dv5_30870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dv5_30870/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2026/7dv5_30870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2026/7dv5_30870.map" model { file = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2026/7dv5_30870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2026/7dv5_30870.cif" } 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-5986/lib/python3.9/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: 1.95, 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: 0.53 Conformation dependent library (CDL) restraints added in 477.7 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: 0.27 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: 1.10 Time building geometry restraints manager: 0.74 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 - 24.37: 5479 24.37 - 48.75: 250 48.75 - 73.12: 22 73.12 - 97.49: 8 97.49 - 121.87: 3 Dihedral angle restraints: 5762 sinusoidal: 2351 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 5759 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: 0.500 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.330 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 14.003 121.866 3572 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 covalent geometry : bond 0.01054 ( 9503) covalent geometry : angle 1.46224 (12866) hydrogen bonds : bond 0.33037 ( 183) hydrogen bonds : angle 11.16376 ( 513) Misc. bond : bond 0.84260 ( 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 : 0.339 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: 0.1193 time to fit residues: 32.4282 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 : 0.344 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.167605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126628 restraints weight = 13584.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125227 restraints weight = 10877.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126495 restraints weight = 9114.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126962 restraints weight = 6657.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127162 restraints weight = 6283.654| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9504 Z= 0.135 Angle : 0.687 8.191 12866 Z= 0.354 Chirality : 0.043 0.154 1473 Planarity : 0.005 0.053 1632 Dihedral : 10.029 134.102 1464 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.14 % Allowed : 14.07 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.78 (0.17), residues: 1185 helix: -4.16 (0.12), residues: 640 sheet: -3.77 (0.71), residues: 26 loop : -3.24 (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 0.013 0.001 TRP U 330 HIS 0.005 0.001 HIS U 484 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9503) covalent geometry : angle 0.68739 (12866) hydrogen bonds : bond 0.04063 ( 183) hydrogen bonds : angle 5.55880 ( 513) Misc. bond : bond 0.00017 ( 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 171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8204 (m-10) cc_final: 0.7933 (m-80) REVERT: U 154 ILE cc_start: 0.8830 (tp) cc_final: 0.8279 (tp) REVERT: U 173 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8369 (mtmm) REVERT: U 191 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: U 424 ASN cc_start: 0.5262 (p0) cc_final: 0.4912 (p0) REVERT: U 478 MET cc_start: 0.6442 (ppp) cc_final: 0.5776 (mmt) REVERT: U 533 LYS cc_start: 0.7601 (tttm) cc_final: 0.7283 (pttt) REVERT: U 576 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7341 (t0) REVERT: U 610 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8037 (mp) REVERT: U 913 LEU cc_start: 0.8431 (tm) cc_final: 0.7981 (mt) REVERT: U 918 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5462 (tp-100) REVERT: U 920 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5078 (mtt90) REVERT: U 921 MET cc_start: 0.5685 (tpt) cc_final: 0.4475 (ttp) REVERT: U 928 ARG cc_start: 0.7148 (tpt170) cc_final: 0.6064 (ptp90) REVERT: U 946 ASN cc_start: 0.8432 (p0) cc_final: 0.8200 (p0) REVERT: U 966 GLU cc_start: 0.7610 (tp30) cc_final: 0.7399 (tp30) REVERT: U 1006 LEU cc_start: 0.9037 (mp) cc_final: 0.8808 (mt) REVERT: U 1037 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: U 1145 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7479 (ptmt) REVERT: U 1161 GLN cc_start: 0.6858 (tt0) cc_final: 0.6492 (tp40) REVERT: U 1171 MET cc_start: 0.8114 (tmm) cc_final: 0.7809 (tmm) REVERT: U 1270 CYS cc_start: 0.7494 (t) cc_final: 0.6862 (m) outliers start: 31 outliers final: 8 residues processed: 164 average time/residue: 0.1046 time to fit residues: 23.4966 Evaluate side-chains 133 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4039 r_free = 0.4039 target = 0.169695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128790 restraints weight = 13475.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126940 restraints weight = 10782.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128455 restraints weight = 9837.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.128798 restraints weight = 6442.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128913 restraints weight = 5757.590| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9504 Z= 0.104 Angle : 0.609 8.033 12866 Z= 0.310 Chirality : 0.041 0.149 1473 Planarity : 0.004 0.041 1632 Dihedral : 8.933 135.358 1448 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.95 % Allowed : 14.57 % 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: -5.15 (0.19), residues: 1185 helix: -3.49 (0.15), residues: 651 sheet: -3.29 (0.73), residues: 26 loop : -3.16 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 792 TYR 0.013 0.001 TYR U 274 PHE 0.011 0.001 PHE U 811 TRP 0.015 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9503) covalent geometry : angle 0.60887 (12866) hydrogen bonds : bond 0.03035 ( 183) hydrogen bonds : angle 4.64077 ( 513) Misc. bond : bond 0.00010 ( 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 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8094 (m-10) cc_final: 0.7856 (m-80) REVERT: U 154 ILE cc_start: 0.8869 (tp) cc_final: 0.8373 (tp) REVERT: U 173 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: U 183 MET cc_start: 0.8916 (mmm) cc_final: 0.8482 (mmm) REVERT: U 371 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8585 (mt) REVERT: U 424 ASN cc_start: 0.5341 (p0) cc_final: 0.5030 (p0) REVERT: U 478 MET cc_start: 0.6414 (ppp) cc_final: 0.5779 (mmt) REVERT: U 533 LYS cc_start: 0.7563 (tttm) cc_final: 0.7254 (pttt) REVERT: U 576 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7231 (t0) REVERT: U 578 LYS cc_start: 0.8097 (mppt) cc_final: 0.7693 (mmtt) REVERT: U 878 MET cc_start: 0.8211 (tmm) cc_final: 0.7984 (tmm) REVERT: U 913 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7959 (mt) REVERT: U 918 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5507 (tp-100) REVERT: U 920 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.5055 (mtt90) REVERT: U 921 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.4580 (ttp) REVERT: U 928 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6092 (ptp90) REVERT: U 966 GLU cc_start: 0.7523 (tp30) cc_final: 0.7281 (tp30) REVERT: U 1031 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8538 (tt) REVERT: U 1037 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: U 1145 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7315 (ptmt) REVERT: U 1161 GLN cc_start: 0.6955 (tt0) cc_final: 0.6608 (tp40) REVERT: U 1270 CYS cc_start: 0.7311 (t) cc_final: 0.6822 (m) outliers start: 39 outliers final: 15 residues processed: 161 average time/residue: 0.1105 time to fit residues: 24.3719 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 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 764 VAL 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 921 MET 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 1174 ILE 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: 4.9990 chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 93 optimal weight: 4.9990 chunk 116 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4039 r_free = 0.4039 target = 0.169461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127670 restraints weight = 13429.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125231 restraints weight = 12064.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127042 restraints weight = 10033.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126962 restraints weight = 7242.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127273 restraints weight = 6700.027| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9504 Z= 0.146 Angle : 0.622 9.598 12866 Z= 0.314 Chirality : 0.042 0.138 1473 Planarity : 0.004 0.041 1632 Dihedral : 8.786 134.659 1446 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.47 % Allowed : 14.47 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.20), residues: 1185 helix: -3.17 (0.16), residues: 650 sheet: -3.00 (0.73), residues: 26 loop : -3.06 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 299 TYR 0.014 0.002 TYR U 274 PHE 0.026 0.001 PHE U 427 TRP 0.013 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9503) covalent geometry : angle 0.62197 (12866) hydrogen bonds : bond 0.03054 ( 183) hydrogen bonds : angle 4.52422 ( 513) Misc. bond : bond 0.00027 ( 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 177 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8096 (m-10) cc_final: 0.7877 (m-80) REVERT: U 154 ILE cc_start: 0.8881 (tp) cc_final: 0.8337 (tp) REVERT: U 173 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: U 183 MET cc_start: 0.8912 (mmm) cc_final: 0.8431 (mmm) REVERT: U 299 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7803 (tmm-80) REVERT: U 373 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8792 (tp) REVERT: U 424 ASN cc_start: 0.5311 (p0) cc_final: 0.4952 (p0) REVERT: U 478 MET cc_start: 0.6510 (ppp) cc_final: 0.5889 (mmt) REVERT: U 533 LYS cc_start: 0.7565 (tttm) cc_final: 0.7233 (pttt) REVERT: U 576 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7174 (t0) REVERT: U 578 LYS cc_start: 0.8113 (mppt) cc_final: 0.7603 (mmtt) REVERT: U 610 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8085 (mp) REVERT: U 878 MET cc_start: 0.8216 (tmm) cc_final: 0.7916 (tmm) REVERT: U 913 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7987 (mt) REVERT: U 918 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5512 (tp-100) REVERT: U 920 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5163 (mtt90) REVERT: U 921 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.4588 (ttp) REVERT: U 933 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7570 (tt) REVERT: U 966 GLU cc_start: 0.7588 (tp30) cc_final: 0.7364 (tp30) REVERT: U 1031 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8492 (tt) REVERT: U 1037 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: U 1145 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7300 (ptmt) REVERT: U 1161 GLN cc_start: 0.7064 (tt0) cc_final: 0.6348 (tp40) REVERT: U 1221 ARG cc_start: 0.6911 (tmm160) cc_final: 0.6669 (ppt170) REVERT: U 1270 CYS cc_start: 0.7373 (t) cc_final: 0.6841 (m) outliers start: 54 outliers final: 23 residues processed: 162 average time/residue: 0.1092 time to fit residues: 24.3971 Evaluate side-chains 149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 921 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.0070 chunk 73 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN 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 = 0.4096 r_free = 0.4096 target = 0.174721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133355 restraints weight = 13412.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129809 restraints weight = 12135.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131260 restraints weight = 10665.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131783 restraints weight = 7418.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132390 restraints weight = 6452.663| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9504 Z= 0.091 Angle : 0.579 9.218 12866 Z= 0.288 Chirality : 0.040 0.143 1473 Planarity : 0.003 0.035 1632 Dihedral : 8.396 135.146 1446 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.05 % Allowed : 16.90 % Favored : 79.05 % 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: -4.32 (0.21), residues: 1185 helix: -2.78 (0.17), residues: 643 sheet: -2.66 (0.78), residues: 26 loop : -2.86 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 299 TYR 0.009 0.001 TYR U 274 PHE 0.018 0.001 PHE U 90 TRP 0.012 0.001 TRP U 846 HIS 0.006 0.001 HIS U 631 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9503) covalent geometry : angle 0.57895 (12866) hydrogen bonds : bond 0.02383 ( 183) hydrogen bonds : angle 4.17262 ( 513) Misc. bond : bond 0.00006 ( 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 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: U 144 TYR cc_start: 0.7995 (m-10) cc_final: 0.7759 (m-80) REVERT: U 154 ILE cc_start: 0.8872 (tp) cc_final: 0.8432 (tp) REVERT: U 173 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8331 (mtmm) REVERT: U 183 MET cc_start: 0.8861 (mmm) cc_final: 0.8359 (mmm) REVERT: U 299 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7804 (tmm-80) REVERT: U 371 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8436 (mt) REVERT: U 373 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8650 (tp) REVERT: U 424 ASN cc_start: 0.5205 (p0) cc_final: 0.4828 (p0) REVERT: U 478 MET cc_start: 0.6466 (ppp) cc_final: 0.5731 (mmt) REVERT: U 517 ARG cc_start: 0.6148 (ttm170) cc_final: 0.5845 (ttm110) REVERT: U 533 LYS cc_start: 0.7539 (tttm) cc_final: 0.7203 (pttt) REVERT: U 576 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7230 (t0) REVERT: U 578 LYS cc_start: 0.8050 (mppt) cc_final: 0.7575 (mmtt) REVERT: U 596 MET cc_start: 0.6449 (tpt) cc_final: 0.5912 (ptt) REVERT: U 610 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8048 (mp) REVERT: U 878 MET cc_start: 0.8154 (tmm) cc_final: 0.7872 (tmm) REVERT: U 913 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7920 (mt) REVERT: U 918 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5385 (tp-100) REVERT: U 920 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.5052 (mtt90) REVERT: U 921 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.4778 (ttp) REVERT: U 933 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7458 (tt) REVERT: U 946 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8205 (p0) REVERT: U 1037 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7095 (m-10) REVERT: U 1161 GLN cc_start: 0.7111 (tt0) cc_final: 0.6223 (tp40) REVERT: U 1221 ARG cc_start: 0.6763 (tmm160) cc_final: 0.6542 (ppt170) REVERT: U 1270 CYS cc_start: 0.7381 (t) cc_final: 0.6828 (m) outliers start: 40 outliers final: 13 residues processed: 155 average time/residue: 0.1108 time to fit residues: 23.5923 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 243 LEU 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 429 TYR Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 486 ILE Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 839 MET 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 921 MET Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129191 restraints weight = 13365.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127034 restraints weight = 12624.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128366 restraints weight = 11390.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129133 restraints weight = 7194.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129144 restraints weight = 6767.494| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9504 Z= 0.125 Angle : 0.586 8.196 12866 Z= 0.294 Chirality : 0.041 0.133 1473 Planarity : 0.003 0.034 1632 Dihedral : 8.387 134.748 1445 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.55 % Allowed : 17.71 % Favored : 77.73 % 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: -4.10 (0.21), residues: 1185 helix: -2.62 (0.18), residues: 642 sheet: -2.53 (0.78), residues: 26 loop : -2.75 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 792 TYR 0.012 0.001 TYR U 274 PHE 0.020 0.001 PHE U1014 TRP 0.011 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9503) covalent geometry : angle 0.58602 (12866) hydrogen bonds : bond 0.02590 ( 183) hydrogen bonds : angle 4.16617 ( 513) Misc. bond : bond 0.00022 ( 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 161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: U 154 ILE cc_start: 0.8860 (tp) cc_final: 0.8440 (tp) REVERT: U 173 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: U 183 MET cc_start: 0.8854 (mmm) cc_final: 0.8323 (mmm) REVERT: U 299 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7756 (tmm-80) REVERT: U 373 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8638 (tp) REVERT: U 424 ASN cc_start: 0.5181 (p0) cc_final: 0.4779 (p0) REVERT: U 478 MET cc_start: 0.6511 (ppp) cc_final: 0.5841 (mmt) REVERT: U 533 LYS cc_start: 0.7540 (tttm) cc_final: 0.7228 (pttt) REVERT: U 576 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7224 (t0) REVERT: U 578 LYS cc_start: 0.8096 (mppt) cc_final: 0.7634 (mmtt) REVERT: U 596 MET cc_start: 0.6372 (tpt) cc_final: 0.5986 (ptt) REVERT: U 610 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8107 (mp) REVERT: U 878 MET cc_start: 0.8194 (tmm) cc_final: 0.7871 (tmm) REVERT: U 913 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7987 (mt) REVERT: U 918 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5328 (tp-100) REVERT: U 920 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5070 (mtt90) REVERT: U 921 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.4679 (ttp) REVERT: U 933 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (tt) REVERT: U 946 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8284 (p0) REVERT: U 1031 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8465 (tt) REVERT: U 1037 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: U 1161 GLN cc_start: 0.7127 (tt0) cc_final: 0.6329 (tp40) REVERT: U 1270 CYS cc_start: 0.7315 (t) cc_final: 0.6803 (m) REVERT: U 1289 MET cc_start: 0.3506 (pmm) cc_final: 0.2392 (mmt) outliers start: 45 outliers final: 25 residues processed: 148 average time/residue: 0.1074 time to fit residues: 21.5841 Evaluate side-chains 149 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 91 ILE 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 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 486 ILE Chi-restraints excluded: chain U residue 515 ASN 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 839 MET 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 921 MET 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 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 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: 0.0670 chunk 38 optimal weight: 0.0870 chunk 102 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN 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 = 0.4095 r_free = 0.4095 target = 0.174773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133573 restraints weight = 13419.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130907 restraints weight = 11238.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132367 restraints weight = 9946.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132900 restraints weight = 6797.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132980 restraints weight = 6001.751| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9504 Z= 0.089 Angle : 0.556 8.125 12866 Z= 0.280 Chirality : 0.040 0.154 1473 Planarity : 0.003 0.031 1632 Dihedral : 8.213 134.550 1445 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.96 % Allowed : 17.91 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.76 (0.21), residues: 1185 helix: -2.28 (0.18), residues: 639 sheet: -2.41 (0.81), residues: 26 loop : -2.67 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 517 TYR 0.026 0.001 TYR U 538 PHE 0.021 0.001 PHE U1014 TRP 0.010 0.001 TRP U 846 HIS 0.006 0.001 HIS U 631 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9503) covalent geometry : angle 0.55637 (12866) hydrogen bonds : bond 0.02364 ( 183) hydrogen bonds : angle 3.99415 ( 513) Misc. bond : bond 0.00007 ( 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 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.336 Fit side-chains REVERT: U 80 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8447 (mm) REVERT: U 154 ILE cc_start: 0.8847 (tp) cc_final: 0.8448 (tp) REVERT: U 173 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (mtmm) REVERT: U 183 MET cc_start: 0.8879 (mmm) cc_final: 0.8357 (mmm) REVERT: U 299 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7772 (tmm-80) REVERT: U 371 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8443 (mt) REVERT: U 373 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8635 (tp) REVERT: U 424 ASN cc_start: 0.5158 (p0) cc_final: 0.4748 (p0) REVERT: U 478 MET cc_start: 0.6466 (ppp) cc_final: 0.5805 (mmt) REVERT: U 533 LYS cc_start: 0.7542 (tttm) cc_final: 0.7169 (pttt) REVERT: U 576 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7265 (t0) REVERT: U 578 LYS cc_start: 0.8055 (mppt) cc_final: 0.7590 (mmtt) REVERT: U 596 MET cc_start: 0.6563 (tpt) cc_final: 0.5897 (ptm) REVERT: U 610 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8081 (mp) REVERT: U 631 HIS cc_start: 0.5511 (OUTLIER) cc_final: 0.5303 (m-70) REVERT: U 878 MET cc_start: 0.8165 (tmm) cc_final: 0.7846 (tmm) REVERT: U 913 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7930 (mt) REVERT: U 918 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5303 (tp-100) REVERT: U 920 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5007 (mtt90) REVERT: U 921 MET cc_start: 0.5573 (tpt) cc_final: 0.4708 (ttp) REVERT: U 933 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7469 (tt) REVERT: U 1031 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8435 (tt) REVERT: U 1037 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: U 1161 GLN cc_start: 0.7133 (tt0) cc_final: 0.6855 (tp40) REVERT: U 1221 ARG cc_start: 0.7038 (tmm160) cc_final: 0.6835 (ppt170) REVERT: U 1226 ARG cc_start: 0.6722 (mtm180) cc_final: 0.6372 (mmm-85) REVERT: U 1227 ILE cc_start: 0.7378 (mp) cc_final: 0.7141 (tp) REVERT: U 1270 CYS cc_start: 0.7330 (t) cc_final: 0.6799 (m) outliers start: 49 outliers final: 24 residues processed: 158 average time/residue: 0.0954 time to fit residues: 20.6440 Evaluate side-chains 153 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 335 LEU Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 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 515 ASN 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 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 839 MET Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 903 VAL 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 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 1265 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN U 631 HIS U 946 ASN U1198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.170326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128253 restraints weight = 13494.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127244 restraints weight = 12828.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128397 restraints weight = 11281.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128955 restraints weight = 7476.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128973 restraints weight = 7135.810| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9504 Z= 0.195 Angle : 0.649 8.581 12866 Z= 0.330 Chirality : 0.044 0.141 1473 Planarity : 0.004 0.039 1632 Dihedral : 8.456 134.357 1445 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.66 % Allowed : 18.62 % Favored : 76.72 % 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: -3.88 (0.22), residues: 1185 helix: -2.36 (0.18), residues: 645 sheet: -2.79 (0.71), residues: 39 loop : -2.72 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 566 TYR 0.014 0.002 TYR U 144 PHE 0.021 0.001 PHE U1014 TRP 0.013 0.001 TRP U 493 HIS 0.016 0.001 HIS U 631 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9503) covalent geometry : angle 0.64907 (12866) hydrogen bonds : bond 0.03032 ( 183) hydrogen bonds : angle 4.32699 ( 513) Misc. bond : bond 0.00020 ( 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 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.299 Fit side-chains REVERT: U 80 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8514 (mm) REVERT: U 154 ILE cc_start: 0.8909 (tp) cc_final: 0.8450 (tp) REVERT: U 173 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: U 183 MET cc_start: 0.8899 (mmm) cc_final: 0.8374 (mmm) REVERT: U 373 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8650 (tp) REVERT: U 424 ASN cc_start: 0.5202 (p0) cc_final: 0.4767 (p0) REVERT: U 450 MET cc_start: 0.7136 (ptp) cc_final: 0.6925 (ptm) REVERT: U 478 MET cc_start: 0.6402 (ppp) cc_final: 0.5842 (mmt) REVERT: U 533 LYS cc_start: 0.7603 (tttm) cc_final: 0.7285 (pttt) REVERT: U 576 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7281 (t0) REVERT: U 596 MET cc_start: 0.6541 (tpt) cc_final: 0.5920 (ptm) REVERT: U 610 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8157 (mp) REVERT: U 631 HIS cc_start: 0.5349 (OUTLIER) cc_final: 0.5110 (m-70) REVERT: U 913 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8003 (mt) REVERT: U 918 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5163 (tp-100) REVERT: U 920 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.4932 (mtt90) REVERT: U 921 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.4633 (ttp) REVERT: U 933 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7837 (tt) REVERT: U 1031 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8557 (tt) REVERT: U 1145 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7154 (ptmt) REVERT: U 1161 GLN cc_start: 0.7177 (tt0) cc_final: 0.6871 (tp40) REVERT: U 1221 ARG cc_start: 0.7088 (tmm160) cc_final: 0.6670 (ppt170) REVERT: U 1289 MET cc_start: 0.3495 (mpp) cc_final: 0.1798 (mmm) outliers start: 46 outliers final: 25 residues processed: 153 average time/residue: 0.1055 time to fit residues: 22.0048 Evaluate side-chains 151 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 903 VAL 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 921 MET Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1234 VAL Chi-restraints excluded: chain U residue 1265 ARG 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: 2.9990 chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN 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 = 0.4022 r_free = 0.4022 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128636 restraints weight = 13013.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127399 restraints weight = 12596.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128527 restraints weight = 11278.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128988 restraints weight = 7690.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129401 restraints weight = 6669.585| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 9504 Z= 0.100 Angle : 0.592 9.797 12866 Z= 0.298 Chirality : 0.040 0.189 1473 Planarity : 0.003 0.031 1632 Dihedral : 8.137 134.405 1443 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.25 % Allowed : 19.43 % Favored : 76.32 % 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: -3.56 (0.22), residues: 1185 helix: -2.08 (0.19), residues: 638 sheet: -2.57 (0.75), residues: 39 loop : -2.60 (0.25), residues: 508 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 0.011 0.001 TRP U 846 HIS 0.014 0.001 HIS U 631 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9503) covalent geometry : angle 0.59235 (12866) hydrogen bonds : bond 0.02340 ( 183) hydrogen bonds : angle 4.04635 ( 513) Misc. bond : bond 0.00004 ( 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 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.346 Fit side-chains REVERT: U 80 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8494 (mm) REVERT: U 154 ILE cc_start: 0.8853 (tp) cc_final: 0.8452 (tp) REVERT: U 173 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8392 (mtmm) REVERT: U 183 MET cc_start: 0.8841 (mmm) cc_final: 0.8275 (mmm) REVERT: U 299 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7701 (tmm-80) REVERT: U 373 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8747 (tp) REVERT: U 424 ASN cc_start: 0.5043 (p0) cc_final: 0.4598 (p0) REVERT: U 478 MET cc_start: 0.6346 (ppp) cc_final: 0.5792 (mmt) REVERT: U 533 LYS cc_start: 0.7607 (tttm) cc_final: 0.7300 (pttt) REVERT: U 576 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7223 (t0) REVERT: U 578 LYS cc_start: 0.8082 (mppt) cc_final: 0.7667 (mmtt) REVERT: U 596 MET cc_start: 0.6660 (tpt) cc_final: 0.6007 (ptm) REVERT: U 610 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8185 (mp) REVERT: U 631 HIS cc_start: 0.5309 (OUTLIER) cc_final: 0.5006 (m-70) REVERT: U 913 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7946 (mt) REVERT: U 918 GLN cc_start: 0.6213 (OUTLIER) cc_final: 0.5191 (tp-100) REVERT: U 920 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.4748 (mtt90) REVERT: U 933 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7568 (tt) REVERT: U 1031 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8464 (tt) REVERT: U 1161 GLN cc_start: 0.7137 (tt0) cc_final: 0.6133 (tp40) REVERT: U 1221 ARG cc_start: 0.6958 (tmm160) cc_final: 0.6683 (ppt170) REVERT: U 1226 ARG cc_start: 0.6688 (mtm180) cc_final: 0.6457 (mtp-110) REVERT: U 1289 MET cc_start: 0.4138 (mpp) cc_final: 0.2980 (mpp) outliers start: 42 outliers final: 23 residues processed: 147 average time/residue: 0.1086 time to fit residues: 21.9695 Evaluate side-chains 148 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain U residue 248 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 515 ASN 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 621 ARG Chi-restraints excluded: chain U residue 631 HIS 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 839 MET Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 903 VAL 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 1031 LEU 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 1265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 8.9990 chunk 78 optimal weight: 0.0050 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN 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 = 0.4028 r_free = 0.4028 target = 0.170390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129479 restraints weight = 13150.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128150 restraints weight = 13225.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129658 restraints weight = 11664.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129855 restraints weight = 8326.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130191 restraints weight = 7118.352| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 9504 Z= 0.107 Angle : 0.599 10.115 12866 Z= 0.302 Chirality : 0.041 0.191 1473 Planarity : 0.003 0.043 1632 Dihedral : 8.111 134.478 1443 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.85 % Allowed : 20.04 % Favored : 76.11 % 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: -3.40 (0.22), residues: 1185 helix: -1.93 (0.19), residues: 634 sheet: -2.51 (0.77), residues: 39 loop : -2.56 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 299 TYR 0.040 0.001 TYR U 538 PHE 0.014 0.001 PHE U1085 TRP 0.010 0.001 TRP U 846 HIS 0.006 0.001 HIS U 631 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9503) covalent geometry : angle 0.59946 (12866) hydrogen bonds : bond 0.02408 ( 183) hydrogen bonds : angle 4.04699 ( 513) Misc. bond : bond 0.00006 ( 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 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8478 (mm) REVERT: U 154 ILE cc_start: 0.8803 (tp) cc_final: 0.8404 (tp) REVERT: U 173 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8406 (mtmm) REVERT: U 183 MET cc_start: 0.8832 (mmm) cc_final: 0.8256 (mmm) REVERT: U 224 MET cc_start: 0.8167 (tpt) cc_final: 0.7891 (tpp) REVERT: U 299 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7712 (tmm-80) REVERT: U 371 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8499 (mt) REVERT: U 373 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8663 (tp) REVERT: U 424 ASN cc_start: 0.5032 (p0) cc_final: 0.4577 (p0) REVERT: U 478 MET cc_start: 0.6364 (ppp) cc_final: 0.5804 (mmt) REVERT: U 533 LYS cc_start: 0.7593 (tttm) cc_final: 0.7291 (pttt) REVERT: U 576 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7230 (t0) REVERT: U 578 LYS cc_start: 0.8084 (mppt) cc_final: 0.7670 (mmtt) REVERT: U 596 MET cc_start: 0.6801 (tpt) cc_final: 0.6046 (ptm) REVERT: U 610 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8179 (mp) REVERT: U 913 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7929 (mt) REVERT: U 918 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5193 (tp-100) REVERT: U 920 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4722 (mtt90) REVERT: U 933 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7532 (tt) REVERT: U 1031 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8472 (tt) REVERT: U 1151 PHE cc_start: 0.7564 (t80) cc_final: 0.7159 (t80) REVERT: U 1161 GLN cc_start: 0.7136 (tt0) cc_final: 0.6130 (tp40) REVERT: U 1221 ARG cc_start: 0.6901 (tmm160) cc_final: 0.6653 (ppt170) REVERT: U 1289 MET cc_start: 0.4112 (mpp) cc_final: 0.2979 (mpp) outliers start: 38 outliers final: 22 residues processed: 146 average time/residue: 0.1161 time to fit residues: 22.8245 Evaluate side-chains 150 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 429 TYR Chi-restraints excluded: chain U residue 468 ILE 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 621 ARG 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 846 TRP Chi-restraints excluded: chain U residue 903 VAL 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 1031 LEU 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 1265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 94 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 515 ASN U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131042 restraints weight = 13230.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131848 restraints weight = 10227.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132392 restraints weight = 7838.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132575 restraints weight = 5961.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132698 restraints weight = 5224.562| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9504 Z= 0.216 Angle : 0.673 9.616 12866 Z= 0.342 Chirality : 0.046 0.191 1473 Planarity : 0.004 0.043 1632 Dihedral : 8.457 134.202 1443 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.25 % Allowed : 19.53 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.22), residues: 1185 helix: -2.28 (0.18), residues: 658 sheet: -2.86 (0.73), residues: 40 loop : -2.71 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 299 TYR 0.014 0.002 TYR U1176 PHE 0.014 0.001 PHE U 90 TRP 0.012 0.002 TRP U 752 HIS 0.003 0.001 HIS U 72 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9503) covalent geometry : angle 0.67255 (12866) hydrogen bonds : bond 0.03216 ( 183) hydrogen bonds : angle 4.49687 ( 513) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.98 seconds wall clock time: 27 minutes 1.04 seconds (1621.04 seconds total)