Starting phenix.real_space_refine on Fri Jul 3 19:13:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y4c_72478/07_2026/9y4c_72478_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y4c_72478/07_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_72478/07_2026/9y4c_72478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y4c_72478/07_2026/9y4c_72478.map" model { file = "/net/cci-nas-00/data/ceres_data/9y4c_72478/07_2026/9y4c_72478_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y4c_72478/07_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-6108/lib/python3.11/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, 30 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.19 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: 1.18 Conformation dependent library (CDL) restraints added in 619.0 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: 1.79 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: 2.61 Time building geometry restraints manager: 1.63 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: 21618 3.26 - 6.51: 90 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: 1789 0.049 - 0.097: 432 0.097 - 0.146: 104 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 3.250 nonbonded pdb="CA CA A4001 " pdb=" O2G DTP A4002 " model vdw 2.254 3.250 nonbonded pdb=" O VAL A 891 " pdb="CA CA A4001 " model vdw 2.259 3.250 nonbonded pdb=" OD1 ASP A 890 " pdb="CA CA A4001 " model vdw 2.294 3.250 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: 2.880 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.570 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 : 0.005 0.186 15843 Z= 0.324 Angle : 0.670 16.285 21723 Z= 0.423 Chirality : 0.043 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/Z covalent geometry : bond 0.00456 / 0.32 (15842) covalent geometry : angle 0.66994 / 0.42 (21721) SS BOND : bond 0.01424 / 0.75 ( 1) SS BOND : angle 2.87972 / 1.53 ( 2) hydrogen bonds : bond 0.19606 / 13.05 ( 659) hydrogen bonds : angle 6.26985 / 4.34 ( 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 : 0.453 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: 0.0993 time to fit residues: 68.3484 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 : 0.402 ------------------------------------------------------------------------------- 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... A 493 GLN A 659 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090124 restraints weight = 29311.243| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.49 r_work: 0.3057 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 15843 Z= 0.349 Angle : 0.753 8.637 21723 Z= 0.405 Chirality : 0.049 0.179 2327 Planarity : 0.006 0.060 2577 Dihedral : 17.479 93.364 2653 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 8.43 % Allowed : 22.65 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1727 helix: 0.68 (0.20), residues: 714 sheet: -0.00 (0.36), residues: 210 loop : -1.07 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 88 TYR 0.020 0.002 TYR A1108 PHE 0.017 0.002 PHE A 407 TRP 0.019 0.002 TRP B 241 HIS 0.008 0.002 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.35 (15842) covalent geometry : angle 0.75221 / 0.40 (21721) SS BOND : bond 0.01925 / 1.01 ( 1) SS BOND : angle 3.39202 / 1.79 ( 2) hydrogen bonds : bond 0.07964 / 5.42 ( 659) hydrogen bonds : angle 5.39650 / 3.76 ( 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 516 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 388 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: A 456 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 474 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 550 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: A 562 ARG cc_start: 0.5397 (mmp-170) cc_final: 0.5120 (mmp-170) REVERT: A 796 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (ptpt) REVERT: A 993 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.5811 (ptm-80) REVERT: A 1112 MET cc_start: 0.8438 (mtm) cc_final: 0.8135 (mtp) REVERT: A 1117 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7643 (ttmm) REVERT: A 1121 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6838 (tm-30) REVERT: B 71 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 234 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: B 287 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8655 (m-40) REVERT: C 92 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8753 (tt) REVERT: C 107 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7772 (mtm110) REVERT: C 256 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8361 (tp) REVERT: C 310 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8300 (mm-30) REVERT: C 427 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 448 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8488 (mm) outliers start: 128 outliers final: 85 residues processed: 472 average time/residue: 0.0983 time to fit residues: 70.6565 Evaluate side-chains 474 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 375 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 272 SER Chi-restraints excluded: chain A residue 343 SER 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 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 825 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 878 VAL 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 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 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 128 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 437 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 446 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 92 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 211 ILE Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL 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 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 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: 0.7980 chunk 0 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 736 ASN A1157 ASN A1214 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093240 restraints weight = 29584.122| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.50 r_work: 0.3124 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15843 Z= 0.151 Angle : 0.593 8.439 21723 Z= 0.323 Chirality : 0.043 0.172 2327 Planarity : 0.005 0.057 2577 Dihedral : 17.100 98.876 2617 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.12 % Allowed : 24.62 % Favored : 69.26 % 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: -0.00 (0.20), residues: 1727 helix: 1.00 (0.20), residues: 713 sheet: 0.14 (0.36), residues: 204 loop : -0.92 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 107 TYR 0.019 0.001 TYR C 291 PHE 0.011 0.001 PHE B 403 TRP 0.015 0.001 TRP B 241 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (15842) covalent geometry : angle 0.59226 / 0.32 (21721) SS BOND : bond 0.02575 / 1.36 ( 1) SS BOND : angle 2.69820 / 1.45 ( 2) hydrogen bonds : bond 0.05854 / 4.02 ( 659) hydrogen bonds : angle 4.92065 / 3.42 ( 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 502 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 409 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7364 (ptp-170) REVERT: A 308 GLN cc_start: 0.8403 (mt0) cc_final: 0.7987 (mt0) REVERT: A 378 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8772 (p) REVERT: A 379 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8326 (tptt) REVERT: A 393 MET cc_start: 0.8353 (tpp) cc_final: 0.8123 (tpp) REVERT: A 456 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: A 474 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8926 (tt) REVERT: A 535 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 550 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: A 796 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8479 (ptpt) REVERT: A 1112 MET cc_start: 0.8440 (mtm) cc_final: 0.8139 (mtp) REVERT: A 1222 GLN cc_start: 0.8042 (mt0) cc_final: 0.7665 (mt0) REVERT: B 71 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: B 234 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8305 (mtmm) REVERT: B 240 VAL cc_start: 0.9187 (t) cc_final: 0.8951 (p) REVERT: C 92 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8726 (tt) REVERT: C 256 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8333 (tp) REVERT: C 262 TRP cc_start: 0.8808 (t60) cc_final: 0.8597 (t60) REVERT: C 400 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8237 (tp40) REVERT: C 427 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8607 (tm-30) outliers start: 93 outliers final: 51 residues processed: 460 average time/residue: 0.0977 time to fit residues: 68.4682 Evaluate side-chains 459 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 SER 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 379 LYS 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 535 GLU 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 793 GLU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 861 THR 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 1097 VAL 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 1193 VAL 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 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 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 464 GLU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 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 238 SER Chi-restraints excluded: chain C residue 256 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 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: 5.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 169 optimal weight: 0.0050 chunk 34 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN 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 = 0.3529 r_free = 0.3529 target = 0.111265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095150 restraints weight = 29217.316| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.50 r_work: 0.3160 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15843 Z= 0.118 Angle : 0.549 6.744 21723 Z= 0.298 Chirality : 0.041 0.168 2327 Planarity : 0.004 0.058 2577 Dihedral : 16.803 98.037 2590 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.79 % Allowed : 25.48 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1727 helix: 1.22 (0.20), residues: 714 sheet: 0.24 (0.37), residues: 203 loop : -0.79 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.014 0.001 TYR C 291 PHE 0.010 0.001 PHE A 197 TRP 0.013 0.001 TRP B 241 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (15842) covalent geometry : angle 0.54802 / 0.30 (21721) SS BOND : bond 0.01170 / 0.62 ( 1) SS BOND : angle 2.83925 / 1.50 ( 2) hydrogen bonds : bond 0.04737 / 3.28 ( 659) hydrogen bonds : angle 4.61788 / 3.20 ( 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 504 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 416 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7222 (ptp90) REVERT: A 308 GLN cc_start: 0.8377 (mt0) cc_final: 0.7990 (mt0) REVERT: A 378 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8704 (p) REVERT: A 393 MET cc_start: 0.8242 (tpp) cc_final: 0.8012 (tpp) REVERT: A 456 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 474 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 535 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 550 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: A 913 CYS cc_start: 0.8107 (p) cc_final: 0.7808 (p) REVERT: A 993 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6652 (ttm170) REVERT: A 1112 MET cc_start: 0.8374 (mtm) cc_final: 0.8045 (mtp) REVERT: A 1222 GLN cc_start: 0.8000 (mt0) cc_final: 0.7614 (mt0) REVERT: B 71 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: B 92 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 191 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 234 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: B 240 VAL cc_start: 0.9158 (t) cc_final: 0.8952 (p) REVERT: C 92 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 346 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7139 (mtp) REVERT: C 397 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7564 (mm-40) REVERT: C 400 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8186 (tp40) REVERT: C 427 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 88 outliers final: 53 residues processed: 460 average time/residue: 0.1034 time to fit residues: 72.5735 Evaluate side-chains 472 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 406 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 378 VAL 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 535 GLU Chi-restraints excluded: chain A residue 538 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 748 TRP Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 861 THR 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 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1193 VAL 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 213 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 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 385 LEU 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 92 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 268 MET Chi-restraints excluded: chain C residue 346 MET 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 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 475 LEU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 122 optimal weight: 0.0970 chunk 99 optimal weight: 0.0000 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 736 ASN B 85 GLN B 287 ASN C 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096563 restraints weight = 29314.829| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.50 r_work: 0.3185 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15843 Z= 0.111 Angle : 0.533 8.416 21723 Z= 0.288 Chirality : 0.040 0.150 2327 Planarity : 0.004 0.056 2577 Dihedral : 16.680 96.202 2579 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.27 % Allowed : 25.54 % 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: 0.41 (0.21), residues: 1727 helix: 1.41 (0.21), residues: 709 sheet: 0.20 (0.36), residues: 205 loop : -0.70 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 579 TYR 0.012 0.001 TYR A1166 PHE 0.009 0.001 PHE A 389 TRP 0.012 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (15842) covalent geometry : angle 0.53279 / 0.29 (21721) SS BOND : bond 0.03593 / 1.89 ( 1) SS BOND : angle 2.19172 / 1.19 ( 2) hydrogen bonds : bond 0.04127 / 2.86 ( 659) hydrogen bonds : angle 4.43948 / 3.07 ( 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 505 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 425 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7005 (ptp90) REVERT: A 308 GLN cc_start: 0.8369 (mt0) cc_final: 0.8019 (mt0) REVERT: A 393 MET cc_start: 0.8190 (tpp) cc_final: 0.7946 (tpp) REVERT: A 443 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.8104 (ttt90) REVERT: A 456 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 474 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 535 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 913 CYS cc_start: 0.8083 (p) cc_final: 0.7797 (p) REVERT: A 993 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6462 (ttm170) REVERT: A 1204 THR cc_start: 0.8911 (p) cc_final: 0.8501 (t) REVERT: A 1207 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7854 (tt0) REVERT: A 1222 GLN cc_start: 0.8021 (mt0) cc_final: 0.7684 (mt0) REVERT: B 71 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: B 92 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8638 (mt) REVERT: B 234 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8225 (mtmm) REVERT: B 236 GLU cc_start: 0.7376 (tt0) cc_final: 0.7107 (tt0) REVERT: B 240 VAL cc_start: 0.9135 (t) cc_final: 0.8915 (p) REVERT: C 88 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6889 (tmm-80) REVERT: C 92 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8711 (tt) REVERT: C 268 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8309 (ttt) REVERT: C 346 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7131 (mtp) REVERT: C 397 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7418 (mm110) REVERT: C 427 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8561 (tm-30) REVERT: C 470 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.6925 (mmmm) outliers start: 80 outliers final: 50 residues processed: 458 average time/residue: 0.1054 time to fit residues: 73.2467 Evaluate side-chains 474 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 411 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 LEU Chi-restraints excluded: chain A residue 236 THR 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 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 535 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 861 THR 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 1075 LEU Chi-restraints excluded: chain A residue 1078 CYS 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 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 234 LYS Chi-restraints excluded: chain B residue 243 THR 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 437 ILE 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 C residue 86 LEU Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 346 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 139 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 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: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3479 r_free = 0.3479 target = 0.108400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092569 restraints weight = 29206.170| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.49 r_work: 0.3107 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15843 Z= 0.230 Angle : 0.630 8.368 21723 Z= 0.338 Chirality : 0.044 0.168 2327 Planarity : 0.005 0.062 2577 Dihedral : 16.792 89.464 2577 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 6.85 % Allowed : 24.36 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1727 helix: 1.19 (0.20), residues: 711 sheet: 0.04 (0.36), residues: 214 loop : -0.91 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 328 TYR 0.018 0.002 TYR C 291 PHE 0.011 0.002 PHE A 766 TRP 0.012 0.002 TRP A 607 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (15842) covalent geometry : angle 0.62886 / 0.34 (21721) SS BOND : bond 0.01564 / 0.82 ( 1) SS BOND : angle 3.07802 / 1.67 ( 2) hydrogen bonds : bond 0.05906 / 4.07 ( 659) hydrogen bonds : angle 4.68117 / 3.27 ( 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 504 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 400 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 279 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.6787 (ptp90) REVERT: A 379 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8158 (tptt) REVERT: A 393 MET cc_start: 0.8319 (tpp) cc_final: 0.8087 (tpp) REVERT: A 443 ARG cc_start: 0.8669 (ttt-90) cc_final: 0.8270 (ttt90) REVERT: A 456 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 474 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8967 (tt) REVERT: A 535 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 550 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: A 796 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8494 (ptpt) REVERT: A 913 CYS cc_start: 0.8097 (p) cc_final: 0.7784 (p) REVERT: A 993 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.5852 (ptm-80) REVERT: A 1112 MET cc_start: 0.8402 (mtm) cc_final: 0.8076 (mtp) REVERT: A 1207 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7902 (tt0) REVERT: A 1222 GLN cc_start: 0.8022 (mt0) cc_final: 0.7606 (mt0) REVERT: B 71 GLU cc_start: 0.8617 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 234 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8271 (mtmm) REVERT: B 240 VAL cc_start: 0.9198 (t) cc_final: 0.8966 (p) REVERT: C 268 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8423 (ttt) REVERT: C 346 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7264 (mtp) REVERT: C 400 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: C 427 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8530 (tm-30) REVERT: C 470 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7114 (mmmm) outliers start: 104 outliers final: 70 residues processed: 457 average time/residue: 0.1064 time to fit residues: 74.1098 Evaluate side-chains 476 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 393 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 195 LEU 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 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 534 SER Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 562 ARG 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 793 GLU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 931 LEU 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 185 LEU Chi-restraints excluded: chain B residue 211 ILE 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 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 385 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 398 VAL 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 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 197 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 346 MET 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 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 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: 0.8980 chunk 105 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN 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 = 0.3514 r_free = 0.3514 target = 0.110518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094837 restraints weight = 28971.265| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.47 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1192 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= 0.140 Angle : 0.584 8.473 21723 Z= 0.312 Chirality : 0.042 0.151 2327 Planarity : 0.004 0.062 2577 Dihedral : 16.770 91.447 2577 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.12 % Allowed : 25.35 % Favored : 68.53 % 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 (0.20), residues: 1727 helix: 1.23 (0.20), residues: 716 sheet: 0.11 (0.36), residues: 212 loop : -0.84 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 328 TYR 0.013 0.001 TYR C 291 PHE 0.011 0.001 PHE A 389 TRP 0.013 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (15842) covalent geometry : angle 0.58320 / 0.31 (21721) SS BOND : bond 0.01354 / 0.71 ( 1) SS BOND : angle 2.81469 / 1.50 ( 2) hydrogen bonds : bond 0.04954 / 3.43 ( 659) hydrogen bonds : angle 4.51451 / 3.14 ( 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 502 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 409 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 279 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.6473 (ptp90) REVERT: A 299 MET cc_start: 0.8896 (tpp) cc_final: 0.8594 (mmm) REVERT: A 308 GLN cc_start: 0.8410 (mt0) cc_final: 0.8006 (mt0) REVERT: A 379 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8126 (tptt) REVERT: A 393 MET cc_start: 0.8262 (tpp) cc_final: 0.8030 (tpp) REVERT: A 443 ARG cc_start: 0.8620 (ttt-90) cc_final: 0.8250 (ttt90) REVERT: A 456 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 474 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8918 (tt) REVERT: A 535 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: A 550 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 792 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 796 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8476 (ptpt) REVERT: A 913 CYS cc_start: 0.8082 (p) cc_final: 0.7765 (p) REVERT: A 993 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6087 (ptm-80) REVERT: A 1112 MET cc_start: 0.8333 (mtm) cc_final: 0.8011 (mtp) REVERT: A 1207 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7942 (tt0) REVERT: A 1222 GLN cc_start: 0.8013 (mt0) cc_final: 0.7605 (mt0) REVERT: B 71 GLU cc_start: 0.8586 (tt0) cc_final: 0.8270 (tm-30) REVERT: B 234 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: B 240 VAL cc_start: 0.9174 (t) cc_final: 0.8950 (p) REVERT: C 87 SER cc_start: 0.8137 (t) cc_final: 0.7587 (p) REVERT: C 88 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6915 (tmm-80) REVERT: C 268 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8409 (ttt) REVERT: C 346 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7177 (mtp) REVERT: C 400 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: C 427 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 470 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7052 (mmmm) outliers start: 93 outliers final: 62 residues processed: 458 average time/residue: 0.1071 time to fit residues: 74.3337 Evaluate side-chains 479 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 402 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 195 LEU 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 245 ILE 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 748 TRP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 796 LYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 931 LEU 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 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 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN 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 385 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 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 88 ARG 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 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 346 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3515 r_free = 0.3515 target = 0.110634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094877 restraints weight = 29305.712| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.49 r_work: 0.3147 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15843 Z= 0.132 Angle : 0.571 8.662 21723 Z= 0.306 Chirality : 0.041 0.154 2327 Planarity : 0.004 0.064 2577 Dihedral : 16.740 90.576 2577 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.99 % Allowed : 25.21 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1727 helix: 1.30 (0.21), residues: 716 sheet: 0.13 (0.35), residues: 212 loop : -0.81 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 328 TYR 0.013 0.001 TYR C 291 PHE 0.010 0.001 PHE A 389 TRP 0.014 0.001 TRP B 241 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15842) covalent geometry : angle 0.57061 / 0.31 (21721) SS BOND : bond 0.01403 / 0.74 ( 1) SS BOND : angle 2.83131 / 1.50 ( 2) hydrogen bonds : bond 0.04662 / 3.23 ( 659) hydrogen bonds : angle 4.43807 / 3.09 ( 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 497 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 406 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 279 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6385 (ptp90) REVERT: A 299 MET cc_start: 0.8886 (tpp) cc_final: 0.8582 (mmm) REVERT: A 308 GLN cc_start: 0.8406 (mt0) cc_final: 0.8000 (mt0) REVERT: A 379 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8134 (tptt) REVERT: A 393 MET cc_start: 0.8250 (tpp) cc_final: 0.8008 (tpp) REVERT: A 443 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.8240 (ttt90) REVERT: A 456 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 474 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8891 (tt) REVERT: A 535 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 550 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 774 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: A 792 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 796 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8472 (ptpt) REVERT: A 913 CYS cc_start: 0.8082 (p) cc_final: 0.7766 (p) REVERT: A 993 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6008 (ptm-80) REVERT: A 1207 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7955 (tt0) REVERT: A 1222 GLN cc_start: 0.8013 (mt0) cc_final: 0.7605 (mt0) REVERT: B 71 GLU cc_start: 0.8562 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 234 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: B 240 VAL cc_start: 0.9171 (t) cc_final: 0.8948 (p) REVERT: C 87 SER cc_start: 0.8053 (t) cc_final: 0.7518 (p) REVERT: C 88 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6869 (tmm-80) REVERT: C 268 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8393 (ttt) REVERT: C 400 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: C 427 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 470 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.6967 (mmmm) outliers start: 91 outliers final: 64 residues processed: 456 average time/residue: 0.1065 time to fit residues: 73.8600 Evaluate side-chains 483 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 404 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 195 LEU 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 245 ILE 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 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 748 TRP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 796 LYS 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 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1199 THR 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 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN 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 385 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 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 88 ARG 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 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 346 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3522 r_free = 0.3522 target = 0.111023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095352 restraints weight = 29067.553| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.48 r_work: 0.3156 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 0.037 15843 Z= 0.125 Angle : 0.569 8.512 21723 Z= 0.302 Chirality : 0.041 0.154 2327 Planarity : 0.004 0.063 2577 Dihedral : 16.711 89.974 2576 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.92 % Allowed : 25.48 % 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: 0.34 (0.21), residues: 1727 helix: 1.34 (0.21), residues: 716 sheet: 0.22 (0.35), residues: 213 loop : -0.78 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 328 TYR 0.012 0.001 TYR C 291 PHE 0.010 0.001 PHE A 389 TRP 0.014 0.001 TRP B 241 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15842) covalent geometry : angle 0.56861 / 0.30 (21721) SS BOND : bond 0.01368 / 0.72 ( 1) SS BOND : angle 2.79676 / 1.48 ( 2) hydrogen bonds : bond 0.04443 / 3.08 ( 659) hydrogen bonds : angle 4.38520 / 3.05 ( 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 498 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 408 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 279 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.6363 (ptp90) REVERT: A 299 MET cc_start: 0.8883 (tpp) cc_final: 0.8586 (mmm) REVERT: A 308 GLN cc_start: 0.8399 (mt0) cc_final: 0.8001 (mt0) REVERT: A 379 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8121 (tptt) REVERT: A 393 MET cc_start: 0.8206 (tpp) cc_final: 0.7959 (tpp) REVERT: A 443 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8183 (ttt90) REVERT: A 456 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: A 535 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 550 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: A 774 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7949 (ttt) REVERT: A 792 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 796 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8487 (ptpt) REVERT: A 913 CYS cc_start: 0.8072 (p) cc_final: 0.7754 (p) REVERT: A 993 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6574 (ttm170) REVERT: A 1207 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7952 (tt0) REVERT: A 1222 GLN cc_start: 0.8018 (mt0) cc_final: 0.7614 (mt0) REVERT: B 71 GLU cc_start: 0.8568 (tt0) cc_final: 0.8308 (tm-30) REVERT: B 92 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 234 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8293 (mtmm) REVERT: B 240 VAL cc_start: 0.9167 (t) cc_final: 0.8942 (p) REVERT: C 87 SER cc_start: 0.8048 (t) cc_final: 0.7536 (p) REVERT: C 88 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6828 (tmm-80) REVERT: C 268 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8392 (ttt) REVERT: C 397 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7425 (mm110) REVERT: C 400 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8081 (tp40) REVERT: C 427 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 470 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.6968 (mmmm) outliers start: 90 outliers final: 65 residues processed: 457 average time/residue: 0.1028 time to fit residues: 71.7891 Evaluate side-chains 479 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 399 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 195 LEU 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 245 ILE 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 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 748 TRP Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 792 LEU 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 931 LEU 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 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 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN 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 423 SER Chi-restraints excluded: chain B residue 437 ILE 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 88 ARG 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 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 346 MET 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 383 VAL Chi-restraints excluded: chain C residue 394 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 53 optimal weight: 0.0070 chunk 105 optimal weight: 3.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3509 r_free = 0.3509 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094482 restraints weight = 29465.586| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.50 r_work: 0.3141 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15843 Z= 0.153 Angle : 0.584 9.101 21723 Z= 0.310 Chirality : 0.042 0.159 2327 Planarity : 0.004 0.066 2577 Dihedral : 16.724 89.633 2576 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.53 % Allowed : 25.94 % Favored : 68.53 % 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: 1.37 (0.21), residues: 709 sheet: 0.18 (0.35), residues: 213 loop : -0.78 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 328 TYR 0.015 0.001 TYR A 884 PHE 0.010 0.001 PHE A 389 TRP 0.012 0.001 TRP B 241 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15842) covalent geometry : angle 0.58319 / 0.31 (21721) SS BOND : bond 0.01447 / 0.76 ( 1) SS BOND : angle 2.85554 / 1.51 ( 2) hydrogen bonds : bond 0.04771 / 3.31 ( 659) hydrogen bonds : angle 4.42322 / 3.08 ( 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 486 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 402 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 279 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.6385 (ptp90) REVERT: A 299 MET cc_start: 0.8893 (tpp) cc_final: 0.8594 (mmm) REVERT: A 308 GLN cc_start: 0.8422 (mt0) cc_final: 0.8017 (mt0) REVERT: A 379 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8106 (tptt) REVERT: A 393 MET cc_start: 0.8253 (tpp) cc_final: 0.8012 (tpp) REVERT: A 443 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.8242 (ttt90) REVERT: A 456 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 535 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: A 550 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: A 792 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 796 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8469 (ptpt) REVERT: A 913 CYS cc_start: 0.8083 (p) cc_final: 0.7764 (p) REVERT: A 993 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.5786 (ptm-80) REVERT: A 1207 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7968 (tt0) REVERT: A 1222 GLN cc_start: 0.8040 (mt0) cc_final: 0.7628 (mt0) REVERT: B 71 GLU cc_start: 0.8579 (tt0) cc_final: 0.8254 (tm-30) REVERT: B 234 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8306 (mtmm) REVERT: B 236 GLU cc_start: 0.7311 (tt0) cc_final: 0.6952 (tt0) REVERT: B 240 VAL cc_start: 0.9180 (t) cc_final: 0.8953 (p) REVERT: C 87 SER cc_start: 0.8072 (t) cc_final: 0.7559 (p) REVERT: C 88 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6854 (tmm-80) REVERT: C 268 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8420 (ttt) REVERT: C 400 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8073 (tp40) REVERT: C 427 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8524 (tm-30) REVERT: C 470 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.6975 (mmmm) outliers start: 84 outliers final: 67 residues processed: 452 average time/residue: 0.1013 time to fit residues: 70.2173 Evaluate side-chains 479 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 399 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 195 LEU 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 245 ILE 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 792 LEU 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 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 1157 ASN Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1199 THR 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 234 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 ASN 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 423 SER Chi-restraints excluded: chain B residue 437 ILE 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 88 ARG 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 268 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 346 MET 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 383 VAL Chi-restraints excluded: chain C residue 394 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 122 optimal weight: 0.0020 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3530 r_free = 0.3530 target = 0.111584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095874 restraints weight = 28991.302| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.49 r_work: 0.3166 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1325 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= 0.119 Angle : 0.569 9.553 21723 Z= 0.301 Chirality : 0.041 0.163 2327 Planarity : 0.004 0.063 2577 Dihedral : 16.691 89.822 2576 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.33 % Allowed : 26.33 % Favored : 68.33 % 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: 0.44 (0.21), residues: 1727 helix: 1.44 (0.21), residues: 710 sheet: 0.21 (0.35), residues: 213 loop : -0.72 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.015 0.001 TYR A 955 PHE 0.010 0.001 PHE A 389 TRP 0.014 0.001 TRP B 241 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15842) covalent geometry : angle 0.56811 / 0.30 (21721) SS BOND : bond 0.01334 / 0.70 ( 1) SS BOND : angle 2.73185 / 1.44 ( 2) hydrogen bonds : bond 0.04243 / 2.95 ( 659) hydrogen bonds : angle 4.32375 / 3.01 ( 1823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.50 seconds wall clock time: 52 minutes 39.53 seconds (3159.53 seconds total)