Starting phenix.real_space_refine on Wed Mar 4 19:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4c_72478/03_2026/9y4c_72478_neut.cif" } resolution = 3.23 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= 0.203 sd= 0.732 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 62 5.49 5 S 82 5.16 5 C 9572 2.51 5 N 2712 2.21 5 O 2902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15331 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: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1209 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.11, per 1000 atoms: 0.20 Number of scatterers: 15331 At special positions: 0 Unit cell: (101.48, 106.64, 162.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 62 15.00 O 2902 8.00 N 2712 7.00 C 9572 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=2.05 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: 1.35 Conformation dependent library (CDL) restraints added in 742.6 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: 70 helices and 16 sheets defined 46.1% alpha, 12.0% beta 27 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.098A pdb=" N VAL A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.385A 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: 3.654A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 removed outlier: 4.328A pdb=" N GLY A 206 " --> pdb=" O LEU A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 removed outlier: 4.016A pdb=" N LEU A 244 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.024A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.952A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.619A 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: 3.533A pdb=" N GLU A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.324A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.997A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 4.544A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.561A pdb=" N LEU A 558 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 559 " --> pdb=" O THR A 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 555 through 559' Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.597A pdb=" N LYS A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.787A pdb=" N ALA A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 810 " --> pdb=" O LYS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.536A pdb=" N VAL A 878 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 removed outlier: 4.192A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 986 Processing helix chain 'A' and resid 998 through 1009 Processing helix chain 'A' and resid 1021 through 1033 removed outlier: 3.509A pdb=" N GLU A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.528A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.858A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A1119 " --> pdb=" O ALA A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1167 removed outlier: 4.210A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.700A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1211 Processing helix chain 'A' and resid 1219 through 1228 removed outlier: 3.590A pdb=" N GLU A1225 " --> pdb=" O TYR A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.553A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.843A pdb=" N CYS B 196 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 197 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.723A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 removed outlier: 4.125A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.646A pdb=" N TYR B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.525A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.510A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 4.337A pdb=" N SER B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.770A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.658A pdb=" N LYS B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 198 through 201 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 267 removed outlier: 4.415A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.597A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.719A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 410 removed outlier: 3.620A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.608A pdb=" N SER C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 431 " --> pdb=" O GLN C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.001A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.567A 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: 3.717A pdb=" N VAL A 187 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 222 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 178 " --> pdb=" O TRP A 220 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.652A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 622 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.856A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 995 through 997 removed outlier: 6.410A pdb=" N ARG A 996 " --> pdb=" O ALA A1045 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.414A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 234 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 341 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 288 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AB1, first strand: chain 'B' and resid 383 through 385 removed outlier: 7.450A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.770A pdb=" N HIS B 454 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 80 removed outlier: 4.271A pdb=" N GLY C 98 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.989A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 243 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.703A pdb=" N LYS C 134 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB7, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.118A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS C 454 " --> pdb=" O LEU C 442 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4835 1.34 - 1.47: 4090 1.47 - 1.59: 6674 1.59 - 1.72: 114 1.72 - 1.85: 129 Bond restraints: 15842 Sorted by residual: bond pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 1.579 1.765 -0.186 1.10e-02 8.26e+03 2.86e+02 bond pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " ideal model delta sigma weight residual 1.443 1.346 0.097 1.00e-02 1.00e+04 9.41e+01 bond pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 1.592 1.672 -0.080 1.10e-02 8.26e+03 5.23e+01 bond pdb=" C6 DTP A4002 " pdb=" N6 DTP A4002 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.10e-02 8.26e+03 1.44e+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 1.34e+01 ... (remaining 15837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 21620 3.26 - 6.51: 88 6.51 - 9.77: 7 9.77 - 13.03: 1 13.03 - 16.28: 5 Bond angle restraints: 21721 Sorted by residual: angle pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " pdb=" PB DTP A4002 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" O2A DTP A4002 " pdb=" PA DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 106.94 121.65 -14.71 1.88e+00 2.83e-01 6.12e+01 angle pdb=" C5' DTP A4002 " pdb=" O5' DTP A4002 " pdb=" PA DTP A4002 " ideal model delta sigma weight residual 121.27 114.93 6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" O1B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3A DTP A4002 " ideal model delta sigma weight residual 111.24 94.96 16.28 2.72e+00 1.35e-01 3.59e+01 angle pdb=" O2B DTP A4002 " pdb=" PB DTP A4002 " pdb=" O3B DTP A4002 " ideal model delta sigma weight residual 106.94 116.51 -9.57 1.88e+00 2.83e-01 2.59e+01 ... (remaining 21716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.49: 7742 19.49 - 38.99: 1110 38.99 - 58.48: 366 58.48 - 77.98: 36 77.98 - 97.47: 19 Dihedral angle restraints: 9273 sinusoidal: 4218 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 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 54.62 38.38 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA ARG A1047 " pdb=" C ARG A1047 " pdb=" N ALA A1048 " pdb=" CA ALA A1048 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1842 0.049 - 0.097: 392 0.097 - 0.146: 91 0.146 - 0.194: 1 0.194 - 0.243: 1 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A 104 " pdb=" CA VAL A 104 " pdb=" CG1 VAL A 104 " pdb=" CG2 VAL A 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA VAL B 338 " pdb=" N VAL B 338 " pdb=" C VAL B 338 " pdb=" CB VAL B 338 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2324 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 115 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 116 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1207 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" CD GLU A1207 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU A1207 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A1207 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 301 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" CD GLU B 301 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU B 301 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2842 2.77 - 3.30: 13499 3.30 - 3.84: 24415 3.84 - 4.37: 26870 4.37 - 4.90: 46682 Nonbonded interactions: 114308 Sorted by model distance: nonbonded pdb="CA CA A4001 " pdb=" O1A DTP A4002 " model vdw 2.240 2.510 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.254 2.510 nonbonded pdb=" O VAL A 891 " pdb="CA CA A4001 " model vdw 2.259 2.510 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.294 2.510 nonbonded pdb=" N SER A 343 " pdb=" OG SER A 343 " model vdw 2.504 2.496 ... (remaining 114303 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: 3.000 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.860 Find NCS groups from input model: 0.260 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.186 15843 Z= 0.244 Angle : 0.643 16.285 21723 Z= 0.350 Chirality : 0.041 0.243 2327 Planarity : 0.004 0.065 2577 Dihedral : 19.475 97.474 6010 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.69 % Allowed : 26.73 % Favored : 69.59 % 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: 0.16 (0.20), residues: 1727 helix: 1.18 (0.21), residues: 679 sheet: -0.15 (0.36), residues: 211 loop : -0.68 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 328 TYR 0.013 0.001 TYR A1166 PHE 0.010 0.001 PHE A 389 TRP 0.011 0.001 TRP A 441 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00418 (15842) covalent geometry : angle 0.64221 (21721) SS BOND : bond 0.01424 ( 1) SS BOND : angle 2.87972 ( 2) hydrogen bonds : bond 0.19606 ( 659) hydrogen bonds : angle 6.26985 ( 1823) *********************** 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 480 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 424 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.8077 (m-80) cc_final: 0.7872 (m-80) REVERT: A 279 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7572 (ptp-170) REVERT: A 308 GLN cc_start: 0.8494 (mt0) cc_final: 0.8056 (mt0) REVERT: A 378 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 393 MET cc_start: 0.8393 (tpp) cc_final: 0.8127 (tpp) REVERT: A 443 ARG cc_start: 0.8673 (ttt180) cc_final: 0.8296 (ttt90) REVERT: A 562 ARG cc_start: 0.5155 (mmp-170) cc_final: 0.4925 (mmp-170) REVERT: A 796 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8412 (ptpt) REVERT: A 873 GLU cc_start: 0.8664 (pm20) cc_final: 0.8463 (pm20) REVERT: A 913 CYS cc_start: 0.8083 (p) cc_final: 0.7807 (p) REVERT: A 993 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6582 (ttm170) REVERT: A 1121 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 71 GLU cc_start: 0.8499 (tt0) cc_final: 0.8207 (tm-30) REVERT: B 234 LYS cc_start: 0.8635 (mttp) cc_final: 0.8247 (mtmm) REVERT: C 87 SER cc_start: 0.7802 (m) cc_final: 0.7566 (p) REVERT: C 107 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7744 (mtm110) REVERT: C 310 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 342 LEU cc_start: 0.8990 (mp) cc_final: 0.8716 (mm) REVERT: C 346 MET cc_start: 0.8348 (ttt) cc_final: 0.8047 (mtp) REVERT: C 427 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 56 outliers final: 47 residues processed: 455 average time/residue: 0.1108 time to fit residues: 75.9408 Evaluate side-chains 468 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 416 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 SER 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 264 GLN Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 736 ASN A1214 GLN B 249 ASN B 404 ASN B 422 GLN C 210 GLN C 292 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089747 restraints weight = 29421.764| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.47 r_work: 0.3060 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 15843 Z= 0.356 Angle : 0.737 8.614 21723 Z= 0.394 Chirality : 0.048 0.158 2327 Planarity : 0.006 0.060 2577 Dihedral : 17.523 90.674 2653 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 8.76 % Allowed : 22.05 % Favored : 69.19 % 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: -0.36 (0.20), residues: 1727 helix: 0.65 (0.20), residues: 715 sheet: -0.08 (0.35), residues: 210 loop : -1.06 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 88 TYR 0.020 0.002 TYR A1108 PHE 0.019 0.002 PHE A 766 TRP 0.018 0.002 TRP B 241 HIS 0.009 0.002 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00813 (15842) covalent geometry : angle 0.73625 (21721) SS BOND : bond 0.01852 ( 1) SS BOND : angle 3.47891 ( 2) hydrogen bonds : bond 0.07831 ( 659) hydrogen bonds : angle 5.34382 ( 1823) *********************** 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 522 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 389 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: A 379 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8323 (tptt) REVERT: A 456 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: A 474 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9016 (tt) REVERT: A 535 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 550 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: A 562 ARG cc_start: 0.5315 (mmp-170) cc_final: 0.5090 (mmp-170) REVERT: A 796 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8419 (ptpt) REVERT: A 993 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5792 (ptm-80) REVERT: A 1117 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: A 1121 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6860 (tm-30) REVERT: B 71 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: B 234 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8385 (mttp) REVERT: B 287 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (m-40) REVERT: C 76 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8268 (tpp-160) REVERT: C 107 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7738 (mtm110) REVERT: C 256 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (tp) REVERT: C 262 TRP cc_start: 0.8862 (t60) cc_final: 0.8623 (t60) REVERT: C 427 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8593 (tm-30) REVERT: C 448 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8518 (mm) outliers start: 133 outliers final: 87 residues processed: 472 average time/residue: 0.1046 time to fit residues: 75.2225 Evaluate side-chains 474 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 371 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 475 LEU 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 100 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 129 optimal weight: 0.0010 chunk 142 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 736 ASN A1157 ASN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092885 restraints weight = 29583.825| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.50 r_work: 0.3111 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15843 Z= 0.162 Angle : 0.582 8.384 21723 Z= 0.311 Chirality : 0.042 0.149 2327 Planarity : 0.005 0.058 2577 Dihedral : 17.052 94.037 2620 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.78 % Allowed : 23.90 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1727 helix: 0.99 (0.20), residues: 714 sheet: 0.01 (0.36), residues: 203 loop : -0.94 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.018 0.001 TYR C 291 PHE 0.010 0.001 PHE B 403 TRP 0.016 0.001 TRP B 241 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00366 (15842) covalent geometry : angle 0.58190 (21721) SS BOND : bond 0.01327 ( 1) SS BOND : angle 2.80646 ( 2) hydrogen bonds : bond 0.05489 ( 659) hydrogen bonds : angle 4.82328 ( 1823) *********************** 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 514 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 411 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7136 (ptp90) REVERT: A 308 GLN cc_start: 0.8413 (mt0) cc_final: 0.7991 (mt0) REVERT: A 378 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8768 (p) REVERT: A 379 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8323 (tptt) REVERT: A 393 MET cc_start: 0.8312 (tpp) cc_final: 0.8087 (tpp) REVERT: A 456 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 474 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 550 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 562 ARG cc_start: 0.5274 (mmp-170) cc_final: 0.5069 (mmp-170) REVERT: A 792 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 796 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8450 (ptpt) REVERT: A 1112 MET cc_start: 0.8398 (mtm) cc_final: 0.8096 (mtp) REVERT: A 1222 GLN cc_start: 0.8069 (mt0) cc_final: 0.7697 (mt0) REVERT: B 71 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: B 234 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: B 236 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: B 240 VAL cc_start: 0.9195 (t) cc_final: 0.8971 (p) REVERT: C 408 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 427 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8529 (tm-30) outliers start: 103 outliers final: 63 residues processed: 467 average time/residue: 0.1068 time to fit residues: 75.3303 Evaluate side-chains 473 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 399 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE 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 63 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.0170 chunk 122 optimal weight: 0.9980 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 736 ASN B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093816 restraints weight = 29238.487| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.48 r_work: 0.3129 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15843 Z= 0.141 Angle : 0.554 7.321 21723 Z= 0.296 Chirality : 0.041 0.159 2327 Planarity : 0.004 0.059 2577 Dihedral : 16.765 91.168 2594 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.45 % Allowed : 24.95 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.20), residues: 1727 helix: 1.15 (0.20), residues: 715 sheet: 0.11 (0.36), residues: 208 loop : -0.88 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.014 0.001 TYR C 291 PHE 0.010 0.001 PHE B 403 TRP 0.015 0.001 TRP B 241 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00318 (15842) covalent geometry : angle 0.55377 (21721) SS BOND : bond 0.01467 ( 1) SS BOND : angle 2.96903 ( 2) hydrogen bonds : bond 0.04893 ( 659) hydrogen bonds : angle 4.61901 ( 1823) *********************** 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 512 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 414 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7192 (ptp90) REVERT: A 308 GLN cc_start: 0.8424 (mt0) cc_final: 0.8016 (mt0) REVERT: A 378 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8732 (p) REVERT: A 379 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8269 (tptt) REVERT: A 393 MET cc_start: 0.8283 (tpp) cc_final: 0.8053 (tpp) REVERT: A 443 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.8312 (ttt90) REVERT: A 456 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: A 474 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8929 (tt) REVERT: A 550 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: A 792 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 993 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6061 (ptm-80) REVERT: A 1112 MET cc_start: 0.8369 (mtm) cc_final: 0.8048 (mtp) REVERT: A 1121 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 1207 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7846 (tt0) REVERT: A 1222 GLN cc_start: 0.8031 (mt0) cc_final: 0.7650 (mt0) REVERT: B 71 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 234 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8295 (mtmm) REVERT: B 240 VAL cc_start: 0.9179 (t) cc_final: 0.8963 (p) REVERT: C 427 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8523 (tm-30) outliers start: 98 outliers final: 72 residues processed: 465 average time/residue: 0.1057 time to fit residues: 73.9968 Evaluate side-chains 485 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 403 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1214 GLN Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE 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 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 736 ASN B 85 GLN B 249 ASN B 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094966 restraints weight = 29325.669| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.50 r_work: 0.3150 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15843 Z= 0.122 Angle : 0.534 6.802 21723 Z= 0.283 Chirality : 0.040 0.146 2327 Planarity : 0.004 0.059 2577 Dihedral : 16.565 89.121 2584 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.32 % Allowed : 25.21 % Favored : 68.47 % 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: 0.29 (0.21), residues: 1727 helix: 1.32 (0.21), residues: 716 sheet: 0.15 (0.36), residues: 208 loop : -0.82 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 88 TYR 0.012 0.001 TYR C 291 PHE 0.009 0.001 PHE B 403 TRP 0.013 0.001 TRP B 241 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00271 (15842) covalent geometry : angle 0.53323 (21721) SS BOND : bond 0.01327 ( 1) SS BOND : angle 2.84673 ( 2) hydrogen bonds : bond 0.04297 ( 659) hydrogen bonds : angle 4.41229 ( 1823) *********************** 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 511 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 415 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7101 (ptp90) REVERT: A 308 GLN cc_start: 0.8398 (mt0) cc_final: 0.8005 (mt0) REVERT: A 393 MET cc_start: 0.8245 (tpp) cc_final: 0.8006 (tpp) REVERT: A 443 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8198 (ttt90) REVERT: A 456 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: A 535 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: A 550 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: A 792 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 796 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8474 (ptpt) REVERT: A 993 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6576 (ttm170) REVERT: A 1207 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7897 (tt0) REVERT: A 1222 GLN cc_start: 0.8036 (mt0) cc_final: 0.7671 (mt0) REVERT: B 71 GLU cc_start: 0.8514 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 234 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8292 (mtmm) REVERT: B 240 VAL cc_start: 0.9159 (t) cc_final: 0.8937 (p) REVERT: C 268 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: C 397 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7376 (mm110) REVERT: C 427 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 470 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6993 (mmmm) outliers start: 96 outliers final: 65 residues processed: 464 average time/residue: 0.1088 time to fit residues: 75.9153 Evaluate side-chains 475 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 139 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1157 ASN B 249 ASN B 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090736 restraints weight = 29264.104| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.49 r_work: 0.3074 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15843 Z= 0.288 Angle : 0.681 9.061 21723 Z= 0.362 Chirality : 0.046 0.154 2327 Planarity : 0.005 0.066 2577 Dihedral : 16.839 89.478 2576 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 7.90 % Allowed : 24.09 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.20), residues: 1727 helix: 0.88 (0.20), residues: 718 sheet: -0.11 (0.36), residues: 208 loop : -1.02 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 328 TYR 0.019 0.002 TYR C 291 PHE 0.015 0.002 PHE A 766 TRP 0.016 0.002 TRP A 607 HIS 0.013 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00660 (15842) covalent geometry : angle 0.68010 (21721) SS BOND : bond 0.02639 ( 1) SS BOND : angle 3.20518 ( 2) hydrogen bonds : bond 0.06750 ( 659) hydrogen bonds : angle 4.86152 ( 1823) *********************** 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 514 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 394 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.6972 (ptp90) REVERT: A 379 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8166 (tptt) REVERT: A 456 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: A 474 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9019 (tt) REVERT: A 535 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 550 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 796 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (ptpt) REVERT: A 1112 MET cc_start: 0.8431 (mtm) cc_final: 0.8124 (mtp) REVERT: A 1222 GLN cc_start: 0.8079 (mt0) cc_final: 0.7668 (mt0) REVERT: B 71 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: B 234 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8246 (mttp) REVERT: B 236 GLU cc_start: 0.7423 (tt0) cc_final: 0.7209 (tt0) REVERT: C 400 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8209 (tp40) REVERT: C 427 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8530 (tm-30) REVERT: C 470 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7352 (mmmm) outliers start: 120 outliers final: 84 residues processed: 463 average time/residue: 0.1032 time to fit residues: 72.6406 Evaluate side-chains 480 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 385 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain C residue 475 LEU 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 112 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN B 249 ASN C 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093604 restraints weight = 29088.371| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.47 r_work: 0.3125 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15843 Z= 0.151 Angle : 0.587 8.649 21723 Z= 0.309 Chirality : 0.042 0.202 2327 Planarity : 0.004 0.065 2577 Dihedral : 16.672 89.158 2576 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 6.25 % Allowed : 26.00 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.20), residues: 1727 helix: 1.13 (0.20), residues: 717 sheet: -0.02 (0.36), residues: 208 loop : -0.92 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 579 TYR 0.016 0.001 TYR C 291 PHE 0.009 0.001 PHE B 403 TRP 0.016 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00344 (15842) covalent geometry : angle 0.58651 (21721) SS BOND : bond 0.01584 ( 1) SS BOND : angle 2.73990 ( 2) hydrogen bonds : bond 0.04933 ( 659) hydrogen bonds : angle 4.54431 ( 1823) *********************** 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 495 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 400 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.6493 (ptp90) REVERT: A 308 GLN cc_start: 0.8420 (mt0) cc_final: 0.8009 (mt0) REVERT: A 379 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8124 (tptt) REVERT: A 393 MET cc_start: 0.8266 (tpp) cc_final: 0.8027 (tpp) REVERT: A 456 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: A 474 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8918 (tt) REVERT: A 535 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 550 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: A 993 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6222 (ptm-80) REVERT: A 1112 MET cc_start: 0.8335 (mtm) cc_final: 0.8019 (mtp) REVERT: A 1222 GLN cc_start: 0.8022 (mt0) cc_final: 0.7622 (mt0) REVERT: B 71 GLU cc_start: 0.8561 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 234 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: C 400 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: C 427 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 470 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7135 (mmmm) outliers start: 95 outliers final: 63 residues processed: 449 average time/residue: 0.1089 time to fit residues: 73.8305 Evaluate side-chains 465 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 392 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 748 TRP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1157 ASN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093822 restraints weight = 29377.327| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.50 r_work: 0.3128 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15843 Z= 0.148 Angle : 0.578 8.645 21723 Z= 0.304 Chirality : 0.041 0.155 2327 Planarity : 0.004 0.065 2577 Dihedral : 16.610 89.338 2576 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.79 % Allowed : 26.27 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1727 helix: 1.18 (0.20), residues: 718 sheet: 0.02 (0.36), residues: 208 loop : -0.87 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.015 0.001 TYR C 291 PHE 0.010 0.001 PHE B 403 TRP 0.014 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00338 (15842) covalent geometry : angle 0.57734 (21721) SS BOND : bond 0.01508 ( 1) SS BOND : angle 2.76411 ( 2) hydrogen bonds : bond 0.04776 ( 659) hydrogen bonds : angle 4.47353 ( 1823) *********************** 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 488 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 400 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7133 (ptp90) REVERT: A 308 GLN cc_start: 0.8427 (mt0) cc_final: 0.8026 (mt0) REVERT: A 379 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8070 (tptt) REVERT: A 393 MET cc_start: 0.8245 (tpp) cc_final: 0.7999 (tpp) REVERT: A 443 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.8319 (ttt90) REVERT: A 456 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: A 474 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 535 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 550 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6373 (tm-30) REVERT: A 796 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8428 (ptpt) REVERT: A 993 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6228 (ptm-80) REVERT: A 1112 MET cc_start: 0.8356 (mtm) cc_final: 0.8027 (mtp) REVERT: A 1207 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7840 (tt0) REVERT: A 1222 GLN cc_start: 0.8053 (mt0) cc_final: 0.7646 (mt0) REVERT: B 71 GLU cc_start: 0.8573 (tt0) cc_final: 0.8333 (tm-30) REVERT: B 234 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8294 (mtmm) REVERT: B 240 VAL cc_start: 0.9186 (t) cc_final: 0.8972 (p) REVERT: C 268 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8422 (ttt) REVERT: C 427 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8485 (tm-30) REVERT: C 470 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7057 (mmmm) outliers start: 88 outliers final: 68 residues processed: 448 average time/residue: 0.1069 time to fit residues: 72.5534 Evaluate side-chains 475 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 LYS 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 38 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 152 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS A 736 ASN B 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095287 restraints weight = 29160.669| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.49 r_work: 0.3156 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15843 Z= 0.121 Angle : 0.569 9.533 21723 Z= 0.298 Chirality : 0.040 0.159 2327 Planarity : 0.004 0.064 2577 Dihedral : 16.490 89.015 2576 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.66 % Allowed : 26.60 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.21), residues: 1727 helix: 1.36 (0.21), residues: 711 sheet: 0.12 (0.36), residues: 208 loop : -0.75 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 579 TYR 0.014 0.001 TYR C 291 PHE 0.009 0.001 PHE B 403 TRP 0.016 0.001 TRP B 241 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00272 (15842) covalent geometry : angle 0.56805 (21721) SS BOND : bond 0.01331 ( 1) SS BOND : angle 2.67861 ( 2) hydrogen bonds : bond 0.04179 ( 659) hydrogen bonds : angle 4.34511 ( 1823) *********************** 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 493 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 407 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7037 (ptp90) REVERT: A 308 GLN cc_start: 0.8398 (mt0) cc_final: 0.8013 (mt0) REVERT: A 379 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8043 (tptt) REVERT: A 393 MET cc_start: 0.8206 (tpp) cc_final: 0.7954 (tpp) REVERT: A 443 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8260 (ttt90) REVERT: A 456 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 535 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: A 550 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: A 796 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8437 (ptpt) REVERT: A 993 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.5870 (ptm-80) REVERT: A 1207 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7856 (tt0) REVERT: A 1222 GLN cc_start: 0.8069 (mt0) cc_final: 0.7727 (mt0) REVERT: B 71 GLU cc_start: 0.8547 (tt0) cc_final: 0.8231 (tm-30) REVERT: B 191 GLU cc_start: 0.8234 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 234 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8263 (mtmm) REVERT: B 240 VAL cc_start: 0.9182 (t) cc_final: 0.8979 (p) REVERT: C 180 LYS cc_start: 0.8395 (tppt) cc_final: 0.8100 (tppt) REVERT: C 268 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8408 (ttt) REVERT: C 427 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8474 (tm-30) REVERT: C 470 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.6930 (mmmm) outliers start: 86 outliers final: 64 residues processed: 451 average time/residue: 0.1090 time to fit residues: 74.2409 Evaluate side-chains 470 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 396 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 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 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1157 ASN B 249 ASN B 313 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093270 restraints weight = 29522.827| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.50 r_work: 0.3119 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15843 Z= 0.183 Angle : 0.611 10.034 21723 Z= 0.320 Chirality : 0.042 0.149 2327 Planarity : 0.005 0.066 2577 Dihedral : 16.522 89.591 2573 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.66 % Allowed : 26.86 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1727 helix: 1.25 (0.20), residues: 712 sheet: 0.06 (0.36), residues: 208 loop : -0.83 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 579 TYR 0.018 0.002 TYR C 291 PHE 0.010 0.001 PHE A 389 TRP 0.010 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00422 (15842) covalent geometry : angle 0.61016 (21721) SS BOND : bond 0.01482 ( 1) SS BOND : angle 2.80862 ( 2) hydrogen bonds : bond 0.05126 ( 659) hydrogen bonds : angle 4.47181 ( 1823) ********************** 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 478 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 392 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6459 (ptp90) REVERT: A 308 GLN cc_start: 0.8450 (mt0) cc_final: 0.8053 (mt0) REVERT: A 379 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8061 (tptt) REVERT: A 393 MET cc_start: 0.8268 (tpp) cc_final: 0.8023 (tpp) REVERT: A 443 ARG cc_start: 0.8638 (ttt-90) cc_final: 0.8332 (ttt90) REVERT: A 456 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: A 474 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 535 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 550 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: A 796 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8404 (ptpt) REVERT: A 993 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.5819 (ptm-80) REVERT: A 1207 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7862 (tt0) REVERT: A 1222 GLN cc_start: 0.8035 (mt0) cc_final: 0.7611 (mt0) REVERT: B 71 GLU cc_start: 0.8570 (tt0) cc_final: 0.8252 (tm-30) REVERT: B 234 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: B 240 VAL cc_start: 0.9222 (t) cc_final: 0.9017 (p) REVERT: C 180 LYS cc_start: 0.8435 (tppt) cc_final: 0.8113 (tppt) REVERT: C 427 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 470 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7062 (mmmm) outliers start: 86 outliers final: 71 residues processed: 442 average time/residue: 0.1056 time to fit residues: 70.7113 Evaluate side-chains 466 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 993 ARG Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 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 48 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1157 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093452 restraints weight = 29084.695| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.48 r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15843 Z= 0.171 Angle : 0.794 59.013 21723 Z= 0.457 Chirality : 0.051 1.464 2327 Planarity : 0.005 0.066 2577 Dihedral : 16.521 89.594 2572 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.46 % Allowed : 27.32 % Favored : 67.22 % Cbeta Deviations : 0.06 % 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: 0.20 (0.21), residues: 1727 helix: 1.23 (0.20), residues: 712 sheet: 0.06 (0.36), residues: 208 loop : -0.83 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 579 TYR 0.017 0.001 TYR C 291 PHE 0.010 0.001 PHE B 403 TRP 0.011 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00389 (15842) covalent geometry : angle 0.79399 (21721) SS BOND : bond 0.01341 ( 1) SS BOND : angle 2.78724 ( 2) hydrogen bonds : bond 0.05063 ( 659) hydrogen bonds : angle 4.47862 ( 1823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.22 seconds wall clock time: 52 minutes 0.47 seconds (3120.47 seconds total)