Starting phenix.real_space_refine on Thu Aug 6 12:50:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855.map" model { file = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2026/8wui_37855_neut.cif" } resolution = 3.4 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= 0.002 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 10130 2.51 5 N 2498 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15340 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.41, per 1000 atoms: 0.22 Number of scatterers: 15340 At special positions: 0 Unit cell: (117.52, 115.44, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 2 15.00 O 2618 8.00 N 2498 7.00 C 10130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 650.5 milliseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 10 sheets defined 67.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 79 through 97 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.895A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.514A pdb=" N VAL B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.240A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 243 removed outlier: 3.670A pdb=" N ILE B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 287 Processing helix chain 'B' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.575A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.837A pdb=" N ILE B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.720A pdb=" N SER A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 187' Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 194 through 208 removed outlier: 4.187A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.847A pdb=" N CYS A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 330 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 97 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.894A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.515A pdb=" N VAL D 184 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.241A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.670A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.217A pdb=" N THR D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 287 Processing helix chain 'D' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE D 336 " --> pdb=" O LYS D 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 369 Processing helix chain 'D' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.576A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.838A pdb=" N ILE D 476 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 509 Processing helix chain 'D' and resid 509 through 524 Processing helix chain 'C' and resid 79 through 98 removed outlier: 3.719A pdb=" N SER C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 187' Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 194 through 208 removed outlier: 4.188A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.961A pdb=" N CYS C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 238 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR C 251 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 330 Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'C' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 418 " --> pdb=" O GLN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 541 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 137 through 139 removed outlier: 3.758A pdb=" N TYR B 137 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU B 422 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 494 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 493 " --> pdb=" O CYS B 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 441 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 471 " --> pdb=" O TYR B 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 460 through 465 removed outlier: 6.620A pdb=" N GLU B 450 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 464 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 448 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 449 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 447 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.759A pdb=" N TYR D 137 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU D 422 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 494 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 493 " --> pdb=" O CYS D 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 441 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 471 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 460 through 465 removed outlier: 6.621A pdb=" N GLU D 450 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL D 464 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 448 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 449 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB1, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 447 " --> pdb=" O ALA C 489 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2302 1.30 - 1.43: 4363 1.43 - 1.56: 8865 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15694 Sorted by residual: bond pdb=" C ASN A 355 " pdb=" O ASN A 355 " ideal model delta sigma weight residual 1.235 1.310 -0.075 1.26e-02 6.30e+03 3.52e+01 bond pdb=" C ASN C 355 " pdb=" O ASN C 355 " ideal model delta sigma weight residual 1.235 1.309 -0.074 1.26e-02 6.30e+03 3.45e+01 bond pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.32e-02 5.74e+03 2.40e+01 bond pdb=" C SER C 331 " pdb=" O SER C 331 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.32e-02 5.74e+03 2.35e+01 bond pdb=" C GLN A 359 " pdb=" O GLN A 359 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 ... (remaining 15689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 20930 3.58 - 7.16: 177 7.16 - 10.75: 25 10.75 - 14.33: 0 14.33 - 17.91: 2 Bond angle restraints: 21134 Sorted by residual: angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 112.23 101.94 10.29 1.26e+00 6.30e-01 6.67e+01 angle pdb=" N ASN C 348 " pdb=" CA ASN C 348 " pdb=" C ASN C 348 " ideal model delta sigma weight residual 112.23 101.96 10.27 1.26e+00 6.30e-01 6.65e+01 angle pdb=" N LEU D 226 " pdb=" CA LEU D 226 " pdb=" C LEU D 226 " ideal model delta sigma weight residual 113.72 104.00 9.72 1.30e+00 5.92e-01 5.60e+01 angle pdb=" N LYS C 332 " pdb=" CA LYS C 332 " pdb=" C LYS C 332 " ideal model delta sigma weight residual 111.14 103.08 8.06 1.08e+00 8.57e-01 5.58e+01 angle pdb=" N LYS A 332 " pdb=" CA LYS A 332 " pdb=" C LYS A 332 " ideal model delta sigma weight residual 111.14 103.10 8.04 1.08e+00 8.57e-01 5.54e+01 ... (remaining 21129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7694 17.75 - 35.50: 1141 35.50 - 53.25: 408 53.25 - 71.00: 91 71.00 - 88.75: 22 Dihedral angle restraints: 9356 sinusoidal: 3958 harmonic: 5398 Sorted by residual: dihedral pdb=" CA GLU D 112 " pdb=" C GLU D 112 " pdb=" N ASN D 113 " pdb=" CA ASN D 113 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLU B 112 " pdb=" C GLU B 112 " pdb=" N ASN B 113 " pdb=" CA ASN B 113 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C CYS D 228 " pdb=" N CYS D 228 " pdb=" CA CYS D 228 " pdb=" CB CYS D 228 " ideal model delta harmonic sigma weight residual -122.60 -131.35 8.75 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 9353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1916 0.061 - 0.121: 331 0.121 - 0.182: 52 0.182 - 0.243: 22 0.243 - 0.304: 7 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 350 " pdb=" N ASN C 350 " pdb=" C ASN C 350 " pdb=" CB ASN C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2325 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C ASP C 380 " 0.094 2.00e-02 2.50e+03 pdb=" O ASP C 380 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE C 381 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 380 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASP A 380 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP A 380 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE A 381 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 270 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 271 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.054 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 198 2.59 - 3.36: 20841 3.36 - 4.13: 37714 4.13 - 4.90: 68846 Nonbonded interactions: 127610 Sorted by model distance: nonbonded pdb=" CG1 ILE A 360 " pdb=" CD1 ILE D 385 " model vdw 1.049 3.860 nonbonded pdb=" CG1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.127 3.840 nonbonded pdb=" NH2 ARG A 345 " pdb=" OE1 GLU D 374 " model vdw 1.261 3.120 nonbonded pdb=" CD1 ILE B 385 " pdb=" CG1 ILE C 360 " model vdw 1.395 3.860 nonbonded pdb=" CD1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.405 3.860 ... (remaining 127605 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'B' and (resid 73 through 452 or resid 462 through 901 or (resid 902 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C29 or name C2A)) or resid 903)) selection = (chain 'C' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'D' and (resid 73 through 452 or resid 462 through 901 or (resid 902 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C29 or name C2A)) or resid 903)) } 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: 1.340 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 : 0.012 0.884 15702 Z= 1.124 Angle : 0.838 17.910 21134 Z= 0.532 Chirality : 0.053 0.304 2328 Planarity : 0.006 0.100 2592 Dihedral : 19.522 88.748 5888 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 27.30 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.15 (0.20), residues: 1810 helix: -0.98 (0.16), residues: 1040 sheet: -0.97 (0.97), residues: 34 loop : -0.12 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 TYR 0.013 0.001 TYR B 237 PHE 0.030 0.002 PHE D 223 TRP 0.018 0.001 TRP C 171 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.37 (15694) covalent geometry : angle 0.83753 / 0.53 (21134) hydrogen bonds : bond 0.26261 / 16.45 ( 837) hydrogen bonds : angle 9.26269 / 6.49 ( 2355) Misc. bond : bond 0.47052 / 29.29 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 235 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6435 (t) REVERT: B 468 ASP cc_start: 0.5185 (t0) cc_final: 0.4524 (t0) REVERT: A 145 MET cc_start: 0.6947 (tpp) cc_final: 0.6699 (tpp) REVERT: A 351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3582 (mttp) REVERT: A 365 ARG cc_start: 0.0570 (OUTLIER) cc_final: 0.0068 (ttp-170) REVERT: D 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7657 (t70) REVERT: D 468 ASP cc_start: 0.5363 (t0) cc_final: 0.5022 (t0) REVERT: C 183 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5435 (tt0) REVERT: C 365 ARG cc_start: 0.1331 (OUTLIER) cc_final: 0.0352 (ttp-170) REVERT: C 369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2456 (pt0) outliers start: 83 outliers final: 31 residues processed: 306 average time/residue: 0.1285 time to fit residues: 57.2660 Evaluate side-chains 227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 GLN D 295 HIS D 312 ASN D 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.261150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193200 restraints weight = 18871.919| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.24 r_work: 0.3738 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15702 Z= 0.166 Angle : 0.658 11.205 21134 Z= 0.345 Chirality : 0.044 0.165 2328 Planarity : 0.006 0.073 2592 Dihedral : 11.756 93.630 2358 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.52 % Favored : 94.03 % Rotamer: Outliers : 4.91 % Allowed : 25.58 % Favored : 69.51 % 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: -0.39 (0.20), residues: 1810 helix: -0.27 (0.16), residues: 1074 sheet: -0.63 (1.18), residues: 20 loop : 0.07 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.016 0.001 TYR A 368 PHE 0.024 0.002 PHE D 281 TRP 0.014 0.001 TRP D 92 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (15694) covalent geometry : angle 0.65784 / 0.34 (21134) hydrogen bonds : bond 0.05523 / 3.52 ( 837) hydrogen bonds : angle 5.83922 / 4.13 ( 2355) Misc. bond : bond 0.00267 / 0.17 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7507 (mmp) cc_final: 0.6453 (mmm) REVERT: B 218 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5360 (tt) REVERT: B 367 GLN cc_start: 0.7924 (mt0) cc_final: 0.7530 (mp10) REVERT: A 89 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 145 MET cc_start: 0.8240 (tpp) cc_final: 0.7749 (tpp) REVERT: A 260 ASP cc_start: 0.8116 (m-30) cc_final: 0.7780 (t70) REVERT: A 339 LYS cc_start: 0.6560 (mmtt) cc_final: 0.6168 (pttm) REVERT: A 355 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.5533 (p0) REVERT: A 360 ILE cc_start: 0.4277 (OUTLIER) cc_final: 0.3868 (mm) REVERT: A 368 TYR cc_start: 0.3829 (OUTLIER) cc_final: 0.3177 (p90) REVERT: A 369 GLU cc_start: 0.0290 (OUTLIER) cc_final: 0.0060 (pt0) REVERT: A 404 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 421 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6503 (tm-30) REVERT: C 89 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7483 (tp) REVERT: C 92 TRP cc_start: 0.7724 (m100) cc_final: 0.7497 (m100) REVERT: C 171 TRP cc_start: 0.7761 (m100) cc_final: 0.7311 (m100) REVERT: C 211 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7282 (mp) REVERT: C 221 LEU cc_start: 0.7953 (mm) cc_final: 0.7560 (mt) REVERT: C 359 GLN cc_start: 0.4510 (tm-30) cc_final: 0.4132 (mm110) REVERT: C 369 GLU cc_start: 0.1305 (OUTLIER) cc_final: 0.0986 (pt0) REVERT: C 393 LEU cc_start: 0.7230 (tt) cc_final: 0.6836 (pp) REVERT: C 404 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (t80) outliers start: 80 outliers final: 37 residues processed: 286 average time/residue: 0.1061 time to fit residues: 47.4757 Evaluate side-chains 230 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 124 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.1714 > 50:) chunk 6 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.262358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196962 restraints weight = 19746.265| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.50 r_work: 0.3752 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15702 Z= 0.136 Angle : 0.597 10.616 21134 Z= 0.309 Chirality : 0.043 0.156 2328 Planarity : 0.005 0.057 2592 Dihedral : 9.833 81.993 2304 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.03 % Favored : 94.53 % Rotamer: Outliers : 4.29 % Allowed : 25.52 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1810 helix: 0.09 (0.16), residues: 1080 sheet: -1.27 (0.80), residues: 40 loop : 0.03 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 349 TYR 0.014 0.001 TYR D 237 PHE 0.016 0.001 PHE D 281 TRP 0.014 0.001 TRP D 92 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15694) covalent geometry : angle 0.59704 / 0.31 (21134) hydrogen bonds : bond 0.04671 / 2.95 ( 837) hydrogen bonds : angle 5.25810 / 3.74 ( 2355) Misc. bond : bond 0.00164 / 0.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.6770 (tttm) REVERT: B 421 GLU cc_start: 0.6807 (tp30) cc_final: 0.6467 (mt-10) REVERT: A 89 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 126 LEU cc_start: 0.7109 (mt) cc_final: 0.6581 (mt) REVERT: A 145 MET cc_start: 0.8116 (tpp) cc_final: 0.7686 (tpp) REVERT: A 260 ASP cc_start: 0.8124 (m-30) cc_final: 0.7778 (t0) REVERT: A 322 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.6867 (m-40) REVERT: A 339 LYS cc_start: 0.6793 (mmtt) cc_final: 0.6546 (pttp) REVERT: A 344 MET cc_start: 0.4663 (mmt) cc_final: 0.3793 (pmm) REVERT: A 368 TYR cc_start: 0.3796 (OUTLIER) cc_final: 0.3375 (p90) REVERT: A 393 LEU cc_start: 0.7584 (tt) cc_final: 0.7046 (pp) REVERT: A 404 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7212 (t80) REVERT: D 218 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5322 (tt) REVERT: D 299 MET cc_start: 0.8150 (ttm) cc_final: 0.7928 (ttp) REVERT: D 421 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6480 (tm-30) REVERT: C 89 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7588 (tp) REVERT: C 92 TRP cc_start: 0.7725 (m100) cc_final: 0.7477 (m100) REVERT: C 211 ILE cc_start: 0.7716 (tp) cc_final: 0.7216 (mp) REVERT: C 221 LEU cc_start: 0.7950 (mm) cc_final: 0.7509 (mt) REVERT: C 260 ASP cc_start: 0.8218 (m-30) cc_final: 0.7830 (t0) REVERT: C 322 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7173 (m-40) REVERT: C 339 LYS cc_start: 0.6655 (mmtt) cc_final: 0.6115 (pttm) REVERT: C 340 MET cc_start: 0.4388 (mmt) cc_final: 0.3857 (ptp) REVERT: C 359 GLN cc_start: 0.4602 (tm-30) cc_final: 0.3985 (mp10) REVERT: C 365 ARG cc_start: 0.1987 (OUTLIER) cc_final: 0.1578 (ttp-170) REVERT: C 393 LEU cc_start: 0.7212 (tt) cc_final: 0.6823 (pp) REVERT: C 404 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7057 (t80) REVERT: C 503 MET cc_start: 0.8368 (ppp) cc_final: 0.7744 (ppp) outliers start: 70 outliers final: 24 residues processed: 265 average time/residue: 0.1181 time to fit residues: 48.2446 Evaluate side-chains 219 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 149 optimal weight: 0.0870 chunk 165 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN C 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.259677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.186103 restraints weight = 19634.439| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.21 r_work: 0.3705 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15702 Z= 0.159 Angle : 0.592 12.069 21134 Z= 0.307 Chirality : 0.044 0.205 2328 Planarity : 0.004 0.057 2592 Dihedral : 8.954 68.560 2289 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.64 % Favored : 93.92 % Rotamer: Outliers : 4.23 % Allowed : 26.32 % Favored : 69.45 % 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: -0.02 (0.20), residues: 1810 helix: 0.19 (0.16), residues: 1080 sheet: -0.81 (0.71), residues: 60 loop : -0.01 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 210 TYR 0.041 0.001 TYR A 82 PHE 0.015 0.002 PHE A 304 TRP 0.011 0.001 TRP B 92 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15694) covalent geometry : angle 0.59227 / 0.31 (21134) hydrogen bonds : bond 0.04435 / 2.83 ( 837) hydrogen bonds : angle 5.09313 / 3.62 ( 2355) Misc. bond : bond 0.00139 / 0.08 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7609 (mmp) cc_final: 0.6362 (mmm) REVERT: B 158 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6764 (tttm) REVERT: B 202 PHE cc_start: 0.7102 (m-10) cc_final: 0.6838 (m-10) REVERT: B 218 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5400 (tt) REVERT: B 236 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7694 (t80) REVERT: A 89 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 126 LEU cc_start: 0.7447 (mt) cc_final: 0.6806 (mt) REVERT: A 145 MET cc_start: 0.8123 (tpp) cc_final: 0.7700 (tpp) REVERT: A 239 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 306 MET cc_start: 0.8312 (mmp) cc_final: 0.8020 (mmt) REVERT: A 322 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.6898 (m-40) REVERT: A 344 MET cc_start: 0.4584 (mmt) cc_final: 0.3803 (pmm) REVERT: A 368 TYR cc_start: 0.3646 (OUTLIER) cc_final: 0.3445 (p90) REVERT: A 393 LEU cc_start: 0.7482 (tt) cc_final: 0.6848 (pp) REVERT: A 404 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7079 (t80) REVERT: D 186 TYR cc_start: 0.7330 (m-10) cc_final: 0.7118 (m-10) REVERT: D 218 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.5669 (tt) REVERT: D 299 MET cc_start: 0.8179 (ttm) cc_final: 0.7928 (ttp) REVERT: D 421 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6414 (tm-30) REVERT: C 89 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7764 (tp) REVERT: C 211 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7271 (mp) REVERT: C 221 LEU cc_start: 0.8036 (mm) cc_final: 0.7528 (mt) REVERT: C 322 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7122 (m-40) REVERT: C 393 LEU cc_start: 0.7220 (tt) cc_final: 0.6851 (pp) REVERT: C 404 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7064 (t80) outliers start: 69 outliers final: 32 residues processed: 250 average time/residue: 0.1080 time to fit residues: 41.3125 Evaluate side-chains 226 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 121 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 chunk 13 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.258934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174341 restraints weight = 19201.920| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.18 r_work: 0.3703 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15702 Z= 0.129 Angle : 0.572 11.263 21134 Z= 0.294 Chirality : 0.043 0.178 2328 Planarity : 0.004 0.055 2592 Dihedral : 8.520 67.970 2280 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.36 % Favored : 94.20 % Rotamer: Outliers : 4.17 % Allowed : 26.44 % Favored : 69.39 % 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: 0.10 (0.20), residues: 1810 helix: 0.33 (0.16), residues: 1078 sheet: -0.90 (0.70), residues: 60 loop : -0.03 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.024 0.001 TYR A 82 PHE 0.015 0.001 PHE D 281 TRP 0.014 0.001 TRP B 92 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (15694) covalent geometry : angle 0.57247 / 0.29 (21134) hydrogen bonds : bond 0.04289 / 2.76 ( 837) hydrogen bonds : angle 4.91058 / 3.50 ( 2355) Misc. bond : bond 0.00079 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.5900 (tp) REVERT: B 90 LEU cc_start: 0.7389 (tp) cc_final: 0.6884 (tt) REVERT: B 236 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 89 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 115 PHE cc_start: 0.7675 (t80) cc_final: 0.7458 (t80) REVERT: A 125 PHE cc_start: 0.6382 (m-10) cc_final: 0.6164 (m-10) REVERT: A 126 LEU cc_start: 0.7557 (mt) cc_final: 0.6939 (mt) REVERT: A 145 MET cc_start: 0.8204 (tpp) cc_final: 0.7675 (tpp) REVERT: A 260 ASP cc_start: 0.7657 (m-30) cc_final: 0.7329 (t0) REVERT: A 319 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 322 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.6829 (m-40) REVERT: A 344 MET cc_start: 0.4366 (mmt) cc_final: 0.3769 (pmm) REVERT: A 368 TYR cc_start: 0.3725 (OUTLIER) cc_final: 0.3525 (p90) REVERT: A 393 LEU cc_start: 0.7252 (tt) cc_final: 0.6708 (pp) REVERT: A 404 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7154 (t80) REVERT: D 87 MET cc_start: 0.7366 (mmp) cc_final: 0.6186 (mmm) REVERT: D 218 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.5428 (tt) REVERT: D 222 ILE cc_start: 0.7879 (tt) cc_final: 0.7601 (tt) REVERT: D 421 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6315 (tm-30) REVERT: D 432 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7118 (tp30) REVERT: C 89 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7739 (tp) REVERT: C 211 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7229 (mp) REVERT: C 221 LEU cc_start: 0.7958 (mm) cc_final: 0.7430 (mt) REVERT: C 260 ASP cc_start: 0.8238 (m-30) cc_final: 0.7858 (t0) REVERT: C 322 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7111 (m-40) REVERT: C 393 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6791 (pp) REVERT: C 404 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7096 (t80) REVERT: C 410 GLU cc_start: 0.8401 (pm20) cc_final: 0.7961 (mt-10) outliers start: 68 outliers final: 38 residues processed: 260 average time/residue: 0.1036 time to fit residues: 43.0737 Evaluate side-chains 236 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 295 HIS ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.248857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.171866 restraints weight = 19048.621| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.88 r_work: 0.3585 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 15702 Z= 0.366 Angle : 0.778 16.690 21134 Z= 0.403 Chirality : 0.051 0.243 2328 Planarity : 0.006 0.056 2592 Dihedral : 9.364 58.421 2280 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.24 % Favored : 93.26 % Rotamer: Outliers : 5.46 % Allowed : 26.87 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1810 helix: -0.22 (0.15), residues: 1076 sheet: -1.07 (0.71), residues: 60 loop : -0.25 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 337 TYR 0.041 0.002 TYR B 346 PHE 0.026 0.003 PHE D 304 TRP 0.013 0.002 TRP A 171 HIS 0.010 0.002 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.37 (15694) covalent geometry : angle 0.77790 / 0.40 (21134) hydrogen bonds : bond 0.04872 / 3.15 ( 837) hydrogen bonds : angle 5.34061 / 3.79 ( 2355) Misc. bond : bond 0.00177 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 178 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7687 (mmp) cc_final: 0.6346 (mmm) REVERT: B 89 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6616 (tp) REVERT: B 218 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.5471 (tt) REVERT: B 236 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 421 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6748 (tp30) REVERT: A 131 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 145 MET cc_start: 0.7913 (tpp) cc_final: 0.7532 (tpp) REVERT: A 393 LEU cc_start: 0.7471 (tt) cc_final: 0.6931 (pp) REVERT: A 404 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7064 (t80) REVERT: D 89 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6574 (tp) REVERT: D 218 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.5570 (tt) REVERT: D 222 ILE cc_start: 0.8199 (tt) cc_final: 0.7888 (tt) REVERT: D 432 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7047 (tp30) REVERT: C 89 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8077 (tp) REVERT: C 145 MET cc_start: 0.8134 (tpp) cc_final: 0.7746 (tpp) REVERT: C 217 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7275 (mmm-85) REVERT: C 306 MET cc_start: 0.8382 (mmt) cc_final: 0.7961 (mmp) REVERT: C 322 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7138 (m-40) REVERT: C 393 LEU cc_start: 0.7314 (tt) cc_final: 0.6972 (pp) REVERT: C 404 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7101 (t80) outliers start: 89 outliers final: 49 residues processed: 253 average time/residue: 0.1087 time to fit residues: 43.4911 Evaluate side-chains 227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 193 TYR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 3 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.256751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.4084 r_free = 0.4084 target = 0.171164 restraints weight = 18915.233| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 4.08 r_work: 0.3659 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15702 Z= 0.135 Angle : 0.627 11.341 21134 Z= 0.317 Chirality : 0.044 0.224 2328 Planarity : 0.004 0.055 2592 Dihedral : 8.540 59.816 2280 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.41 % Favored : 94.09 % Rotamer: Outliers : 3.93 % Allowed : 28.83 % Favored : 67.24 % 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: -0.15 (0.20), residues: 1810 helix: 0.15 (0.16), residues: 1078 sheet: -1.05 (0.71), residues: 60 loop : -0.17 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 365 TYR 0.028 0.001 TYR B 346 PHE 0.017 0.001 PHE D 281 TRP 0.019 0.001 TRP B 92 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15694) covalent geometry : angle 0.62714 / 0.32 (21134) hydrogen bonds : bond 0.04315 / 2.78 ( 837) hydrogen bonds : angle 4.95971 / 3.52 ( 2355) Misc. bond : bond 0.00062 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7540 (mmp) cc_final: 0.6439 (mmm) REVERT: B 236 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 299 MET cc_start: 0.8188 (ttm) cc_final: 0.7936 (ttp) REVERT: B 421 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6651 (tp30) REVERT: A 145 MET cc_start: 0.7933 (tpp) cc_final: 0.7622 (tpp) REVERT: A 260 ASP cc_start: 0.8173 (m-30) cc_final: 0.7764 (t70) REVERT: A 340 MET cc_start: 0.3847 (mmm) cc_final: 0.2971 (mmt) REVERT: A 344 MET cc_start: 0.4186 (mmp) cc_final: 0.3105 (pmm) REVERT: A 393 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6804 (pp) REVERT: A 404 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 445 HIS cc_start: 0.4151 (m90) cc_final: 0.3545 (t70) REVERT: D 87 MET cc_start: 0.7468 (mmp) cc_final: 0.6293 (mmm) REVERT: D 218 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.4941 (tt) REVERT: D 222 ILE cc_start: 0.8038 (tt) cc_final: 0.7755 (tt) REVERT: D 294 ILE cc_start: 0.8934 (mt) cc_final: 0.8734 (mt) REVERT: D 432 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7143 (tp30) REVERT: C 89 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8088 (tp) REVERT: C 126 LEU cc_start: 0.7246 (mt) cc_final: 0.6940 (mt) REVERT: C 211 ILE cc_start: 0.7612 (tp) cc_final: 0.7250 (mp) REVERT: C 221 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 322 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7079 (m-40) REVERT: C 368 TYR cc_start: 0.3530 (OUTLIER) cc_final: 0.2452 (t80) REVERT: C 393 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6893 (pp) outliers start: 64 outliers final: 43 residues processed: 235 average time/residue: 0.1063 time to fit residues: 40.0928 Evaluate side-chains 231 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 0.0030 chunk 57 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.257812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.4098 r_free = 0.4098 target = 0.172767 restraints weight = 19029.543| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 4.15 r_work: 0.3677 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15702 Z= 0.131 Angle : 0.606 11.198 21134 Z= 0.307 Chirality : 0.044 0.246 2328 Planarity : 0.004 0.054 2592 Dihedral : 8.135 59.764 2280 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.41 % Favored : 94.20 % Rotamer: Outliers : 3.87 % Allowed : 28.90 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1810 helix: 0.33 (0.16), residues: 1076 sheet: -0.99 (0.72), residues: 60 loop : -0.11 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 349 TYR 0.027 0.001 TYR B 346 PHE 0.023 0.001 PHE D 411 TRP 0.016 0.001 TRP B 92 HIS 0.004 0.000 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15694) covalent geometry : angle 0.60590 / 0.31 (21134) hydrogen bonds : bond 0.04243 / 2.73 ( 837) hydrogen bonds : angle 4.86127 / 3.45 ( 2355) Misc. bond : bond 0.00069 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7603 (mmp) cc_final: 0.6478 (mmm) REVERT: B 89 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6039 (tp) REVERT: B 202 PHE cc_start: 0.6954 (m-80) cc_final: 0.6683 (m-10) REVERT: B 236 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7700 (t80) REVERT: B 347 MET cc_start: 0.3375 (OUTLIER) cc_final: 0.3168 (mpp) REVERT: B 421 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6630 (tp30) REVERT: A 131 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 165 LEU cc_start: 0.8879 (tp) cc_final: 0.8591 (pp) REVERT: A 260 ASP cc_start: 0.8063 (m-30) cc_final: 0.7690 (t70) REVERT: A 344 MET cc_start: 0.4231 (mmp) cc_final: 0.3254 (pmm) REVERT: A 393 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6699 (pp) REVERT: A 404 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7106 (t80) REVERT: A 445 HIS cc_start: 0.4209 (m90) cc_final: 0.3606 (t70) REVERT: D 87 MET cc_start: 0.7479 (mmp) cc_final: 0.6352 (mmm) REVERT: D 222 ILE cc_start: 0.8059 (tt) cc_final: 0.7768 (tt) REVERT: D 294 ILE cc_start: 0.8856 (mt) cc_final: 0.8354 (mp) REVERT: D 432 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7371 (tp30) REVERT: C 89 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8040 (tp) REVERT: C 126 LEU cc_start: 0.7257 (mt) cc_final: 0.6949 (mt) REVERT: C 211 ILE cc_start: 0.7724 (tp) cc_final: 0.7375 (mp) REVERT: C 221 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7345 (mt) REVERT: C 279 MET cc_start: 0.8407 (mmm) cc_final: 0.8114 (tpt) REVERT: C 322 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: C 393 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6797 (pp) REVERT: C 404 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7046 (t80) REVERT: C 445 HIS cc_start: 0.4157 (m90) cc_final: 0.3609 (t70) outliers start: 63 outliers final: 42 residues processed: 237 average time/residue: 0.0919 time to fit residues: 35.0918 Evaluate side-chains 235 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 62 optimal weight: 0.2980 chunk 46 optimal weight: 0.2980 chunk 160 optimal weight: 0.9980 chunk 140 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.259243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.4151 r_free = 0.4151 target = 0.177375 restraints weight = 19126.932| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.76 r_work: 0.3718 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15702 Z= 0.127 Angle : 0.619 12.231 21134 Z= 0.310 Chirality : 0.044 0.227 2328 Planarity : 0.004 0.055 2592 Dihedral : 7.916 60.242 2278 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.47 % Favored : 94.14 % Rotamer: Outliers : 4.23 % Allowed : 28.28 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1810 helix: 0.42 (0.16), residues: 1062 sheet: -1.05 (0.71), residues: 60 loop : -0.08 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 418 TYR 0.046 0.001 TYR B 346 PHE 0.025 0.001 PHE D 411 TRP 0.015 0.001 TRP B 92 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (15694) covalent geometry : angle 0.61913 / 0.31 (21134) hydrogen bonds : bond 0.04217 / 2.70 ( 837) hydrogen bonds : angle 4.81501 / 3.42 ( 2355) Misc. bond : bond 0.00057 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7562 (mmp) cc_final: 0.6380 (mmm) REVERT: B 89 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.5961 (tp) REVERT: B 202 PHE cc_start: 0.6804 (m-80) cc_final: 0.6512 (m-80) REVERT: B 236 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7619 (t80) REVERT: B 299 MET cc_start: 0.7978 (ttm) cc_final: 0.7736 (ttp) REVERT: B 347 MET cc_start: 0.3968 (mtm) cc_final: 0.3763 (mpp) REVERT: B 421 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6635 (tp30) REVERT: A 131 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7758 (tt) REVERT: A 165 LEU cc_start: 0.8862 (tp) cc_final: 0.8553 (pp) REVERT: A 260 ASP cc_start: 0.7903 (m-30) cc_final: 0.7558 (t70) REVERT: A 340 MET cc_start: 0.3037 (mmm) cc_final: 0.2424 (mmt) REVERT: A 344 MET cc_start: 0.4533 (mmp) cc_final: 0.3696 (pmm) REVERT: A 393 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6694 (pp) REVERT: A 404 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6999 (t80) REVERT: A 445 HIS cc_start: 0.4387 (m90) cc_final: 0.3673 (t70) REVERT: D 87 MET cc_start: 0.7480 (mmp) cc_final: 0.6327 (mmm) REVERT: D 218 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.4282 (tt) REVERT: D 222 ILE cc_start: 0.7993 (tt) cc_final: 0.7689 (tt) REVERT: D 294 ILE cc_start: 0.8829 (mt) cc_final: 0.8318 (mp) REVERT: D 432 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7384 (tp30) REVERT: C 89 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (tp) REVERT: C 126 LEU cc_start: 0.7329 (mt) cc_final: 0.7033 (mt) REVERT: C 211 ILE cc_start: 0.7711 (tp) cc_final: 0.7398 (mp) REVERT: C 322 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.6904 (m-40) REVERT: C 340 MET cc_start: 0.4760 (mmm) cc_final: 0.4278 (mtp) REVERT: C 393 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6785 (pp) REVERT: C 404 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7063 (t80) REVERT: C 445 HIS cc_start: 0.4156 (m90) cc_final: 0.3574 (t70) outliers start: 69 outliers final: 42 residues processed: 248 average time/residue: 0.0998 time to fit residues: 39.2603 Evaluate side-chains 238 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 20.0000 chunk 139 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.249930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161796 restraints weight = 19066.541| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.99 r_work: 0.3541 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 15702 Z= 0.332 Angle : 0.761 11.791 21134 Z= 0.392 Chirality : 0.051 0.214 2328 Planarity : 0.005 0.054 2592 Dihedral : 9.028 59.141 2278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.80 % Favored : 93.76 % Rotamer: Outliers : 3.44 % Allowed : 28.77 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1810 helix: -0.10 (0.15), residues: 1076 sheet: -0.73 (0.58), residues: 80 loop : -0.35 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 337 TYR 0.039 0.002 TYR B 346 PHE 0.026 0.003 PHE B 336 TRP 0.015 0.002 TRP A 171 HIS 0.008 0.001 HIS C 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.33 (15694) covalent geometry : angle 0.76124 / 0.39 (21134) hydrogen bonds : bond 0.04741 / 3.04 ( 837) hydrogen bonds : angle 5.20700 / 3.70 ( 2355) Misc. bond : bond 0.00144 / 0.09 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7762 (mmp) cc_final: 0.6522 (mmm) REVERT: B 89 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6546 (tp) REVERT: B 236 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7915 (t80) REVERT: A 131 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 165 LEU cc_start: 0.8941 (tp) cc_final: 0.8634 (pp) REVERT: A 260 ASP cc_start: 0.8520 (m-30) cc_final: 0.7942 (t0) REVERT: A 340 MET cc_start: 0.3610 (mmm) cc_final: 0.2566 (ptp) REVERT: A 344 MET cc_start: 0.4316 (mmp) cc_final: 0.3451 (pmm) REVERT: A 393 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6748 (pp) REVERT: A 398 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6929 (pt) REVERT: A 404 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 445 HIS cc_start: 0.4564 (m90) cc_final: 0.3806 (t70) REVERT: D 87 MET cc_start: 0.7651 (mmp) cc_final: 0.6414 (mmm) REVERT: D 218 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.5440 (tt) REVERT: D 222 ILE cc_start: 0.8151 (tt) cc_final: 0.7804 (tt) REVERT: C 89 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8082 (tp) REVERT: C 115 PHE cc_start: 0.7870 (t80) cc_final: 0.7626 (t80) REVERT: C 306 MET cc_start: 0.8663 (mmp) cc_final: 0.8383 (mmt) REVERT: C 340 MET cc_start: 0.4803 (mmm) cc_final: 0.4301 (mtp) REVERT: C 393 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6858 (pp) REVERT: C 404 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6974 (t80) REVERT: C 445 HIS cc_start: 0.4359 (m90) cc_final: 0.3830 (t70) outliers start: 56 outliers final: 41 residues processed: 211 average time/residue: 0.0986 time to fit residues: 34.0041 Evaluate side-chains 212 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.257666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.190412 restraints weight = 18984.581| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.56 r_work: 0.3727 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15702 Z= 0.133 Angle : 0.643 12.084 21134 Z= 0.323 Chirality : 0.045 0.220 2328 Planarity : 0.004 0.053 2592 Dihedral : 8.229 58.233 2278 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.92 % Favored : 94.64 % Rotamer: Outliers : 3.01 % Allowed : 29.26 % Favored : 67.73 % 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: -0.07 (0.20), residues: 1810 helix: 0.27 (0.16), residues: 1070 sheet: -1.11 (0.71), residues: 60 loop : -0.23 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 418 TYR 0.035 0.001 TYR B 346 PHE 0.024 0.002 PHE D 411 TRP 0.020 0.001 TRP B 92 HIS 0.003 0.000 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15694) covalent geometry : angle 0.64344 / 0.32 (21134) hydrogen bonds : bond 0.04220 / 2.69 ( 837) hydrogen bonds : angle 4.91875 / 3.50 ( 2355) Misc. bond : bond 0.00058 / 0.03 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5411.79 seconds wall clock time: 92 minutes 53.54 seconds (5573.54 seconds total)