Starting phenix.real_space_refine on Fri Mar 14 01:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dv5_30870/03_2025/7dv5_30870.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dv5_30870/03_2025/7dv5_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_2025/7dv5_30870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2025/7dv5_30870.map" model { file = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2025/7dv5_30870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dv5_30870/03_2025/7dv5_30870.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.38, per 1000 atoms: 0.58 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 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: 1.07 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: 2.65 Time building geometry restraints manager: 2.88 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: 0.830 Set stop_for_unknowns flag: 0.010 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 : 0.011 0.148 9503 Z= 0.669 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.60 (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 TRP 0.023 0.003 TRP U 163 HIS 0.009 0.002 HIS U 72 PHE 0.026 0.003 PHE U 629 TYR 0.028 0.003 TYR U 981 ARG 0.014 0.001 ARG U1001 *********************** 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 : 1.069 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: 0.4738 (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: 0.5941 (mmt) REVERT: U 516 ILE cc_start: 0.9009 (mt) cc_final: 0.8714 (mm) REVERT: U 533 LYS cc_start: 0.7873 (tttm) cc_final: 0.7367 (pttt) REVERT: U 913 LEU cc_start: 0.8530 (tm) cc_final: 0.8062 (mt) REVERT: U 918 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.5912 (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: 0.6568 (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: 0.8224 (mt) outliers start: 22 outliers final: 10 residues processed: 206 average time/residue: 0.2747 time to fit residues: 73.9931 Evaluate side-chains 128 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 372 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127636 restraints weight = 13534.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126558 restraints weight = 9395.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127709 restraints weight = 9103.723| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9503 Z= 0.169 Angle : 0.678 8.303 12866 Z= 0.349 Chirality : 0.042 0.164 1473 Planarity : 0.004 0.051 1632 Dihedral : 9.928 134.284 1464 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.94 % Allowed : 13.46 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.17), residues: 1185 helix: -4.14 (0.12), residues: 638 sheet: -3.74 (0.72), residues: 26 loop : -3.23 (0.23), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 330 HIS 0.004 0.001 HIS U1142 PHE 0.012 0.001 PHE U1085 TYR 0.019 0.002 TYR U 157 ARG 0.004 0.001 ARG U1128 *********************** 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 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 123 MET cc_start: 0.0341 (mmt) cc_final: 0.0118 (mmt) REVERT: U 144 TYR cc_start: 0.8197 (m-10) cc_final: 0.7921 (m-80) REVERT: U 154 ILE cc_start: 0.8824 (tp) cc_final: 0.8269 (tp) REVERT: U 173 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: U 191 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: U 424 ASN cc_start: 0.5281 (p0) cc_final: 0.4929 (p0) REVERT: U 472 TYR cc_start: 0.8541 (m-80) cc_final: 0.8332 (m-80) REVERT: U 478 MET cc_start: 0.6443 (ppp) cc_final: 0.5744 (mmt) REVERT: U 533 LYS cc_start: 0.7627 (tttm) cc_final: 0.7308 (pttt) REVERT: U 576 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7341 (t0) REVERT: U 610 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8006 (mp) REVERT: U 913 LEU cc_start: 0.8448 (tm) cc_final: 0.7980 (mt) REVERT: U 918 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5472 (tp-100) REVERT: U 920 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5070 (mtt90) REVERT: U 921 MET cc_start: 0.5584 (tpt) cc_final: 0.4457 (ttp) REVERT: U 928 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6044 (ptp90) REVERT: U 946 ASN cc_start: 0.8371 (p0) cc_final: 0.8117 (p0) REVERT: U 1006 LEU cc_start: 0.9025 (mp) cc_final: 0.8792 (mt) REVERT: U 1037 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: U 1145 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7472 (ptmt) REVERT: U 1161 GLN cc_start: 0.6868 (tt0) cc_final: 0.6493 (tp40) REVERT: U 1171 MET cc_start: 0.8120 (tmm) cc_final: 0.7813 (tmm) REVERT: U 1270 CYS cc_start: 0.7464 (t) cc_final: 0.6819 (m) outliers start: 29 outliers final: 8 residues processed: 162 average time/residue: 0.2953 time to fit residues: 65.0138 Evaluate side-chains 128 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8524 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.170291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129035 restraints weight = 13570.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127592 restraints weight = 11528.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128834 restraints weight = 10860.290| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9503 Z= 0.154 Angle : 0.606 8.061 12866 Z= 0.309 Chirality : 0.041 0.150 1473 Planarity : 0.004 0.038 1632 Dihedral : 8.934 135.327 1448 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.44 % Allowed : 14.98 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.19), residues: 1185 helix: -3.55 (0.14), residues: 647 sheet: -3.29 (0.74), residues: 26 loop : -3.15 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 846 HIS 0.003 0.001 HIS U1142 PHE 0.014 0.001 PHE U1014 TYR 0.014 0.001 TYR U 274 ARG 0.004 0.000 ARG U 792 *********************** 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 169 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: U 144 TYR cc_start: 0.8132 (m-10) cc_final: 0.7899 (m-80) REVERT: U 154 ILE cc_start: 0.8891 (tp) cc_final: 0.8371 (tp) REVERT: U 173 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8325 (mtmm) REVERT: U 371 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8593 (mt) REVERT: U 424 ASN cc_start: 0.5300 (p0) cc_final: 0.4967 (p0) REVERT: U 478 MET cc_start: 0.6422 (ppp) cc_final: 0.5782 (mmt) REVERT: U 533 LYS cc_start: 0.7544 (tttm) cc_final: 0.7252 (pttt) REVERT: U 576 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7251 (t0) REVERT: U 578 LYS cc_start: 0.8131 (mppt) cc_final: 0.7705 (mmtt) REVERT: U 878 MET cc_start: 0.8169 (tmm) cc_final: 0.7906 (tmm) REVERT: U 913 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7932 (mt) REVERT: U 918 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5456 (tp-100) REVERT: U 920 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.5038 (mtt90) REVERT: U 921 MET cc_start: 0.5717 (tpt) cc_final: 0.4619 (ttp) REVERT: U 928 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6088 (ptp90) REVERT: U 1037 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: U 1145 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7308 (ptmt) REVERT: U 1161 GLN cc_start: 0.6963 (tt0) cc_final: 0.6389 (tp40) REVERT: U 1171 MET cc_start: 0.8066 (tmm) cc_final: 0.7802 (tmm) REVERT: U 1270 CYS cc_start: 0.7275 (t) cc_final: 0.6786 (m) outliers start: 34 outliers final: 12 residues processed: 160 average time/residue: 0.2485 time to fit residues: 54.4642 Evaluate side-chains 129 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 173 LYS 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 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 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1031 LEU Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** U 640 HIS U 946 ASN U1097 ASN U1124 GLN U1281 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120558 restraints weight = 13345.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118158 restraints weight = 10961.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119121 restraints weight = 12741.141| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9503 Z= 0.440 Angle : 0.762 9.139 12866 Z= 0.391 Chirality : 0.049 0.142 1473 Planarity : 0.005 0.049 1632 Dihedral : 9.405 133.372 1446 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.77 % Allowed : 15.49 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.19), residues: 1185 helix: -3.36 (0.15), residues: 647 sheet: -3.22 (0.71), residues: 26 loop : -3.13 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 846 HIS 0.004 0.001 HIS U 484 PHE 0.026 0.002 PHE U 427 TYR 0.017 0.002 TYR U1176 ARG 0.006 0.001 ARG U1128 *********************** 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 176 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: U 123 MET cc_start: 0.0270 (mmt) cc_final: -0.0141 (mmt) REVERT: U 154 ILE cc_start: 0.8890 (tp) cc_final: 0.8256 (tp) REVERT: U 173 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8489 (mtmm) REVERT: U 183 MET cc_start: 0.8917 (mmm) cc_final: 0.8458 (mmm) REVERT: U 224 MET cc_start: 0.8147 (tpt) cc_final: 0.7778 (tpt) REVERT: U 299 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7888 (tmm-80) REVERT: U 373 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8853 (tp) REVERT: U 424 ASN cc_start: 0.5434 (p0) cc_final: 0.5115 (p0) REVERT: U 478 MET cc_start: 0.6610 (ppp) cc_final: 0.5565 (mmm) REVERT: U 533 LYS cc_start: 0.7628 (tttm) cc_final: 0.7294 (pttt) REVERT: U 576 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7307 (t0) REVERT: U 610 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8282 (mp) REVERT: U 878 MET cc_start: 0.8231 (tmm) cc_final: 0.7862 (tmm) REVERT: U 913 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7898 (mp) REVERT: U 918 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.5540 (tp-100) REVERT: U 920 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5045 (mtt90) REVERT: U 921 MET cc_start: 0.6382 (tpt) cc_final: 0.4755 (ttp) REVERT: U 928 ARG cc_start: 0.7232 (tpt170) cc_final: 0.6212 (ptp90) REVERT: U 933 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8016 (tt) REVERT: U 946 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8421 (p0) REVERT: U 1145 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7449 (ptmt) REVERT: U 1161 GLN cc_start: 0.7122 (tt0) cc_final: 0.6383 (tp40) REVERT: U 1185 MET cc_start: 0.5040 (tpp) cc_final: 0.4802 (tpt) REVERT: U 1238 LYS cc_start: 0.7519 (mmpt) cc_final: 0.7136 (mttt) REVERT: U 1270 CYS cc_start: 0.7579 (t) cc_final: 0.6976 (m) outliers start: 57 outliers final: 28 residues processed: 165 average time/residue: 0.2325 time to fit residues: 52.7590 Evaluate side-chains 146 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 362 ILE 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 407 SER 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 863 THR 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 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 946 ASN Chi-restraints excluded: chain U residue 960 ILE Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL 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 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 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** U1124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131094 restraints weight = 13246.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130810 restraints weight = 9834.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131918 restraints weight = 7702.604| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9503 Z= 0.144 Angle : 0.605 10.403 12866 Z= 0.302 Chirality : 0.040 0.150 1473 Planarity : 0.003 0.037 1632 Dihedral : 8.640 134.947 1444 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.45 % Allowed : 16.60 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.20), residues: 1185 helix: -2.94 (0.17), residues: 638 sheet: -2.72 (0.75), residues: 26 loop : -2.93 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 846 HIS 0.003 0.000 HIS U1142 PHE 0.019 0.001 PHE U 90 TYR 0.012 0.001 TYR U 274 ARG 0.003 0.000 ARG U 299 *********************** 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 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (mm) REVERT: U 154 ILE cc_start: 0.8797 (tp) cc_final: 0.8262 (tp) REVERT: U 173 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: U 299 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7802 (tmm-80) REVERT: U 373 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8812 (tp) REVERT: U 424 ASN cc_start: 0.5131 (p0) cc_final: 0.4759 (p0) REVERT: U 478 MET cc_start: 0.6474 (ppp) cc_final: 0.5859 (mmt) REVERT: U 533 LYS cc_start: 0.7585 (tttm) cc_final: 0.7266 (pttt) REVERT: U 576 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7203 (t0) REVERT: U 578 LYS cc_start: 0.8080 (mppt) cc_final: 0.7613 (mmtt) REVERT: U 610 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8107 (mp) REVERT: U 878 MET cc_start: 0.8196 (tmm) cc_final: 0.7839 (tmm) REVERT: U 913 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7973 (mt) REVERT: U 918 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5449 (tp-100) REVERT: U 920 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.4958 (mtt90) REVERT: U 921 MET cc_start: 0.5914 (tpt) cc_final: 0.4474 (ttp) REVERT: U 933 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7650 (tt) REVERT: U 1037 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: U 1145 LYS cc_start: 0.7760 (mmmm) cc_final: 0.7322 (ptmt) REVERT: U 1161 GLN cc_start: 0.7111 (tt0) cc_final: 0.6308 (tp40) REVERT: U 1221 ARG cc_start: 0.7083 (ptm160) cc_final: 0.6442 (ppt170) REVERT: U 1270 CYS cc_start: 0.7506 (t) cc_final: 0.6939 (m) outliers start: 44 outliers final: 20 residues processed: 154 average time/residue: 0.2350 time to fit residues: 49.6331 Evaluate side-chains 139 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 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 785 ILE Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 922 LEU Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1037 TYR Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- 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** U 631 HIS U 946 ASN U1225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123926 restraints weight = 13110.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122562 restraints weight = 13306.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123640 restraints weight = 12372.692| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9503 Z= 0.276 Angle : 0.647 8.484 12866 Z= 0.327 Chirality : 0.044 0.145 1473 Planarity : 0.004 0.040 1632 Dihedral : 8.737 134.623 1444 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.96 % Allowed : 18.52 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.21), residues: 1185 helix: -2.84 (0.17), residues: 638 sheet: -2.56 (0.79), residues: 26 loop : -2.92 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 493 HIS 0.005 0.001 HIS U 631 PHE 0.017 0.001 PHE U 90 TYR 0.014 0.001 TYR U 274 ARG 0.004 0.000 ARG U1128 *********************** 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 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8498 (mm) REVERT: U 123 MET cc_start: -0.0237 (mmt) cc_final: -0.0996 (mmt) REVERT: U 154 ILE cc_start: 0.8867 (tp) cc_final: 0.8313 (tp) REVERT: U 173 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: U 373 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8622 (tp) REVERT: U 424 ASN cc_start: 0.5169 (p0) cc_final: 0.4774 (p0) REVERT: U 478 MET cc_start: 0.6476 (ppp) cc_final: 0.5759 (mmt) REVERT: U 533 LYS cc_start: 0.7605 (tttm) cc_final: 0.7313 (pttt) REVERT: U 559 MET cc_start: 0.4612 (OUTLIER) cc_final: 0.4375 (mtt) REVERT: U 576 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7293 (t0) REVERT: U 610 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8252 (mp) REVERT: U 913 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7886 (mt) REVERT: U 918 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5351 (tp-100) REVERT: U 920 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.4847 (mtt90) REVERT: U 921 MET cc_start: 0.6125 (tpt) cc_final: 0.4480 (ttp) REVERT: U 933 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7952 (tt) REVERT: U 1145 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7363 (ptmt) REVERT: U 1162 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7153 (tm-30) REVERT: U 1238 LYS cc_start: 0.7505 (mmpt) cc_final: 0.7189 (mttt) REVERT: U 1270 CYS cc_start: 0.7618 (t) cc_final: 0.6988 (m) outliers start: 49 outliers final: 30 residues processed: 154 average time/residue: 0.2589 time to fit residues: 55.8416 Evaluate side-chains 156 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 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 559 MET Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 764 VAL Chi-restraints excluded: chain U residue 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 1012 LEU Chi-restraints excluded: chain U residue 1025 VAL Chi-restraints excluded: chain U residue 1125 LEU Chi-restraints excluded: chain U residue 1126 LEU Chi-restraints excluded: chain U residue 1149 VAL Chi-restraints excluded: chain U residue 1174 ILE Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** U 946 ASN U1225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.125937 restraints weight = 13289.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.123877 restraints weight = 12894.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125134 restraints weight = 13551.774| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9503 Z= 0.224 Angle : 0.615 8.318 12866 Z= 0.312 Chirality : 0.042 0.190 1473 Planarity : 0.004 0.039 1632 Dihedral : 8.577 134.787 1444 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.06 % Allowed : 19.13 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.21), residues: 1185 helix: -2.66 (0.18), residues: 641 sheet: -2.41 (0.82), residues: 26 loop : -2.83 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 752 HIS 0.003 0.001 HIS U 631 PHE 0.021 0.001 PHE U 90 TYR 0.031 0.001 TYR U 538 ARG 0.006 0.000 ARG U 299 *********************** 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 169 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8484 (mm) REVERT: U 123 MET cc_start: -0.0271 (mmt) cc_final: -0.0983 (mmt) REVERT: U 154 ILE cc_start: 0.8851 (tp) cc_final: 0.8415 (tp) REVERT: U 173 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8422 (mtmm) REVERT: U 299 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7819 (tmm-80) REVERT: U 373 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8708 (tp) REVERT: U 424 ASN cc_start: 0.5078 (p0) cc_final: 0.4635 (p0) REVERT: U 450 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6142 (ptm) REVERT: U 478 MET cc_start: 0.6495 (ppp) cc_final: 0.5801 (mmt) REVERT: U 533 LYS cc_start: 0.7533 (tttm) cc_final: 0.7284 (pttt) REVERT: U 576 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7331 (t0) REVERT: U 610 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8255 (mp) REVERT: U 913 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7946 (mt) REVERT: U 918 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5303 (tp-100) REVERT: U 920 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.4821 (mtt90) REVERT: U 921 MET cc_start: 0.6021 (tpt) cc_final: 0.4576 (ttp) REVERT: U 933 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7696 (tt) REVERT: U 1145 LYS cc_start: 0.7706 (mmmm) cc_final: 0.7367 (ptmt) REVERT: U 1161 GLN cc_start: 0.7104 (tp40) cc_final: 0.6768 (tp40) REVERT: U 1270 CYS cc_start: 0.7615 (t) cc_final: 0.7002 (m) outliers start: 50 outliers final: 32 residues processed: 155 average time/residue: 0.2331 time to fit residues: 49.5579 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 185 MET Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 426 THR Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 621 ARG 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 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 1025 VAL 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 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 0.0070 chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 overall best weight: 1.2806 ------------------------------------------------------------------------------- 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** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128652 restraints weight = 13396.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126297 restraints weight = 10283.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127630 restraints weight = 8702.547| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 9503 Z= 0.181 Angle : 0.599 10.007 12866 Z= 0.298 Chirality : 0.041 0.191 1473 Planarity : 0.003 0.035 1632 Dihedral : 8.348 134.974 1444 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.06 % Allowed : 19.33 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.22), residues: 1185 helix: -2.42 (0.18), residues: 640 sheet: -2.22 (0.85), residues: 26 loop : -2.72 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 846 HIS 0.005 0.001 HIS U 631 PHE 0.022 0.001 PHE U 90 TYR 0.011 0.001 TYR U 274 ARG 0.005 0.000 ARG U 299 *********************** 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 175 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8381 (mm) REVERT: U 123 MET cc_start: -0.0181 (mmt) cc_final: -0.0798 (mmt) REVERT: U 154 ILE cc_start: 0.8829 (tp) cc_final: 0.8406 (tp) REVERT: U 173 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8336 (mtmm) REVERT: U 299 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7772 (tmm-80) REVERT: U 373 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8711 (tp) REVERT: U 424 ASN cc_start: 0.5220 (p0) cc_final: 0.4776 (p0) REVERT: U 478 MET cc_start: 0.6604 (ppp) cc_final: 0.5736 (mmt) REVERT: U 533 LYS cc_start: 0.7652 (tttm) cc_final: 0.7266 (pttt) REVERT: U 576 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7307 (t0) REVERT: U 596 MET cc_start: 0.6534 (tpt) cc_final: 0.5943 (ptm) REVERT: U 610 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8001 (mp) REVERT: U 631 HIS cc_start: 0.5360 (OUTLIER) cc_final: 0.4947 (m-70) REVERT: U 878 MET cc_start: 0.8202 (tmm) cc_final: 0.7777 (tmm) REVERT: U 913 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7849 (mt) REVERT: U 918 GLN cc_start: 0.6164 (OUTLIER) cc_final: 0.5106 (tp-100) REVERT: U 920 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.4386 (mtt90) REVERT: U 933 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7339 (tt) REVERT: U 1037 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: U 1145 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7253 (ptmt) REVERT: U 1151 PHE cc_start: 0.7747 (t80) cc_final: 0.7057 (t80) REVERT: U 1161 GLN cc_start: 0.7215 (tp40) cc_final: 0.6887 (tp40) REVERT: U 1162 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7376 (tm-30) REVERT: U 1221 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6507 (tmm160) REVERT: U 1270 CYS cc_start: 0.7781 (t) cc_final: 0.6940 (m) outliers start: 50 outliers final: 27 residues processed: 162 average time/residue: 0.2468 time to fit residues: 54.7358 Evaluate side-chains 151 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 576 ASN Chi-restraints excluded: chain U residue 580 LEU Chi-restraints excluded: chain U residue 600 VAL Chi-restraints excluded: chain U residue 610 ILE Chi-restraints excluded: chain U residue 621 ARG 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 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 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 1201 VAL Chi-restraints excluded: chain U residue 1265 ARG Chi-restraints excluded: chain U residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130805 restraints weight = 13087.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130885 restraints weight = 9589.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131853 restraints weight = 6941.420| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 9503 Z= 0.177 Angle : 0.599 10.346 12866 Z= 0.299 Chirality : 0.041 0.187 1473 Planarity : 0.003 0.033 1632 Dihedral : 8.229 134.913 1444 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.15 % Allowed : 19.84 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.22), residues: 1185 helix: -2.18 (0.19), residues: 641 sheet: -2.57 (0.75), residues: 31 loop : -2.69 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 846 HIS 0.017 0.001 HIS U 631 PHE 0.020 0.001 PHE U1014 TYR 0.011 0.001 TYR U 354 ARG 0.005 0.000 ARG U 299 *********************** 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 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 123 MET cc_start: -0.0153 (mmt) cc_final: -0.0735 (mmt) REVERT: U 154 ILE cc_start: 0.8849 (tp) cc_final: 0.8449 (tp) REVERT: U 173 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8422 (mtmm) REVERT: U 183 MET cc_start: 0.8915 (mmm) cc_final: 0.8233 (mmm) REVERT: U 299 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7758 (tmm-80) REVERT: U 373 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8761 (tp) REVERT: U 424 ASN cc_start: 0.5008 (p0) cc_final: 0.4562 (p0) REVERT: U 478 MET cc_start: 0.6469 (ppp) cc_final: 0.5744 (mmt) REVERT: U 533 LYS cc_start: 0.7616 (tttm) cc_final: 0.7290 (pttt) REVERT: U 576 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7299 (t0) REVERT: U 596 MET cc_start: 0.6585 (tpt) cc_final: 0.6088 (ptm) REVERT: U 610 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8130 (mp) REVERT: U 631 HIS cc_start: 0.5192 (OUTLIER) cc_final: 0.4935 (m-70) REVERT: U 878 MET cc_start: 0.8193 (tmm) cc_final: 0.7837 (tmm) REVERT: U 913 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7933 (mt) REVERT: U 918 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5284 (tp-100) REVERT: U 920 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.4696 (mtt90) REVERT: U 933 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7521 (tt) REVERT: U 1037 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: U 1145 LYS cc_start: 0.7754 (mmmm) cc_final: 0.7244 (ptmt) REVERT: U 1151 PHE cc_start: 0.7563 (t80) cc_final: 0.7049 (t80) REVERT: U 1161 GLN cc_start: 0.7203 (tp40) cc_final: 0.6861 (tp40) REVERT: U 1162 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7272 (tm-30) REVERT: U 1289 MET cc_start: 0.3139 (mmt) cc_final: 0.2143 (mpp) outliers start: 41 outliers final: 27 residues processed: 151 average time/residue: 0.2403 time to fit residues: 49.6507 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 : 1.041 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 511 THR 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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** U 631 HIS U 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.173915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130554 restraints weight = 13265.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130902 restraints weight = 9227.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131629 restraints weight = 7020.457| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 9503 Z= 0.185 Angle : 0.598 10.584 12866 Z= 0.302 Chirality : 0.041 0.196 1473 Planarity : 0.003 0.033 1632 Dihedral : 8.196 134.760 1444 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.35 % Allowed : 20.24 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.22), residues: 1185 helix: -2.05 (0.19), residues: 648 sheet: -2.30 (0.78), residues: 39 loop : -2.62 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 846 HIS 0.014 0.001 HIS U 631 PHE 0.021 0.001 PHE U1014 TYR 0.010 0.001 TYR U1176 ARG 0.005 0.000 ARG U 299 ********************** 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: 43 poor density : 115 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: U 80 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8491 (mm) REVERT: U 123 MET cc_start: -0.0264 (mmt) cc_final: -0.0872 (mmt) REVERT: U 154 ILE cc_start: 0.8843 (tp) cc_final: 0.8447 (tp) REVERT: U 173 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8432 (mtmm) REVERT: U 183 MET cc_start: 0.8952 (mmm) cc_final: 0.8224 (mmm) REVERT: U 299 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7767 (tmm-80) REVERT: U 373 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8745 (tp) REVERT: U 478 MET cc_start: 0.6474 (ppp) cc_final: 0.5753 (mmt) REVERT: U 533 LYS cc_start: 0.7616 (tttm) cc_final: 0.7286 (pttt) REVERT: U 576 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7323 (t0) REVERT: U 596 MET cc_start: 0.6508 (tpt) cc_final: 0.6062 (ptm) REVERT: U 610 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8113 (mp) REVERT: U 631 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4740 (m-70) REVERT: U 878 MET cc_start: 0.8200 (tmm) cc_final: 0.7829 (tmm) REVERT: U 913 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7928 (mt) REVERT: U 918 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5323 (tp-100) REVERT: U 920 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.4552 (mtt90) REVERT: U 933 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7490 (tt) REVERT: U 1037 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7267 (m-10) REVERT: U 1151 PHE cc_start: 0.7601 (t80) cc_final: 0.7053 (t80) REVERT: U 1161 GLN cc_start: 0.7157 (tp40) cc_final: 0.6825 (tp40) REVERT: U 1162 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7276 (tm-30) REVERT: U 1226 ARG cc_start: 0.6072 (mtp-110) cc_final: 0.5776 (mtp85) REVERT: U 1270 CYS cc_start: 0.7423 (t) cc_final: 0.6828 (m) outliers start: 43 outliers final: 29 residues processed: 145 average time/residue: 0.2462 time to fit residues: 49.6648 Evaluate side-chains 155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 80 LEU Chi-restraints excluded: chain U residue 91 ILE Chi-restraints excluded: chain U residue 173 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain U residue 222 GLN Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 248 VAL Chi-restraints excluded: chain U residue 348 VAL Chi-restraints excluded: chain U residue 368 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 373 LEU Chi-restraints excluded: chain U residue 413 LEU Chi-restraints excluded: chain U residue 429 TYR Chi-restraints excluded: chain U residue 468 ILE Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 511 THR 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 767 THR Chi-restraints excluded: chain U residue 785 ILE Chi-restraints excluded: chain U residue 799 CYS Chi-restraints excluded: chain U residue 800 LEU Chi-restraints excluded: chain U residue 846 TRP Chi-restraints excluded: chain U residue 899 LYS Chi-restraints excluded: chain U residue 905 LEU Chi-restraints excluded: chain U residue 913 LEU Chi-restraints excluded: chain U residue 918 GLN Chi-restraints excluded: chain U residue 920 ARG Chi-restraints excluded: chain U residue 933 LEU Chi-restraints excluded: chain U residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 484 HIS ** U 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 631 HIS U 946 ASN U1198 HIS U1225 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130545 restraints weight = 13294.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130664 restraints weight = 9881.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131795 restraints weight = 7339.352| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9503 Z= 0.321 Angle : 0.667 10.349 12866 Z= 0.339 Chirality : 0.045 0.190 1473 Planarity : 0.004 0.040 1632 Dihedral : 8.483 134.503 1444 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.35 % Allowed : 20.65 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.22), residues: 1185 helix: -2.22 (0.19), residues: 654 sheet: -2.52 (0.77), residues: 39 loop : -2.70 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 752 HIS 0.022 0.002 HIS U 631 PHE 0.025 0.002 PHE U1014 TYR 0.037 0.002 TYR U 538 ARG 0.005 0.001 ARG U 792 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.88 seconds wall clock time: 55 minutes 12.44 seconds (3312.44 seconds total)