Starting phenix.real_space_refine on Wed Mar 4 18:55:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4e_72480/03_2026/9y4e_72480_neut.cif" } resolution = 3.05 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= 0.210 sd= 0.734 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 57 5.49 5 S 82 5.16 5 C 9523 2.51 5 N 2692 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15227 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8229 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 67, 'TRANS': 961} 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: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1105 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.36, per 1000 atoms: 0.22 Number of scatterers: 15227 At special positions: 0 Unit cell: (103.2, 106.64, 163.4, 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 57 15.00 O 2872 8.00 N 2692 7.00 C 9523 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: 1.24 Conformation dependent library (CDL) restraints added in 601.9 milliseconds 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 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: 74 helices and 10 sheets defined 47.0% alpha, 13.4% beta 25 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 removed outlier: 3.585A pdb=" N HIS A 110 " --> pdb=" O HIS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.549A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) 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: 3.603A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.159A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 6.982A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.674A pdb=" N MET A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.608A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.827A pdb=" N ARG A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 418 removed outlier: 4.060A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 386 " --> pdb=" O MET A 382 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.213A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.990A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 648 through 661 removed outlier: 3.512A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) 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: 4.001A pdb=" N ALA A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.848A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 822 through 827' Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.957A pdb=" N GLY A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 956 removed outlier: 4.184A 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 987 Processing helix chain 'A' and resid 998 through 1009 removed outlier: 4.776A pdb=" N LEU A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A1005 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A1009 " --> pdb=" O VAL A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 4.123A pdb=" N ARG A1034 " --> pdb=" O ARG A1030 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A1036 " --> pdb=" O THR A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 removed outlier: 3.823A 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: 4.077A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1167 removed outlier: 3.968A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1211 removed outlier: 4.232A pdb=" N ARG A1208 " --> pdb=" O THR A1204 " (cutoff:3.500A) removed outlier: 3.953A 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 82 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 184 through 190 removed outlier: 4.697A pdb=" N GLY B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 removed outlier: 4.211A pdb=" N VAL B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 196 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 199 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) 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 266 removed outlier: 3.585A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (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 315 removed outlier: 3.777A pdb=" N MET B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.691A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.631A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.817A pdb=" N SER B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.737A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.834A pdb=" N LEU C 86 " --> pdb=" O LYS C 83 " (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 186 through 191 removed outlier: 3.563A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 193 No H-bonds generated for 'chain 'C' and resid 192 through 193' Processing helix chain 'C' and resid 194 through 201 removed outlier: 4.243A pdb=" N ASP C 198 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 199 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 200 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 3.542A pdb=" N ASP C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.536A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 434 removed outlier: 3.673A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.124A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.658A 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: 3.841A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 174 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.849A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.821A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1183 " --> pdb=" O LEU A1218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1218 " --> pdb=" O VAL A1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 994 through 997 removed outlier: 3.861A pdb=" N GLU A1046 " --> pdb=" O ARG A 996 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.537A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 212 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 234 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 288 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.587A pdb=" N LYS B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.196A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.372A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 232 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 243 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 3.557A pdb=" N VAL C 443 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 454 " --> pdb=" O LEU C 442 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4834 1.34 - 1.47: 4066 1.47 - 1.60: 6626 1.60 - 1.73: 70 1.73 - 1.85: 129 Bond restraints: 15725 Sorted by residual: bond pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 1.579 1.754 -0.175 1.10e-02 8.26e+03 2.53e+02 bond pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " ideal model delta sigma weight residual 1.443 1.341 0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 1.592 1.671 -0.079 1.10e-02 8.26e+03 5.17e+01 bond pdb=" C6 DTP A4002 " pdb=" N6 DTP A4002 " ideal model delta sigma weight residual 1.337 1.382 -0.045 1.10e-02 8.26e+03 1.68e+01 bond pdb=" O3B DTP A4002 " pdb=" PG DTP A4002 " ideal model delta sigma weight residual 1.600 1.703 -0.103 2.80e-02 1.28e+03 1.36e+01 ... (remaining 15720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 21438 3.25 - 6.50: 82 6.50 - 9.75: 12 9.75 - 13.00: 2 13.00 - 16.26: 6 Bond angle restraints: 21540 Sorted by residual: angle pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 136.83 122.15 14.68 1.00e+00 1.00e+00 2.15e+02 angle pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 121.27 113.02 8.25 1.00e+00 1.00e+00 6.80e+01 angle pdb=" O2A DTP A4002 " pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 106.94 121.51 -14.57 1.88e+00 2.83e-01 6.01e+01 angle pdb=" O1B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 111.24 94.98 16.26 2.72e+00 1.35e-01 3.57e+01 angle pdb=" O2B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3B DTP A4002 " ideal model delta sigma weight residual 106.94 116.69 -9.75 1.88e+00 2.83e-01 2.69e+01 ... (remaining 21535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.38: 8236 25.38 - 50.77: 855 50.77 - 76.15: 113 76.15 - 101.53: 14 101.53 - 126.92: 1 Dihedral angle restraints: 9219 sinusoidal: 4164 harmonic: 5055 Sorted by residual: dihedral pdb=" CA CYS A1077 " pdb=" C CYS A1077 " pdb=" N CYS A1078 " pdb=" CA CYS A1078 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+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 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA VAL C 118 " pdb=" C VAL C 118 " pdb=" N VAL C 119 " pdb=" CA VAL C 119 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 9216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1475 0.031 - 0.063: 572 0.063 - 0.094: 147 0.094 - 0.126: 102 0.126 - 0.157: 11 Chirality restraints: 2307 Sorted by residual: chirality pdb=" CB VAL A 901 " pdb=" CA VAL A 901 " pdb=" CG1 VAL A 901 " pdb=" CG2 VAL A 901 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE A1131 " pdb=" N ILE A1131 " pdb=" C ILE A1131 " pdb=" CB ILE A1131 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2304 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A1200 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 73 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 421 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C MET C 421 " 0.029 2.00e-02 2.50e+03 pdb=" O MET C 421 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN C 422 " -0.010 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3163 2.78 - 3.31: 13042 3.31 - 3.84: 23699 3.84 - 4.37: 26981 4.37 - 4.90: 46549 Nonbonded interactions: 113434 Sorted by model distance: nonbonded pdb="CA CA A4001 " pdb=" O1A DTP A4002 " model vdw 2.254 2.510 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.273 2.510 nonbonded pdb=" O VAL A 891 " pdb="CA CA A4001 " model vdw 2.280 2.510 nonbonded pdb=" OD2 ASP A1135 " pdb="CA CA A4001 " model vdw 2.311 2.510 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.333 2.510 ... (remaining 113429 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.880 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 0.175 15726 Z= 0.229 Angle : 0.648 16.256 21542 Z= 0.347 Chirality : 0.041 0.157 2307 Planarity : 0.004 0.047 2572 Dihedral : 18.753 126.918 5956 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.82 % Allowed : 20.80 % Favored : 75.38 % 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: 0.12 (0.21), residues: 1727 helix: 0.99 (0.21), residues: 694 sheet: 0.50 (0.34), residues: 236 loop : -0.83 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 964 TYR 0.013 0.001 TYR A 150 PHE 0.009 0.001 PHE A1092 TRP 0.013 0.001 TRP A 441 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00377 (15725) covalent geometry : angle 0.64642 (21540) SS BOND : bond 0.01235 ( 1) SS BOND : angle 4.12529 ( 2) hydrogen bonds : bond 0.19884 ( 673) hydrogen bonds : angle 6.17138 ( 1838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 378 time to evaluate : 0.548 Fit side-chains REVERT: A 247 LEU cc_start: 0.8651 (tp) cc_final: 0.8406 (tt) REVERT: A 558 LEU cc_start: 0.7839 (mm) cc_final: 0.7556 (mp) REVERT: A 985 MET cc_start: 0.8541 (tpp) cc_final: 0.8097 (tpp) REVERT: A 1108 TYR cc_start: 0.8715 (t80) cc_final: 0.8230 (t80) REVERT: A 1163 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8252 (tpp) REVERT: A 1232 GLU cc_start: 0.8521 (mp0) cc_final: 0.8162 (mm-30) REVERT: B 92 LEU cc_start: 0.9161 (mm) cc_final: 0.8927 (mt) REVERT: B 122 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7259 (mtm-85) REVERT: B 404 ASN cc_start: 0.8709 (m-40) cc_final: 0.8313 (m110) REVERT: B 421 MET cc_start: 0.7589 (tmm) cc_final: 0.7278 (tmm) REVERT: C 74 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8420 (tp-100) outliers start: 58 outliers final: 53 residues processed: 410 average time/residue: 0.1066 time to fit residues: 67.1229 Evaluate side-chains 419 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 364 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 HIS B 124 GLN B 400 GLN C 96 HIS C 258 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092550 restraints weight = 29299.682| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.27 r_work: 0.3134 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15726 Z= 0.197 Angle : 0.603 12.539 21542 Z= 0.322 Chirality : 0.043 0.159 2307 Planarity : 0.004 0.048 2572 Dihedral : 16.532 128.439 2602 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.74 % Allowed : 18.89 % Favored : 76.37 % 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: 0.11 (0.20), residues: 1727 helix: 0.94 (0.20), residues: 718 sheet: 0.76 (0.34), residues: 228 loop : -0.95 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 964 TYR 0.019 0.002 TYR A 221 PHE 0.012 0.001 PHE A 389 TRP 0.015 0.001 TRP A 220 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00449 (15725) covalent geometry : angle 0.60181 (21540) SS BOND : bond 0.01294 ( 1) SS BOND : angle 4.50855 ( 2) hydrogen bonds : bond 0.06645 ( 673) hydrogen bonds : angle 5.00816 ( 1838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 381 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8647 (tp) cc_final: 0.8399 (tt) REVERT: A 374 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: A 443 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7067 (mtt180) REVERT: A 985 MET cc_start: 0.8596 (tpp) cc_final: 0.8123 (tpp) REVERT: A 1232 GLU cc_start: 0.8531 (mp0) cc_final: 0.8190 (mm-30) REVERT: B 400 GLN cc_start: 0.8212 (tt0) cc_final: 0.8011 (tt0) REVERT: B 404 ASN cc_start: 0.8749 (m-40) cc_final: 0.8410 (m110) REVERT: B 421 MET cc_start: 0.7950 (tmm) cc_final: 0.7716 (tmm) REVERT: C 74 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8461 (tp-100) REVERT: C 122 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8149 (mtt-85) outliers start: 72 outliers final: 46 residues processed: 432 average time/residue: 0.1119 time to fit residues: 74.8351 Evaluate side-chains 417 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 368 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 396 CYS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 8 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091292 restraints weight = 29531.737| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.27 r_work: 0.3108 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15726 Z= 0.247 Angle : 0.648 12.721 21542 Z= 0.346 Chirality : 0.045 0.163 2307 Planarity : 0.005 0.049 2572 Dihedral : 16.492 131.629 2535 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.33 % Allowed : 19.35 % Favored : 75.31 % 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: -0.09 (0.20), residues: 1727 helix: 0.75 (0.20), residues: 710 sheet: 0.95 (0.34), residues: 217 loop : -1.07 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 182 TYR 0.021 0.002 TYR A 221 PHE 0.013 0.002 PHE A1123 TRP 0.019 0.002 TRP A 220 HIS 0.006 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00571 (15725) covalent geometry : angle 0.64616 (21540) SS BOND : bond 0.00820 ( 1) SS BOND : angle 4.96688 ( 2) hydrogen bonds : bond 0.06660 ( 673) hydrogen bonds : angle 4.97247 ( 1838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 376 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8699 (tp) cc_final: 0.8459 (tt) REVERT: A 374 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8036 (mtt180) REVERT: A 443 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7097 (mtt180) REVERT: A 558 LEU cc_start: 0.7886 (mm) cc_final: 0.7629 (mp) REVERT: A 662 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: A 954 ILE cc_start: 0.8777 (mm) cc_final: 0.8353 (mm) REVERT: A 985 MET cc_start: 0.8630 (tpp) cc_final: 0.8141 (tpp) REVERT: A 1138 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8072 (mmt-90) REVERT: A 1232 GLU cc_start: 0.8566 (mp0) cc_final: 0.8218 (mm-30) REVERT: B 400 GLN cc_start: 0.8253 (tt0) cc_final: 0.7933 (tt0) REVERT: B 404 ASN cc_start: 0.8736 (m-40) cc_final: 0.8280 (m110) REVERT: B 463 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8388 (mmtp) REVERT: C 122 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8193 (mtt-85) outliers start: 81 outliers final: 56 residues processed: 425 average time/residue: 0.1053 time to fit residues: 68.5770 Evaluate side-chains 423 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 362 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 0.0030 chunk 96 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094620 restraints weight = 29385.807| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.30 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15726 Z= 0.117 Angle : 0.557 13.674 21542 Z= 0.292 Chirality : 0.040 0.152 2307 Planarity : 0.004 0.048 2572 Dihedral : 16.145 128.907 2531 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.69 % Allowed : 21.53 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1727 helix: 1.12 (0.20), residues: 718 sheet: 0.88 (0.34), residues: 229 loop : -0.88 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 361 TYR 0.014 0.001 TYR A 150 PHE 0.009 0.001 PHE C 254 TRP 0.014 0.001 TRP A 220 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00250 (15725) covalent geometry : angle 0.55556 (21540) SS BOND : bond 0.00590 ( 1) SS BOND : angle 3.93667 ( 2) hydrogen bonds : bond 0.04617 ( 673) hydrogen bonds : angle 4.61300 ( 1838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 383 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8607 (tp) cc_final: 0.8383 (tt) REVERT: A 443 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6924 (mtt180) REVERT: A 662 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: A 954 ILE cc_start: 0.8690 (mm) cc_final: 0.8283 (mm) REVERT: A 985 MET cc_start: 0.8500 (tpp) cc_final: 0.8044 (tpp) REVERT: A 1138 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.8107 (mmt-90) REVERT: A 1232 GLU cc_start: 0.8518 (mp0) cc_final: 0.8178 (mm-30) REVERT: B 74 GLN cc_start: 0.8570 (tp40) cc_final: 0.8343 (tp40) REVERT: B 400 GLN cc_start: 0.8227 (tt0) cc_final: 0.7866 (tt0) REVERT: B 404 ASN cc_start: 0.8630 (m-40) cc_final: 0.8150 (m110) REVERT: B 452 LEU cc_start: 0.7528 (mt) cc_final: 0.7310 (mt) REVERT: B 463 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8364 (mmtp) REVERT: C 122 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8114 (mtt-85) outliers start: 56 outliers final: 32 residues processed: 414 average time/residue: 0.1026 time to fit residues: 65.6325 Evaluate side-chains 405 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 113 optimal weight: 0.0570 chunk 78 optimal weight: 6.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093472 restraints weight = 29384.694| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.29 r_work: 0.3149 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15726 Z= 0.162 Angle : 0.579 13.892 21542 Z= 0.305 Chirality : 0.042 0.153 2307 Planarity : 0.004 0.047 2572 Dihedral : 16.062 129.220 2517 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.33 % Allowed : 20.21 % Favored : 74.46 % 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: 0.24 (0.21), residues: 1727 helix: 1.08 (0.20), residues: 714 sheet: 0.87 (0.35), residues: 226 loop : -0.91 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.021 0.002 TYR A 732 PHE 0.013 0.001 PHE A 949 TRP 0.015 0.001 TRP A 220 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00372 (15725) covalent geometry : angle 0.57762 (21540) SS BOND : bond 0.01078 ( 1) SS BOND : angle 4.28427 ( 2) hydrogen bonds : bond 0.05161 ( 673) hydrogen bonds : angle 4.60912 ( 1838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8629 (tp) cc_final: 0.8396 (tt) REVERT: A 374 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8110 (mtt180) REVERT: A 443 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7051 (mtt180) REVERT: A 662 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: A 954 ILE cc_start: 0.8740 (mm) cc_final: 0.8313 (mm) REVERT: A 985 MET cc_start: 0.8541 (tpp) cc_final: 0.8054 (tpp) REVERT: A 1138 ARG cc_start: 0.8577 (mmt-90) cc_final: 0.8110 (mmt-90) REVERT: A 1163 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8176 (tpt) REVERT: A 1232 GLU cc_start: 0.8568 (mp0) cc_final: 0.8239 (mm-30) REVERT: B 74 GLN cc_start: 0.8587 (tp40) cc_final: 0.8364 (tp40) REVERT: B 400 GLN cc_start: 0.8265 (tt0) cc_final: 0.7924 (tt0) REVERT: B 404 ASN cc_start: 0.8613 (m-40) cc_final: 0.8136 (m110) REVERT: B 452 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7397 (mt) REVERT: B 463 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8430 (mmtp) REVERT: C 122 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8141 (mtt-85) outliers start: 81 outliers final: 58 residues processed: 431 average time/residue: 0.1072 time to fit residues: 71.3273 Evaluate side-chains 431 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 366 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095503 restraints weight = 29245.414| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.28 r_work: 0.3187 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15726 Z= 0.116 Angle : 0.550 14.470 21542 Z= 0.286 Chirality : 0.040 0.149 2307 Planarity : 0.004 0.047 2572 Dihedral : 15.827 127.541 2517 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.08 % Allowed : 22.25 % Favored : 73.67 % 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: 0.43 (0.21), residues: 1727 helix: 1.26 (0.20), residues: 717 sheet: 0.89 (0.34), residues: 233 loop : -0.81 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.025 0.001 TYR A 732 PHE 0.009 0.001 PHE C 254 TRP 0.013 0.001 TRP B 241 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00255 (15725) covalent geometry : angle 0.54882 (21540) SS BOND : bond 0.01143 ( 1) SS BOND : angle 3.66676 ( 2) hydrogen bonds : bond 0.04182 ( 673) hydrogen bonds : angle 4.41175 ( 1838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 384 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 443 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6949 (mtt180) REVERT: A 598 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8786 (p) REVERT: A 662 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: A 954 ILE cc_start: 0.8688 (mm) cc_final: 0.8251 (mm) REVERT: A 985 MET cc_start: 0.8491 (tpp) cc_final: 0.7994 (tpp) REVERT: A 1138 ARG cc_start: 0.8534 (mmt-90) cc_final: 0.8104 (mmt-90) REVERT: A 1163 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8141 (tpt) REVERT: A 1232 GLU cc_start: 0.8537 (mp0) cc_final: 0.8218 (mm-30) REVERT: B 74 GLN cc_start: 0.8576 (tp40) cc_final: 0.8347 (tp40) REVERT: B 400 GLN cc_start: 0.8252 (tt0) cc_final: 0.7941 (tt0) REVERT: B 404 ASN cc_start: 0.8573 (m-40) cc_final: 0.8106 (m110) REVERT: B 452 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7233 (mt) REVERT: B 463 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8424 (mmtp) REVERT: C 122 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8094 (mtt-85) outliers start: 62 outliers final: 44 residues processed: 425 average time/residue: 0.1062 time to fit residues: 70.2922 Evaluate side-chains 431 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 380 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 0.0040 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093043 restraints weight = 29260.000| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.27 r_work: 0.3143 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15726 Z= 0.189 Angle : 0.615 14.543 21542 Z= 0.320 Chirality : 0.043 0.148 2307 Planarity : 0.004 0.047 2572 Dihedral : 15.869 129.593 2514 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.07 % Allowed : 22.25 % Favored : 72.68 % 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: 0.25 (0.21), residues: 1727 helix: 1.08 (0.20), residues: 717 sheet: 0.85 (0.35), residues: 228 loop : -0.90 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.023 0.002 TYR A 732 PHE 0.013 0.001 PHE A 389 TRP 0.013 0.001 TRP B 241 HIS 0.005 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00437 (15725) covalent geometry : angle 0.61388 (21540) SS BOND : bond 0.00771 ( 1) SS BOND : angle 4.28004 ( 2) hydrogen bonds : bond 0.05323 ( 673) hydrogen bonds : angle 4.55566 ( 1838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 381 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 222 SER cc_start: 0.8316 (t) cc_final: 0.7803 (p) REVERT: A 374 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8105 (mtt180) REVERT: A 443 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: A 662 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8423 (mm-30) REVERT: A 954 ILE cc_start: 0.8744 (mm) cc_final: 0.8314 (mm) REVERT: A 985 MET cc_start: 0.8590 (tpp) cc_final: 0.8042 (tpp) REVERT: A 1138 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8060 (mmt-90) REVERT: A 1163 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8181 (tpt) REVERT: A 1232 GLU cc_start: 0.8542 (mp0) cc_final: 0.8235 (mm-30) REVERT: B 74 GLN cc_start: 0.8589 (tp40) cc_final: 0.8369 (tp40) REVERT: B 400 GLN cc_start: 0.8273 (tt0) cc_final: 0.7967 (tt0) REVERT: B 404 ASN cc_start: 0.8605 (m-40) cc_final: 0.8145 (m110) REVERT: B 452 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7398 (mt) REVERT: B 463 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8438 (mmtp) REVERT: C 74 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8422 (tp-100) REVERT: C 122 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8137 (mtt-85) outliers start: 77 outliers final: 61 residues processed: 428 average time/residue: 0.1070 time to fit residues: 70.4279 Evaluate side-chains 442 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 374 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 133 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094954 restraints weight = 29485.333| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.31 r_work: 0.3177 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15726 Z= 0.124 Angle : 0.579 14.877 21542 Z= 0.297 Chirality : 0.041 0.155 2307 Planarity : 0.004 0.047 2572 Dihedral : 15.653 128.504 2514 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.54 % Allowed : 22.51 % Favored : 72.94 % 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: 0.42 (0.21), residues: 1727 helix: 1.26 (0.20), residues: 718 sheet: 0.88 (0.34), residues: 233 loop : -0.83 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.028 0.001 TYR A 732 PHE 0.009 0.001 PHE A 949 TRP 0.014 0.001 TRP A 220 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00273 (15725) covalent geometry : angle 0.57755 (21540) SS BOND : bond 0.01169 ( 1) SS BOND : angle 3.80261 ( 2) hydrogen bonds : bond 0.04395 ( 673) hydrogen bonds : angle 4.41241 ( 1838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 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: 69 poor density : 391 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8771 (tt) cc_final: 0.8548 (tp) REVERT: A 222 SER cc_start: 0.8216 (t) cc_final: 0.7740 (p) REVERT: A 374 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8085 (mtt180) REVERT: A 443 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6919 (mtt180) REVERT: A 662 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: A 954 ILE cc_start: 0.8688 (mm) cc_final: 0.8248 (mm) REVERT: A 985 MET cc_start: 0.8514 (tpp) cc_final: 0.8015 (tpp) REVERT: A 1138 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.8061 (mmt-90) REVERT: A 1163 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8148 (tpt) REVERT: A 1232 GLU cc_start: 0.8505 (mp0) cc_final: 0.8206 (mm-30) REVERT: B 74 GLN cc_start: 0.8581 (tp40) cc_final: 0.8355 (tp40) REVERT: B 105 GLU cc_start: 0.8064 (tp30) cc_final: 0.7694 (mp0) REVERT: B 122 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7458 (mtm-85) REVERT: B 400 GLN cc_start: 0.8242 (tt0) cc_final: 0.7923 (tt0) REVERT: B 404 ASN cc_start: 0.8581 (m-40) cc_final: 0.8117 (m110) REVERT: B 452 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7300 (mt) REVERT: B 463 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8423 (mmtp) REVERT: C 122 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8089 (mtt-85) outliers start: 69 outliers final: 55 residues processed: 435 average time/residue: 0.1063 time to fit residues: 71.4720 Evaluate side-chains 445 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 443 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 0.0370 chunk 44 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097335 restraints weight = 29292.391| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.29 r_work: 0.3219 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15726 Z= 0.110 Angle : 0.572 14.714 21542 Z= 0.291 Chirality : 0.040 0.157 2307 Planarity : 0.004 0.047 2572 Dihedral : 15.355 126.241 2514 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.16 % Allowed : 24.75 % Favored : 72.09 % 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: 0.61 (0.21), residues: 1727 helix: 1.45 (0.20), residues: 720 sheet: 0.95 (0.34), residues: 239 loop : -0.79 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 396 TYR 0.036 0.001 TYR A 732 PHE 0.009 0.001 PHE A1092 TRP 0.014 0.001 TRP B 241 HIS 0.003 0.001 HIS A 932 Details of bonding type rmsd covalent geometry : bond 0.00242 (15725) covalent geometry : angle 0.57108 (21540) SS BOND : bond 0.01112 ( 1) SS BOND : angle 3.31219 ( 2) hydrogen bonds : bond 0.03604 ( 673) hydrogen bonds : angle 4.24169 ( 1838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 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: 48 poor density : 392 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8671 (tt) cc_final: 0.8437 (tp) REVERT: A 374 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8070 (mtt180) REVERT: A 598 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (p) REVERT: A 662 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8347 (mm-30) REVERT: A 954 ILE cc_start: 0.8636 (mm) cc_final: 0.8227 (mm) REVERT: A 985 MET cc_start: 0.8460 (tpp) cc_final: 0.8156 (tpp) REVERT: A 1138 ARG cc_start: 0.8506 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: A 1139 TYR cc_start: 0.8961 (m-80) cc_final: 0.8751 (m-80) REVERT: A 1163 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8127 (tpt) REVERT: A 1232 GLU cc_start: 0.8518 (mp0) cc_final: 0.8268 (mm-30) REVERT: B 74 GLN cc_start: 0.8591 (tp40) cc_final: 0.8378 (tp40) REVERT: B 105 GLU cc_start: 0.8031 (tp30) cc_final: 0.7677 (mp0) REVERT: B 122 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7360 (mtm-85) REVERT: B 400 GLN cc_start: 0.8253 (tt0) cc_final: 0.7950 (tt0) REVERT: B 404 ASN cc_start: 0.8560 (m-40) cc_final: 0.8097 (m110) REVERT: B 452 LEU cc_start: 0.7407 (mt) cc_final: 0.7190 (mt) REVERT: B 463 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8428 (mmtp) REVERT: C 74 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8396 (tp-100) REVERT: C 122 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8073 (mtt-85) outliers start: 48 outliers final: 36 residues processed: 424 average time/residue: 0.1102 time to fit residues: 71.6882 Evaluate side-chains 416 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 373 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096198 restraints weight = 29358.545| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.28 r_work: 0.3199 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15726 Z= 0.124 Angle : 0.585 14.990 21542 Z= 0.297 Chirality : 0.041 0.161 2307 Planarity : 0.004 0.046 2572 Dihedral : 15.366 127.493 2509 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.16 % Allowed : 24.69 % Favored : 72.15 % 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: 0.64 (0.21), residues: 1727 helix: 1.47 (0.20), residues: 723 sheet: 0.98 (0.34), residues: 237 loop : -0.77 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.033 0.001 TYR A 732 PHE 0.010 0.001 PHE A 389 TRP 0.012 0.001 TRP C 251 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00281 (15725) covalent geometry : angle 0.58434 (21540) SS BOND : bond 0.01140 ( 1) SS BOND : angle 3.43735 ( 2) hydrogen bonds : bond 0.04017 ( 673) hydrogen bonds : angle 4.26998 ( 1838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 375 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.8723 (tt) cc_final: 0.8492 (tp) REVERT: A 222 SER cc_start: 0.8118 (t) cc_final: 0.7674 (p) REVERT: A 374 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8049 (mtt180) REVERT: A 598 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 662 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: A 796 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8809 (ptpt) REVERT: A 954 ILE cc_start: 0.8667 (mm) cc_final: 0.8222 (mm) REVERT: A 985 MET cc_start: 0.8478 (tpp) cc_final: 0.8138 (tpp) REVERT: A 1138 ARG cc_start: 0.8535 (mmt-90) cc_final: 0.8061 (mmt-90) REVERT: A 1139 TYR cc_start: 0.9001 (m-80) cc_final: 0.8798 (m-80) REVERT: A 1163 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8143 (tpt) REVERT: A 1232 GLU cc_start: 0.8537 (mp0) cc_final: 0.8275 (mm-30) REVERT: B 74 GLN cc_start: 0.8590 (tp40) cc_final: 0.8365 (tp40) REVERT: B 105 GLU cc_start: 0.8054 (tp30) cc_final: 0.7699 (mp0) REVERT: B 122 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7396 (mtm-85) REVERT: B 400 GLN cc_start: 0.8248 (tt0) cc_final: 0.7944 (tt0) REVERT: B 404 ASN cc_start: 0.8541 (m-40) cc_final: 0.8089 (m110) REVERT: B 452 LEU cc_start: 0.7456 (mt) cc_final: 0.7245 (mt) REVERT: B 463 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8427 (mmtp) REVERT: C 74 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8448 (tp-100) REVERT: C 122 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8110 (mtt-85) outliers start: 48 outliers final: 37 residues processed: 408 average time/residue: 0.1034 time to fit residues: 64.8996 Evaluate side-chains 419 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 374 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 GLN Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 0.8980 chunk 100 optimal weight: 0.0370 chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 0.0370 chunk 109 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095758 restraints weight = 29181.732| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.27 r_work: 0.3192 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15726 Z= 0.129 Angle : 0.595 15.149 21542 Z= 0.302 Chirality : 0.041 0.165 2307 Planarity : 0.004 0.046 2572 Dihedral : 15.392 128.688 2509 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.29 % Allowed : 24.75 % Favored : 71.96 % 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: 0.62 (0.21), residues: 1727 helix: 1.47 (0.20), residues: 717 sheet: 0.95 (0.34), residues: 237 loop : -0.78 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.033 0.001 TYR A 732 PHE 0.016 0.001 PHE A1092 TRP 0.012 0.001 TRP B 241 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00295 (15725) covalent geometry : angle 0.59454 (21540) SS BOND : bond 0.01159 ( 1) SS BOND : angle 3.54320 ( 2) hydrogen bonds : bond 0.04170 ( 673) hydrogen bonds : angle 4.28838 ( 1838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.89 seconds wall clock time: 71 minutes 38.52 seconds (4298.52 seconds total)