Starting phenix.real_space_refine on Fri Jul 3 19:12:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4d_72479/07_2026/9y4d_72479.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.212 sd= 0.744 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 62 5.49 5 S 82 5.16 5 C 9574 2.51 5 N 2713 2.21 5 O 2903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15335 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8233 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 67, 'TRANS': 962} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2977 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 352} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2885 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1209 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 15335 At special positions: 0 Unit cell: (100.62, 106.64, 158.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 62 15.00 O 2903 8.00 N 2713 7.00 C 9574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 537.7 milliseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 46.5% alpha, 13.0% beta 23 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.012A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.528A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.989A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 6.900A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 418 removed outlier: 5.944A pdb=" N GLN A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 4.106A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.993A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 473 No H-bonds generated for 'chain 'A' and resid 472 through 473' Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.054A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 555 removed outlier: 4.247A pdb=" N THR A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.021A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 810 " --> pdb=" O LYS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.644A pdb=" N LEU A 821 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.620A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.561A pdb=" N LYS A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.721A pdb=" N ALA A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1009 Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.851A pdb=" N GLU A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A1033 " --> pdb=" O GLN A1029 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 removed outlier: 3.556A pdb=" N PHE A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1084 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.814A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.913A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 4.440A pdb=" N ARG A1208 " --> pdb=" O THR A1204 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A1209 " --> pdb=" O GLY A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.821A pdb=" N GLU B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.559A pdb=" N TRP B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 254 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.047A pdb=" N MET B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 362 through 367 removed outlier: 4.089A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.715A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.684A pdb=" N SER B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 470 through 485 removed outlier: 3.682A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.635A pdb=" N GLN C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 247 through 265 removed outlier: 3.524A pdb=" N TRP C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.620A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.513A pdb=" N TYR C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.714A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 removed outlier: 3.505A pdb=" N SER C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.888A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.886A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.814A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 174 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.603A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.787A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A1183 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1218 " --> pdb=" O VAL A1183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 995 through 997 removed outlier: 6.686A pdb=" N ARG A 996 " --> pdb=" O ALA A1045 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.692A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 243 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.730A pdb=" N SER B 230 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.185A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.349A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 278 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.640A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.500A pdb=" N GLY C 324 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 331 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.305A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS C 454 " --> pdb=" O LEU C 442 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.47 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: 4453 1.33 - 1.45: 3004 1.45 - 1.57: 8143 1.57 - 1.69: 116 1.69 - 1.81: 130 Bond restraints: 15846 Sorted by residual: bond pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 1.579 1.763 -0.184 1.10e-02 8.26e+03 2.80e+02 bond pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " ideal model delta sigma weight residual 1.443 1.344 0.099 1.00e-02 1.00e+04 9.86e+01 bond pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 1.592 1.674 -0.082 1.10e-02 8.26e+03 5.52e+01 bond pdb=" C6 DTP A4002 " pdb=" N6 DTP A4002 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.10e-02 8.26e+03 1.64e+01 bond pdb=" O3B DTP A4002 " pdb=" PG DTP A4002 " ideal model delta sigma weight residual 1.600 1.706 -0.106 2.80e-02 1.28e+03 1.43e+01 ... (remaining 15841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 21611 3.27 - 6.54: 97 6.54 - 9.82: 12 9.82 - 13.09: 1 13.09 - 16.36: 6 Bond angle restraints: 21727 Sorted by residual: angle pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 136.83 122.03 14.80 1.00e+00 1.00e+00 2.19e+02 angle pdb=" O2A DTP A4002 " pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 106.94 121.49 -14.55 1.88e+00 2.83e-01 5.99e+01 angle pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 121.27 114.51 6.76 1.00e+00 1.00e+00 4.56e+01 angle pdb=" O1B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 111.24 94.88 16.36 2.72e+00 1.35e-01 3.62e+01 angle pdb=" N3 DT D 4 " pdb=" C4 DT D 4 " pdb=" O4 DT D 4 " ideal model delta sigma weight residual 119.90 122.97 -3.07 6.00e-01 2.78e+00 2.61e+01 ... (remaining 21722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7600 17.99 - 35.99: 1137 35.99 - 53.98: 414 53.98 - 71.97: 91 71.97 - 89.97: 32 Dihedral angle restraints: 9274 sinusoidal: 4218 harmonic: 5056 Sorted by residual: dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 142.22 -49.22 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA VAL C 200 " pdb=" C VAL C 200 " pdb=" N ASN C 201 " pdb=" CA ASN C 201 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR C 420 " pdb=" C THR C 420 " pdb=" N MET C 421 " pdb=" CA MET C 421 " ideal model delta harmonic sigma weight residual 180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2142 0.084 - 0.168: 184 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.421: 1 Chirality restraints: 2327 Sorted by residual: chirality pdb=" P DG D 12 " pdb=" OP1 DG D 12 " pdb=" OP2 DG D 12 " pdb=" O5' DG D 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CG LEU A 156 " pdb=" CB LEU A 156 " pdb=" CD1 LEU A 156 " pdb=" CD2 LEU A 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ASP A 868 " pdb=" N ASP A 868 " pdb=" C ASP A 868 " pdb=" CB ASP A 868 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2324 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 977 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C GLU A 977 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 977 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 978 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 389 " 0.189 9.50e-02 1.11e+02 8.54e-02 5.75e+00 pdb=" NE ARG B 389 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 389 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 389 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 389 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A1200 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " 0.031 5.00e-02 4.00e+02 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4387 2.83 - 3.34: 13065 3.34 - 3.86: 24178 3.86 - 4.38: 27235 4.38 - 4.90: 46283 Nonbonded interactions: 115148 Sorted by model distance: nonbonded pdb=" O VAL A 891 " pdb="CA CA A4001 " model vdw 2.307 3.250 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.309 3.250 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.345 3.250 nonbonded pdb="CA CA A4001 " pdb=" O1A DTP A4002 " model vdw 2.356 3.250 nonbonded pdb=" O THR A 555 " pdb=" OG1 THR A 555 " model vdw 2.470 3.040 ... (remaining 115143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or resid 228 through 355 or resid 368 through 485)) selection = chain 'C' } 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 individual isotropic 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.004 0.184 15847 Z= 0.316 Angle : 0.691 16.360 21729 Z= 0.424 Chirality : 0.044 0.421 2327 Planarity : 0.005 0.085 2579 Dihedral : 19.838 89.965 6011 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 3.82 % Allowed : 29.43 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1728 helix: 1.16 (0.20), residues: 722 sheet: 0.35 (0.33), residues: 230 loop : -0.87 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 389 TYR 0.021 0.001 TYR A 479 PHE 0.009 0.001 PHE A 539 TRP 0.009 0.001 TRP A 897 HIS 0.003 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.32 (15846) covalent geometry : angle 0.69075 / 0.42 (21727) SS BOND : bond 0.00486 / 0.26 ( 1) SS BOND : angle 0.67845 / 0.38 ( 2) hydrogen bonds : bond 0.20553 / 14.18 ( 680) hydrogen bonds : angle 6.07966 / 4.24 ( 1901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 375 time to evaluate : 0.629 Fit side-chains REVERT: A 232 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7942 (mtp-110) REVERT: A 346 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8670 (t0) REVERT: A 478 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7592 (mmt180) REVERT: A 607 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.7343 (t60) REVERT: A 741 ASP cc_start: 0.8204 (p0) cc_final: 0.7906 (p0) REVERT: A 934 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8337 (mtmm) REVERT: A 1046 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7278 (mp0) REVERT: A 1142 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7333 (mtp180) REVERT: A 1163 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7207 (tpt) REVERT: A 1194 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8658 (m) REVERT: B 465 MET cc_start: 0.8476 (mmt) cc_final: 0.7869 (mmt) REVERT: C 105 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7782 (mm-30) REVERT: C 187 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.8066 (t70) REVERT: C 280 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: C 298 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7681 (mp0) REVERT: C 310 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: C 395 LEU cc_start: 0.8098 (mt) cc_final: 0.7741 (mp) REVERT: C 419 GLU cc_start: 0.8574 (tt0) cc_final: 0.8319 (tp30) REVERT: C 426 GLU cc_start: 0.7544 (pm20) cc_final: 0.7342 (pp20) REVERT: C 449 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7394 (tm-30) outliers start: 58 outliers final: 44 residues processed: 402 average time/residue: 0.5331 time to fit residues: 239.4136 Evaluate side-chains 412 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 261 GLN C 192 HIS C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095348 restraints weight = 27907.444| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.06 r_work: 0.3195 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15847 Z= 0.155 Angle : 0.585 10.182 21729 Z= 0.323 Chirality : 0.042 0.175 2327 Planarity : 0.005 0.053 2579 Dihedral : 16.550 80.627 2658 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.13 % Allowed : 25.74 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1728 helix: 1.37 (0.20), residues: 732 sheet: 0.71 (0.33), residues: 225 loop : -0.92 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 389 TYR 0.018 0.002 TYR A 479 PHE 0.008 0.001 PHE A 539 TRP 0.009 0.001 TRP C 241 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (15846) covalent geometry : angle 0.58451 / 0.32 (21727) SS BOND : bond 0.00438 / 0.23 ( 1) SS BOND : angle 0.75202 / 0.42 ( 2) hydrogen bonds : bond 0.06096 / 4.11 ( 680) hydrogen bonds : angle 4.94683 / 3.49 ( 1901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 362 time to evaluate : 0.614 Fit side-chains REVERT: A 478 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7716 (mmt180) REVERT: A 607 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7593 (t60) REVERT: A 741 ASP cc_start: 0.8173 (p0) cc_final: 0.7884 (p0) REVERT: A 796 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8658 (ttpt) REVERT: A 934 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8339 (mtmm) REVERT: A 1046 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7238 (mp0) REVERT: A 1054 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: B 85 GLN cc_start: 0.8799 (mp10) cc_final: 0.8594 (mp10) REVERT: B 105 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7816 (mt-10) REVERT: B 465 MET cc_start: 0.8595 (mmt) cc_final: 0.8110 (mmt) REVERT: C 105 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 187 HIS cc_start: 0.8465 (OUTLIER) cc_final: 0.8055 (t70) REVERT: C 298 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7776 (mp0) REVERT: C 310 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: C 395 LEU cc_start: 0.8286 (mt) cc_final: 0.8035 (mp) outliers start: 78 outliers final: 33 residues processed: 408 average time/residue: 0.5230 time to fit residues: 238.6960 Evaluate side-chains 390 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 113 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 803 ASN A 976 GLN A1202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093599 restraints weight = 28212.860| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.05 r_work: 0.3169 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15847 Z= 0.196 Angle : 0.606 10.271 21729 Z= 0.333 Chirality : 0.044 0.177 2327 Planarity : 0.005 0.056 2579 Dihedral : 16.414 81.541 2591 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.65 % Allowed : 25.41 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1728 helix: 1.24 (0.19), residues: 737 sheet: 0.64 (0.33), residues: 231 loop : -1.04 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 389 TYR 0.028 0.002 TYR A 479 PHE 0.012 0.002 PHE B 242 TRP 0.012 0.001 TRP B 241 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (15846) covalent geometry : angle 0.60568 / 0.33 (21727) SS BOND : bond 0.00523 / 0.28 ( 1) SS BOND : angle 0.71304 / 0.40 ( 2) hydrogen bonds : bond 0.06408 / 4.37 ( 680) hydrogen bonds : angle 4.81758 / 3.40 ( 1901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 359 time to evaluate : 0.597 Fit side-chains REVERT: A 232 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7938 (mtp-110) REVERT: A 478 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7732 (mmt180) REVERT: A 607 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.7602 (t60) REVERT: A 741 ASP cc_start: 0.8203 (p0) cc_final: 0.7920 (p0) REVERT: A 775 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: A 796 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (ttpt) REVERT: A 934 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8388 (mtmm) REVERT: A 1046 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7248 (mp0) REVERT: A 1054 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: A 1163 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7199 (tpt) REVERT: B 465 MET cc_start: 0.8576 (mmt) cc_final: 0.8087 (mmt) REVERT: C 74 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: C 187 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8129 (t70) REVERT: C 197 LEU cc_start: 0.8864 (tp) cc_final: 0.8639 (tp) REVERT: C 298 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7775 (mp0) REVERT: C 310 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: C 395 LEU cc_start: 0.8322 (mt) cc_final: 0.8101 (mp) REVERT: C 427 GLN cc_start: 0.7931 (mt0) cc_final: 0.7652 (mt0) REVERT: C 449 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: C 465 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7677 (mpp) outliers start: 101 outliers final: 54 residues processed: 413 average time/residue: 0.5240 time to fit residues: 241.6051 Evaluate side-chains 410 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 345 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 497 GLN A 803 ASN A1202 ASN B 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089667 restraints weight = 28057.454| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.02 r_work: 0.3095 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 15847 Z= 0.405 Angle : 0.806 10.002 21729 Z= 0.438 Chirality : 0.053 0.189 2327 Planarity : 0.007 0.071 2579 Dihedral : 16.752 81.909 2589 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 10.07 % Allowed : 23.50 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.19), residues: 1728 helix: 0.48 (0.19), residues: 738 sheet: 0.65 (0.33), residues: 209 loop : -1.54 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.034 0.003 TYR A 479 PHE 0.024 0.003 PHE B 242 TRP 0.020 0.003 TRP B 241 HIS 0.007 0.002 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00924 / 0.41 (15846) covalent geometry : angle 0.80578 / 0.44 (21727) SS BOND : bond 0.00940 / 0.49 ( 1) SS BOND : angle 0.90470 / 0.51 ( 2) hydrogen bonds : bond 0.08727 / 6.01 ( 680) hydrogen bonds : angle 5.26122 / 3.70 ( 1901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 344 time to evaluate : 0.631 Fit side-chains REVERT: A 232 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8004 (mtp-110) REVERT: A 607 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.7691 (t60) REVERT: A 775 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: A 796 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8757 (ttpt) REVERT: A 904 ASP cc_start: 0.7449 (m-30) cc_final: 0.6972 (m-30) REVERT: A 1024 ASP cc_start: 0.8481 (m-30) cc_final: 0.8255 (m-30) REVERT: A 1046 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7239 (mp0) REVERT: A 1054 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: A 1163 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7260 (tpt) REVERT: A 1224 ILE cc_start: 0.8706 (mt) cc_final: 0.8392 (mp) REVERT: B 400 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: B 465 MET cc_start: 0.8643 (mmt) cc_final: 0.8066 (mmt) REVERT: C 74 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: C 105 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 203 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7297 (mtt-85) REVERT: C 298 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7821 (mp0) REVERT: C 310 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 314 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: C 395 LEU cc_start: 0.8414 (mt) cc_final: 0.8197 (mp) REVERT: C 427 GLN cc_start: 0.8017 (mt0) cc_final: 0.7766 (mt0) REVERT: C 449 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: C 465 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.7742 (mpp) outliers start: 153 outliers final: 76 residues processed: 427 average time/residue: 0.4729 time to fit residues: 227.3565 Evaluate side-chains 427 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 338 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 170 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 106 HIS A 110 HIS A 449 GLN A1202 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094518 restraints weight = 27915.208| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.06 r_work: 0.3184 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15847 Z= 0.134 Angle : 0.592 13.275 21729 Z= 0.321 Chirality : 0.042 0.179 2327 Planarity : 0.005 0.057 2579 Dihedral : 16.567 79.712 2587 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.46 % Allowed : 27.58 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1728 helix: 1.19 (0.19), residues: 727 sheet: 0.63 (0.34), residues: 213 loop : -1.19 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.023 0.001 TYR A 479 PHE 0.012 0.001 PHE A 539 TRP 0.013 0.001 TRP A 897 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (15846) covalent geometry : angle 0.59215 / 0.32 (21727) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 0.74878 / 0.41 ( 2) hydrogen bonds : bond 0.05481 / 3.71 ( 680) hydrogen bonds : angle 4.72193 / 3.33 ( 1901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 365 time to evaluate : 0.675 Fit side-chains REVERT: A 232 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8014 (mtp-110) REVERT: A 478 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7678 (mmt180) REVERT: A 607 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.7632 (t60) REVERT: A 775 GLU cc_start: 0.8195 (pt0) cc_final: 0.7967 (pt0) REVERT: A 796 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8632 (ttpt) REVERT: A 1024 ASP cc_start: 0.8416 (m-30) cc_final: 0.8200 (m-30) REVERT: A 1046 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7264 (mp0) REVERT: A 1054 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 1163 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7156 (tpt) REVERT: A 1224 ILE cc_start: 0.8692 (mt) cc_final: 0.8395 (mp) REVERT: B 400 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: B 455 LEU cc_start: 0.8566 (tt) cc_final: 0.8327 (tp) REVERT: B 465 MET cc_start: 0.8575 (mmt) cc_final: 0.8126 (mmt) REVERT: C 105 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 187 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7976 (t70) REVERT: C 298 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7762 (mp0) REVERT: C 310 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 387 VAL cc_start: 0.9056 (t) cc_final: 0.8845 (m) REVERT: C 395 LEU cc_start: 0.8308 (mt) cc_final: 0.8102 (mp) REVERT: C 427 GLN cc_start: 0.7833 (mt0) cc_final: 0.7589 (mt0) outliers start: 83 outliers final: 39 residues processed: 407 average time/residue: 0.5323 time to fit residues: 241.5023 Evaluate side-chains 393 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 346 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A1059 ASN A1202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094897 restraints weight = 28038.080| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.04 r_work: 0.3178 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15847 Z= 0.145 Angle : 0.594 14.334 21729 Z= 0.320 Chirality : 0.042 0.170 2327 Planarity : 0.005 0.056 2579 Dihedral : 16.529 80.012 2584 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.25 % Allowed : 27.19 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1728 helix: 1.33 (0.20), residues: 727 sheet: 0.65 (0.33), residues: 233 loop : -1.10 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 257 TYR 0.015 0.001 TYR B 193 PHE 0.011 0.001 PHE B 403 TRP 0.012 0.001 TRP B 241 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (15846) covalent geometry : angle 0.59446 / 0.32 (21727) SS BOND : bond 0.00450 / 0.24 ( 1) SS BOND : angle 0.72280 / 0.40 ( 2) hydrogen bonds : bond 0.05344 / 3.63 ( 680) hydrogen bonds : angle 4.62976 / 3.26 ( 1901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 355 time to evaluate : 0.561 Fit side-chains REVERT: A 232 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7979 (mtp-110) REVERT: A 478 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7657 (mmt180) REVERT: A 607 TRP cc_start: 0.8633 (OUTLIER) cc_final: 0.7626 (t60) REVERT: A 775 GLU cc_start: 0.8208 (pt0) cc_final: 0.7993 (pt0) REVERT: A 796 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8677 (ttpt) REVERT: A 1024 ASP cc_start: 0.8441 (m-30) cc_final: 0.8235 (m-30) REVERT: A 1046 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7237 (mp0) REVERT: A 1054 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 1163 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7165 (tpt) REVERT: B 400 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: B 455 LEU cc_start: 0.8602 (tt) cc_final: 0.8359 (tp) REVERT: B 465 MET cc_start: 0.8538 (mmt) cc_final: 0.8075 (mmt) REVERT: C 298 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7785 (mp0) REVERT: C 310 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: C 387 VAL cc_start: 0.9048 (t) cc_final: 0.8809 (m) REVERT: C 427 GLN cc_start: 0.7844 (mt0) cc_final: 0.7603 (mt0) REVERT: C 465 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7563 (mpp) outliers start: 95 outliers final: 62 residues processed: 406 average time/residue: 0.5242 time to fit residues: 237.7366 Evaluate side-chains 417 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 159 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095016 restraints weight = 27846.951| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.02 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15847 Z= 0.149 Angle : 0.593 14.068 21729 Z= 0.320 Chirality : 0.042 0.169 2327 Planarity : 0.005 0.062 2579 Dihedral : 16.496 79.867 2584 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.32 % Allowed : 27.52 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1728 helix: 1.38 (0.20), residues: 727 sheet: 0.68 (0.33), residues: 233 loop : -1.10 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 389 TYR 0.015 0.002 TYR B 193 PHE 0.010 0.001 PHE B 403 TRP 0.011 0.001 TRP B 241 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (15846) covalent geometry : angle 0.59325 / 0.32 (21727) SS BOND : bond 0.00437 / 0.23 ( 1) SS BOND : angle 0.72432 / 0.41 ( 2) hydrogen bonds : bond 0.05251 / 3.57 ( 680) hydrogen bonds : angle 4.60033 / 3.24 ( 1901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 348 time to evaluate : 0.612 Fit side-chains REVERT: A 232 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7979 (mtp-110) REVERT: A 478 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7663 (mmt180) REVERT: A 607 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.7620 (t60) REVERT: A 775 GLU cc_start: 0.8167 (pt0) cc_final: 0.7954 (pt0) REVERT: A 796 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8677 (ttpt) REVERT: A 1046 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7249 (mp0) REVERT: A 1054 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 1142 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7343 (mtp180) REVERT: A 1163 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7146 (tpt) REVERT: A 1194 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 400 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: B 455 LEU cc_start: 0.8621 (tt) cc_final: 0.8359 (tp) REVERT: B 465 MET cc_start: 0.8532 (mmt) cc_final: 0.8082 (mmt) REVERT: C 105 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7845 (mm-30) REVERT: C 187 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7939 (t70) REVERT: C 298 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7799 (mp0) REVERT: C 310 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 427 GLN cc_start: 0.7842 (mt0) cc_final: 0.7604 (mt0) REVERT: C 465 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7577 (mpp) outliers start: 96 outliers final: 65 residues processed: 400 average time/residue: 0.5109 time to fit residues: 228.5727 Evaluate side-chains 414 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 124 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 133 optimal weight: 0.0980 chunk 116 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 163 optimal weight: 0.0980 chunk 142 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095671 restraints weight = 28013.698| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.05 r_work: 0.3193 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15847 Z= 0.135 Angle : 0.591 14.734 21729 Z= 0.315 Chirality : 0.042 0.164 2327 Planarity : 0.005 0.055 2579 Dihedral : 16.415 79.659 2581 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.60 % Allowed : 29.10 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1728 helix: 1.36 (0.20), residues: 735 sheet: 0.72 (0.34), residues: 228 loop : -1.09 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 389 TYR 0.015 0.001 TYR A 951 PHE 0.010 0.001 PHE B 403 TRP 0.011 0.001 TRP B 241 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15846) covalent geometry : angle 0.59135 / 0.31 (21727) SS BOND : bond 0.00405 / 0.21 ( 1) SS BOND : angle 0.71619 / 0.40 ( 2) hydrogen bonds : bond 0.04893 / 3.32 ( 680) hydrogen bonds : angle 4.53292 / 3.20 ( 1901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 347 time to evaluate : 0.586 Fit side-chains REVERT: A 232 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7934 (mtp-110) REVERT: A 478 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7652 (mmt180) REVERT: A 607 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7579 (t60) REVERT: A 775 GLU cc_start: 0.8156 (pt0) cc_final: 0.7943 (pt0) REVERT: A 796 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8656 (ttpt) REVERT: A 1046 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7233 (mp0) REVERT: A 1054 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: A 1142 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7327 (mtp180) REVERT: A 1163 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7114 (tpt) REVERT: A 1194 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8726 (m) REVERT: B 400 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (mt0) REVERT: B 455 LEU cc_start: 0.8623 (tt) cc_final: 0.8365 (tp) REVERT: B 465 MET cc_start: 0.8525 (mmt) cc_final: 0.8095 (mmt) REVERT: C 187 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7928 (t70) REVERT: C 298 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7803 (mp0) REVERT: C 310 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 389 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6199 (ppt170) REVERT: C 427 GLN cc_start: 0.7815 (mt0) cc_final: 0.7558 (mt0) REVERT: C 465 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7551 (mpp) outliers start: 85 outliers final: 59 residues processed: 397 average time/residue: 0.5278 time to fit residues: 233.9901 Evaluate side-chains 411 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 341 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 156 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 18 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 803 ASN B 187 HIS C 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096823 restraints weight = 27956.791| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.06 r_work: 0.3212 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15847 Z= 0.124 Angle : 0.593 14.783 21729 Z= 0.312 Chirality : 0.041 0.159 2327 Planarity : 0.005 0.082 2579 Dihedral : 16.332 79.383 2581 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.20 % Allowed : 29.49 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1728 helix: 1.54 (0.20), residues: 723 sheet: 0.74 (0.34), residues: 228 loop : -0.95 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 389 TYR 0.014 0.001 TYR A 479 PHE 0.011 0.001 PHE B 403 TRP 0.012 0.001 TRP A1049 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (15846) covalent geometry : angle 0.59300 / 0.31 (21727) SS BOND : bond 0.00338 / 0.18 ( 1) SS BOND : angle 0.67605 / 0.37 ( 2) hydrogen bonds : bond 0.04453 / 3.01 ( 680) hydrogen bonds : angle 4.42364 / 3.12 ( 1901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 350 time to evaluate : 0.555 Fit side-chains REVERT: A 232 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7901 (mtp-110) REVERT: A 478 ARG cc_start: 0.8354 (mtt180) cc_final: 0.7671 (mmt180) REVERT: A 607 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.7559 (t60) REVERT: A 775 GLU cc_start: 0.8132 (pt0) cc_final: 0.7925 (pt0) REVERT: A 796 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8622 (ttpt) REVERT: A 799 SER cc_start: 0.8798 (t) cc_final: 0.8486 (p) REVERT: A 1046 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7226 (mp0) REVERT: A 1054 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: A 1142 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7279 (mtp180) REVERT: A 1163 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7119 (tpt) REVERT: A 1194 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8690 (m) REVERT: B 400 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: B 455 LEU cc_start: 0.8632 (tt) cc_final: 0.8367 (tp) REVERT: B 465 MET cc_start: 0.8465 (mmt) cc_final: 0.8083 (mmt) REVERT: C 187 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7898 (t70) REVERT: C 298 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7788 (mp0) REVERT: C 310 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: C 389 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.6209 (ppt170) REVERT: C 427 GLN cc_start: 0.7772 (mt0) cc_final: 0.7537 (mt0) outliers start: 79 outliers final: 53 residues processed: 398 average time/residue: 0.5193 time to fit residues: 231.0946 Evaluate side-chains 409 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095909 restraints weight = 27952.808| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.03 r_work: 0.3197 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15847 Z= 0.146 Angle : 0.611 14.780 21729 Z= 0.323 Chirality : 0.042 0.161 2327 Planarity : 0.005 0.089 2579 Dihedral : 16.306 79.499 2581 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.81 % Allowed : 29.76 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1728 helix: 1.48 (0.20), residues: 729 sheet: 0.88 (0.34), residues: 223 loop : -1.02 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 389 TYR 0.029 0.002 TYR A 479 PHE 0.009 0.001 PHE A1180 TRP 0.011 0.001 TRP B 241 HIS 0.003 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (15846) covalent geometry : angle 0.61093 / 0.32 (21727) SS BOND : bond 0.00427 / 0.22 ( 1) SS BOND : angle 0.69554 / 0.39 ( 2) hydrogen bonds : bond 0.04849 / 3.30 ( 680) hydrogen bonds : angle 4.48360 / 3.16 ( 1901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 0.685 Fit side-chains REVERT: A 232 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7904 (mtp-110) REVERT: A 478 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7689 (mmt180) REVERT: A 607 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.7563 (t60) REVERT: A 796 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8630 (ttpt) REVERT: A 799 SER cc_start: 0.8813 (t) cc_final: 0.8489 (p) REVERT: A 1046 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7209 (mp0) REVERT: A 1054 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: A 1142 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7288 (mtp180) REVERT: A 1163 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7115 (tpt) REVERT: A 1194 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8699 (m) REVERT: B 400 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: B 455 LEU cc_start: 0.8643 (tt) cc_final: 0.8380 (tp) REVERT: B 465 MET cc_start: 0.8459 (mmt) cc_final: 0.8050 (mmt) REVERT: C 187 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.7903 (t70) REVERT: C 298 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7789 (mp0) REVERT: C 310 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 389 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.6202 (ppt170) REVERT: C 427 GLN cc_start: 0.7811 (mt0) cc_final: 0.7556 (mt0) outliers start: 73 outliers final: 59 residues processed: 385 average time/residue: 0.5285 time to fit residues: 227.3075 Evaluate side-chains 408 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 44 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095786 restraints weight = 27828.067| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.03 r_work: 0.3199 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15847 Z= 0.147 Angle : 0.618 14.790 21729 Z= 0.327 Chirality : 0.042 0.160 2327 Planarity : 0.005 0.086 2579 Dihedral : 16.270 79.318 2581 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.00 % Allowed : 29.82 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1728 helix: 1.42 (0.20), residues: 729 sheet: 0.90 (0.34), residues: 223 loop : -1.06 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B 389 TYR 0.016 0.001 TYR A 951 PHE 0.009 0.001 PHE A1180 TRP 0.011 0.001 TRP B 241 HIS 0.004 0.001 HIS A 971 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (15846) covalent geometry : angle 0.61823 / 0.33 (21727) SS BOND : bond 0.00453 / 0.24 ( 1) SS BOND : angle 0.73423 / 0.41 ( 2) hydrogen bonds : bond 0.04919 / 3.35 ( 680) hydrogen bonds : angle 4.48533 / 3.17 ( 1901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.32 seconds wall clock time: 100 minutes 38.43 seconds (6038.43 seconds total)