Starting phenix.real_space_refine on Fri Jun 13 19:08:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wui_37855/06_2025/8wui_37855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wui_37855/06_2025/8wui_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_37855/06_2025/8wui_37855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wui_37855/06_2025/8wui_37855.map" model { file = "/net/cci-nas-00/data/ceres_data/8wui_37855/06_2025/8wui_37855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wui_37855/06_2025/8wui_37855_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 3, 'PC1:plan-1': 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-2': 3, 'PC1:plan-1': 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-2': 3, 'PC1:plan-1': 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-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 9.42, per 1000 atoms: 0.61 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: 3.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.40 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: 4.64 Time building geometry restraints manager: 4.33 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: 0.03 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 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 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 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 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: 1.520 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.060 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP C 171 HIS 0.004 0.001 HIS C 295 PHE 0.030 0.002 PHE D 223 TYR 0.013 0.001 TYR B 237 ARG 0.004 0.000 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.26261 ( 837) hydrogen bonds : angle 9.26269 ( 2355) covalent geometry : bond 0.00576 (15694) covalent geometry : angle 0.83753 (21134) Misc. bond : bond 0.47052 ( 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 : 1.554 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: 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 152 ILE cc_start: 0.5216 (OUTLIER) cc_final: 0.4568 (tp) REVERT: B 377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6438 (t) REVERT: B 468 ASP cc_start: 0.5185 (t0) cc_final: 0.4528 (t0) REVERT: A 145 MET cc_start: 0.6947 (tpp) cc_final: 0.6686 (tpp) REVERT: A 351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3589 (mttp) REVERT: A 365 ARG cc_start: 0.0571 (OUTLIER) cc_final: 0.0045 (ttp-170) REVERT: D 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (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: 0.0286 (ttp-170) REVERT: C 369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2512 (pt0) outliers start: 83 outliers final: 31 residues processed: 306 average time/residue: 0.2965 time to fit residues: 129.3240 Evaluate side-chains 227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE 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 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 GLN A 359 GLN D 295 HIS D 312 ASN D 439 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.260546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195455 restraints weight = 19494.329| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.24 r_work: 0.3739 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15702 Z= 0.169 Angle : 0.658 11.054 21134 Z= 0.346 Chirality : 0.044 0.172 2328 Planarity : 0.005 0.064 2592 Dihedral : 11.799 94.086 2360 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.58 % Favored : 93.98 % Rotamer: Outliers : 4.91 % Allowed : 25.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1810 helix: -0.26 (0.16), residues: 1074 sheet: -0.55 (1.21), residues: 20 loop : 0.06 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 92 HIS 0.004 0.001 HIS A 469 PHE 0.024 0.002 PHE D 281 TYR 0.020 0.001 TYR C 368 ARG 0.013 0.001 ARG C 365 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 837) hydrogen bonds : angle 5.86682 ( 2355) covalent geometry : bond 0.00363 (15694) covalent geometry : angle 0.65761 (21134) Misc. bond : bond 0.00310 ( 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 298 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 2.166 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: B 87 MET cc_start: 0.7531 (mmp) cc_final: 0.6452 (mmm) REVERT: B 152 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5235 (tp) REVERT: B 218 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5386 (tt) REVERT: B 367 GLN cc_start: 0.7863 (mt0) cc_final: 0.7493 (mp10) REVERT: B 377 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.7037 (t) REVERT: A 89 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 145 MET cc_start: 0.8229 (tpp) cc_final: 0.7714 (tpp) REVERT: A 260 ASP cc_start: 0.8127 (m-30) cc_final: 0.7794 (t70) REVERT: A 339 LYS cc_start: 0.6521 (mmtt) cc_final: 0.6307 (pttm) REVERT: A 355 ASN cc_start: 0.6423 (OUTLIER) cc_final: 0.5653 (p0) REVERT: A 360 ILE cc_start: 0.4331 (OUTLIER) cc_final: 0.4016 (mm) REVERT: A 369 GLU cc_start: 0.0297 (OUTLIER) cc_final: -0.0113 (pt0) REVERT: A 404 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (t80) REVERT: D 340 MET cc_start: 0.6560 (mpp) cc_final: 0.6358 (mpp) REVERT: D 421 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6501 (tm-30) REVERT: C 89 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7497 (tp) REVERT: C 92 TRP cc_start: 0.7749 (m100) cc_final: 0.7514 (m100) REVERT: C 171 TRP cc_start: 0.7767 (m100) cc_final: 0.7311 (m100) REVERT: C 221 LEU cc_start: 0.7958 (mm) cc_final: 0.7572 (mt) REVERT: C 359 GLN cc_start: 0.4509 (tm-30) cc_final: 0.4103 (mm110) REVERT: C 369 GLU cc_start: 0.1043 (OUTLIER) cc_final: 0.0720 (pt0) REVERT: C 404 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7170 (t80) outliers start: 80 outliers final: 37 residues processed: 282 average time/residue: 0.3221 time to fit residues: 143.6495 Evaluate side-chains 229 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 152 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 211 ILE 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 377 VAL 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 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 338 ASP 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 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 57 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.259246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.190881 restraints weight = 19061.598| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.17 r_work: 0.3719 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15702 Z= 0.166 Angle : 0.622 11.307 21134 Z= 0.322 Chirality : 0.044 0.162 2328 Planarity : 0.005 0.057 2592 Dihedral : 10.092 84.638 2307 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.25 % Favored : 94.31 % Rotamer: Outliers : 4.85 % Allowed : 25.03 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1810 helix: 0.05 (0.16), residues: 1076 sheet: -0.74 (0.71), residues: 60 loop : 0.02 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 92 HIS 0.005 0.001 HIS C 295 PHE 0.017 0.002 PHE D 281 TYR 0.015 0.001 TYR C 238 ARG 0.008 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 837) hydrogen bonds : angle 5.37722 ( 2355) covalent geometry : bond 0.00372 (15694) covalent geometry : angle 0.62174 (21134) Misc. bond : bond 0.00193 ( 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 276 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 1.594 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 218 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.5446 (tt) REVERT: B 421 GLU cc_start: 0.6910 (tp30) cc_final: 0.6544 (mt-10) REVERT: A 89 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 126 LEU cc_start: 0.7065 (mt) cc_final: 0.6528 (mt) REVERT: A 145 MET cc_start: 0.8103 (tpp) cc_final: 0.7692 (tpp) REVERT: A 306 MET cc_start: 0.7767 (mmt) cc_final: 0.7544 (mmp) REVERT: A 322 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.6910 (m-40) REVERT: A 339 LYS cc_start: 0.6773 (mmtt) cc_final: 0.6408 (pttp) REVERT: A 344 MET cc_start: 0.5494 (mmm) cc_final: 0.4591 (pmm) REVERT: A 368 TYR cc_start: 0.3904 (OUTLIER) cc_final: 0.3486 (p90) REVERT: A 393 LEU cc_start: 0.7604 (tp) cc_final: 0.6964 (pp) REVERT: A 404 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7204 (t80) REVERT: A 431 MET cc_start: 0.3661 (mmm) cc_final: 0.3444 (mmm) REVERT: D 128 ASP cc_start: 0.8235 (t0) cc_final: 0.8034 (t0) REVERT: D 218 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.5596 (tt) REVERT: D 258 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8430 (mt) REVERT: D 421 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6523 (tm-30) REVERT: C 89 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7733 (tp) REVERT: C 211 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7352 (mp) REVERT: C 221 LEU cc_start: 0.8041 (mm) cc_final: 0.7577 (mt) REVERT: C 322 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7138 (m-40) REVERT: C 355 ASN cc_start: 0.4809 (OUTLIER) cc_final: 0.4053 (p0) REVERT: C 359 GLN cc_start: 0.4584 (tm-30) cc_final: 0.4021 (mp10) REVERT: C 369 GLU cc_start: 0.2643 (OUTLIER) cc_final: 0.2343 (pt0) REVERT: C 404 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 503 MET cc_start: 0.8419 (ppp) cc_final: 0.7762 (ppp) outliers start: 79 outliers final: 32 residues processed: 259 average time/residue: 0.2770 time to fit residues: 109.2123 Evaluate side-chains 227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 302 MET 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 116 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 258 LEU 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 91 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 344 MET Chi-restraints excluded: chain C residue 355 ASN 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 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 174 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 120 optimal weight: 0.0060 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.259795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.189885 restraints weight = 19426.791| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.07 r_work: 0.3728 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15702 Z= 0.161 Angle : 0.600 10.565 21134 Z= 0.310 Chirality : 0.044 0.284 2328 Planarity : 0.004 0.058 2592 Dihedral : 9.230 73.275 2294 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.52 % Favored : 94.03 % Rotamer: Outliers : 4.91 % Allowed : 25.34 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1810 helix: 0.24 (0.16), residues: 1080 sheet: -0.78 (0.71), residues: 60 loop : -0.10 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 92 HIS 0.004 0.001 HIS B 230 PHE 0.018 0.002 PHE D 281 TYR 0.014 0.001 TYR C 238 ARG 0.006 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 837) hydrogen bonds : angle 5.13388 ( 2355) covalent geometry : bond 0.00356 (15694) covalent geometry : angle 0.60004 (21134) Misc. bond : bond 0.00129 ( 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 290 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 1.551 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: 0.7541 (mmp) cc_final: 0.6345 (mmm) REVERT: B 89 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6113 (tp) REVERT: B 202 PHE cc_start: 0.7123 (m-10) cc_final: 0.6910 (m-10) REVERT: B 218 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5271 (tt) REVERT: B 236 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 306 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8538 (mtm) REVERT: B 421 GLU cc_start: 0.6892 (tp30) cc_final: 0.6579 (mt-10) REVERT: B 431 MET cc_start: 0.1427 (mtm) cc_final: 0.1226 (pmm) REVERT: A 89 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 126 LEU cc_start: 0.7471 (mt) cc_final: 0.6839 (mt) REVERT: A 260 ASP cc_start: 0.8235 (m-30) cc_final: 0.7864 (t70) REVERT: A 319 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 322 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.6819 (m-40) REVERT: A 339 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6400 (pttm) REVERT: A 340 MET cc_start: 0.4281 (mmm) cc_final: 0.3247 (ptp) REVERT: A 344 MET cc_start: 0.4820 (mmm) cc_final: 0.4168 (pmm) REVERT: A 368 TYR cc_start: 0.3849 (OUTLIER) cc_final: 0.3449 (p90) REVERT: A 393 LEU cc_start: 0.7574 (tp) cc_final: 0.6959 (pp) REVERT: A 404 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7122 (t80) REVERT: D 218 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.5397 (tt) REVERT: D 222 ILE cc_start: 0.8048 (tt) cc_final: 0.7749 (tt) REVERT: D 334 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: D 347 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5468 (mmt) REVERT: D 421 GLU cc_start: 0.6822 (mt-10) cc_final: 0.5971 (tm-30) REVERT: D 439 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6388 (pm20) REVERT: C 89 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7810 (tp) REVERT: C 221 LEU cc_start: 0.7943 (mm) cc_final: 0.7409 (mt) REVERT: C 306 MET cc_start: 0.8257 (mmp) cc_final: 0.7984 (mmm) REVERT: C 322 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7100 (m-40) REVERT: C 355 ASN cc_start: 0.4555 (OUTLIER) cc_final: 0.3624 (p0) REVERT: C 359 GLN cc_start: 0.4917 (OUTLIER) cc_final: 0.4698 (mp10) REVERT: C 365 ARG cc_start: 0.2003 (OUTLIER) cc_final: 0.1650 (ttp-170) REVERT: C 404 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7064 (t80) REVERT: C 410 GLU cc_start: 0.8343 (pm20) cc_final: 0.7989 (mt-10) outliers start: 80 outliers final: 35 residues processed: 273 average time/residue: 0.2498 time to fit residues: 103.5340 Evaluate side-chains 239 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 218 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 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 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 116 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 334 GLU 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 91 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 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 355 ASN Chi-restraints excluded: chain C residue 359 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 75 optimal weight: 0.0030 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 82 optimal weight: 40.0000 chunk 5 optimal weight: 0.9990 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.259204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176461 restraints weight = 19486.515| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.80 r_work: 0.3715 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15702 Z= 0.123 Angle : 0.580 12.124 21134 Z= 0.299 Chirality : 0.043 0.222 2328 Planarity : 0.004 0.057 2592 Dihedral : 8.397 67.137 2280 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.58 % Favored : 93.98 % Rotamer: Outliers : 3.50 % Allowed : 27.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1810 helix: 0.37 (0.16), residues: 1066 sheet: -0.89 (0.71), residues: 60 loop : -0.08 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 92 HIS 0.003 0.001 HIS B 363 PHE 0.016 0.001 PHE D 281 TYR 0.014 0.001 TYR C 368 ARG 0.007 0.000 ARG B 496 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 837) hydrogen bonds : angle 4.97117 ( 2355) covalent geometry : bond 0.00259 (15694) covalent geometry : angle 0.58033 (21134) Misc. bond : bond 0.00071 ( 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 257 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.643 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: 0.7511 (mmp) cc_final: 0.6319 (mmm) REVERT: B 236 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7421 (t80) REVERT: A 89 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 126 LEU cc_start: 0.7540 (mt) cc_final: 0.6924 (mt) REVERT: A 260 ASP cc_start: 0.8224 (m-30) cc_final: 0.7731 (t0) REVERT: A 319 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 322 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6818 (m-40) REVERT: A 344 MET cc_start: 0.4209 (mmm) cc_final: 0.3980 (pmm) REVERT: A 393 LEU cc_start: 0.7351 (tp) cc_final: 0.6795 (pp) REVERT: A 404 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7163 (t80) REVERT: D 87 MET cc_start: 0.7354 (mmp) cc_final: 0.6178 (mmm) REVERT: D 218 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.5375 (tt) REVERT: D 222 ILE cc_start: 0.7888 (tt) cc_final: 0.7613 (tt) REVERT: D 347 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5366 (mmt) REVERT: D 432 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7122 (tp30) REVERT: C 89 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7835 (tp) REVERT: C 221 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7393 (mt) REVERT: C 260 ASP cc_start: 0.8220 (m-30) cc_final: 0.7852 (t0) REVERT: C 306 MET cc_start: 0.8189 (mmp) cc_final: 0.7987 (mmm) REVERT: C 322 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: C 398 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6692 (mt) REVERT: C 404 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7101 (t80) outliers start: 57 outliers final: 27 residues processed: 246 average time/residue: 0.2378 time to fit residues: 91.3779 Evaluate side-chains 220 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 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 319 LEU Chi-restraints excluded: chain A residue 322 ASN 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 218 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 347 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 91 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 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 380 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 157 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 HIS B 312 ASN B 420 HIS D 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.251203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182673 restraints weight = 19055.526| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.95 r_work: 0.3465 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15702 Z= 0.291 Angle : 0.703 9.624 21134 Z= 0.365 Chirality : 0.048 0.208 2328 Planarity : 0.005 0.056 2592 Dihedral : 9.034 59.113 2280 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.13 % Favored : 93.37 % Rotamer: Outliers : 5.09 % Allowed : 26.38 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1810 helix: -0.04 (0.15), residues: 1066 sheet: -1.07 (0.71), residues: 60 loop : -0.18 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.007 0.001 HIS A 230 PHE 0.019 0.002 PHE D 304 TYR 0.019 0.002 TYR A 368 ARG 0.009 0.001 ARG B 337 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 837) hydrogen bonds : angle 5.25916 ( 2355) covalent geometry : bond 0.00689 (15694) covalent geometry : angle 0.70279 (21134) Misc. bond : bond 0.00134 ( 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 258 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 1.735 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 86 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7212 (m) REVERT: B 87 MET cc_start: 0.7713 (mmp) cc_final: 0.6291 (mmm) REVERT: B 89 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6069 (tp) REVERT: B 218 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5073 (tt) REVERT: B 236 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7776 (t80) REVERT: B 431 MET cc_start: 0.1598 (mtm) cc_final: 0.1145 (pmm) REVERT: B 476 ILE cc_start: 0.1087 (OUTLIER) cc_final: 0.0662 (mt) REVERT: A 131 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 393 LEU cc_start: 0.7394 (tp) cc_final: 0.6856 (pp) REVERT: A 404 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7164 (t80) REVERT: A 445 HIS cc_start: 0.3986 (m90) cc_final: 0.3383 (t70) REVERT: D 87 MET cc_start: 0.7613 (mmp) cc_final: 0.6323 (mmm) REVERT: D 89 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6293 (tp) REVERT: D 218 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.4906 (tt) REVERT: D 222 ILE cc_start: 0.8018 (tt) cc_final: 0.7676 (tt) REVERT: D 323 MET cc_start: 0.8039 (tpt) cc_final: 0.7814 (tpp) REVERT: D 347 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.5179 (mmp) REVERT: D 432 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7165 (tp30) REVERT: C 89 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7847 (tp) REVERT: C 126 LEU cc_start: 0.7336 (mt) cc_final: 0.7043 (mt) REVERT: C 145 MET cc_start: 0.8201 (tpp) cc_final: 0.7901 (tpp) REVERT: C 322 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.6919 (m-40) REVERT: C 340 MET cc_start: 0.3842 (mmt) cc_final: 0.3507 (ptp) REVERT: C 398 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6620 (mt) REVERT: C 404 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7122 (t80) outliers start: 83 outliers final: 50 residues processed: 248 average time/residue: 0.2704 time to fit residues: 105.8944 Evaluate side-chains 230 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR 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 256 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 476 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 222 ILE 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 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 530 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER 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 347 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 91 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS A 420 HIS A 511 HIS C 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.257097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.187320 restraints weight = 19221.173| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.36 r_work: 0.3727 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3759 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= 0.136 Angle : 0.609 10.895 21134 Z= 0.309 Chirality : 0.044 0.160 2328 Planarity : 0.004 0.071 2592 Dihedral : 8.406 59.960 2280 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.36 % Favored : 94.14 % Rotamer: Outliers : 4.23 % Allowed : 27.91 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1810 helix: 0.20 (0.16), residues: 1078 sheet: -1.08 (0.71), residues: 60 loop : -0.13 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 92 HIS 0.002 0.001 HIS C 295 PHE 0.021 0.001 PHE D 411 TYR 0.024 0.001 TYR A 368 ARG 0.005 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 837) hydrogen bonds : angle 4.95744 ( 2355) covalent geometry : bond 0.00295 (15694) covalent geometry : angle 0.60945 (21134) Misc. bond : bond 0.00068 ( 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 257 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 2.043 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: 0.7587 (mmp) cc_final: 0.6509 (mmm) REVERT: B 202 PHE cc_start: 0.7105 (m-80) cc_final: 0.6781 (m-80) REVERT: B 236 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7593 (t80) REVERT: A 131 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 217 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7036 (mmm-85) REVERT: A 260 ASP cc_start: 0.7687 (m-30) cc_final: 0.7353 (t0) REVERT: A 322 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.6656 (m-40) REVERT: A 344 MET cc_start: 0.7144 (pmm) cc_final: 0.6086 (mpp) REVERT: A 393 LEU cc_start: 0.7458 (tp) cc_final: 0.6871 (pp) REVERT: A 404 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6976 (t80) REVERT: A 445 HIS cc_start: 0.3959 (m90) cc_final: 0.3293 (t70) REVERT: D 87 MET cc_start: 0.7596 (mmp) cc_final: 0.6373 (mmm) REVERT: D 222 ILE cc_start: 0.8043 (tt) cc_final: 0.7737 (tt) REVERT: D 347 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5158 (mmp) REVERT: D 432 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7245 (tp30) REVERT: C 89 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 126 LEU cc_start: 0.7208 (mt) cc_final: 0.6910 (mt) REVERT: C 322 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7072 (m-40) REVERT: C 344 MET cc_start: 0.4962 (mmt) cc_final: 0.4192 (pmm) REVERT: C 404 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7034 (t80) outliers start: 69 outliers final: 43 residues processed: 241 average time/residue: 0.2458 time to fit residues: 92.1773 Evaluate side-chains 233 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 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 309 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 ARG 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 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 380 ASP 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 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 347 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 91 ILE Chi-restraints excluded: chain C residue 106 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 8.9990 chunk 41 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS A 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.255759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165795 restraints weight = 19010.737| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 5.31 r_work: 0.3566 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15702 Z= 0.161 Angle : 0.619 8.601 21134 Z= 0.316 Chirality : 0.044 0.168 2328 Planarity : 0.004 0.065 2592 Dihedral : 8.356 59.997 2280 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.41 % Favored : 94.14 % Rotamer: Outliers : 4.23 % Allowed : 27.55 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1810 helix: 0.22 (0.16), residues: 1076 sheet: -1.18 (0.71), residues: 60 loop : -0.12 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 92 HIS 0.003 0.001 HIS A 295 PHE 0.023 0.002 PHE D 411 TYR 0.024 0.001 TYR A 368 ARG 0.013 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 837) hydrogen bonds : angle 4.92234 ( 2355) covalent geometry : bond 0.00368 (15694) covalent geometry : angle 0.61891 (21134) Misc. bond : bond 0.00077 ( 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 257 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 1.649 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 236 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 274 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6608 (mtm-85) REVERT: A 131 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7470 (tt) REVERT: A 217 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6802 (mmm-85) REVERT: A 260 ASP cc_start: 0.8113 (m-30) cc_final: 0.7636 (t70) REVERT: A 322 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6400 (m-40) REVERT: A 344 MET cc_start: 0.7119 (pmm) cc_final: 0.6347 (mpp) REVERT: A 393 LEU cc_start: 0.7207 (tp) cc_final: 0.6733 (pp) REVERT: A 404 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7078 (t80) REVERT: A 445 HIS cc_start: 0.4240 (m90) cc_final: 0.3687 (t70) REVERT: D 87 MET cc_start: 0.7477 (mmp) cc_final: 0.6249 (mmm) REVERT: D 90 LEU cc_start: 0.6765 (tp) cc_final: 0.6465 (tt) REVERT: D 218 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.4523 (tt) REVERT: D 222 ILE cc_start: 0.7683 (tt) cc_final: 0.7338 (tt) REVERT: D 347 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.5020 (mmp) REVERT: D 432 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7384 (tp30) REVERT: C 126 LEU cc_start: 0.7290 (mt) cc_final: 0.7013 (mt) REVERT: C 217 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6853 (mmm-85) REVERT: C 322 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6685 (m-40) REVERT: C 398 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6757 (mt) REVERT: C 404 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7093 (t80) REVERT: C 445 HIS cc_start: 0.4061 (m90) cc_final: 0.3554 (t70) outliers start: 69 outliers final: 47 residues processed: 244 average time/residue: 0.2555 time to fit residues: 95.1998 Evaluate side-chains 239 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER 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 274 ARG Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 377 VAL 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 217 ARG 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 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 380 ASP 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 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR 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 385 ILE Chi-restraints excluded: chain D residue 445 HIS 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 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 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 37 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS A 420 HIS ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.253852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.181957 restraints weight = 19061.067| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.25 r_work: 0.3614 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 15702 Z= 0.278 Angle : 0.713 11.805 21134 Z= 0.367 Chirality : 0.048 0.172 2328 Planarity : 0.005 0.059 2592 Dihedral : 8.854 59.963 2280 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.86 % Favored : 93.70 % Rotamer: Outliers : 4.23 % Allowed : 27.85 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1810 helix: -0.07 (0.15), residues: 1072 sheet: -0.97 (0.59), residues: 80 loop : -0.27 (0.27), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 171 HIS 0.005 0.001 HIS C 230 PHE 0.022 0.002 PHE D 411 TYR 0.037 0.002 TYR C 368 ARG 0.011 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 837) hydrogen bonds : angle 5.17683 ( 2355) covalent geometry : bond 0.00656 (15694) covalent geometry : angle 0.71260 (21134) Misc. bond : bond 0.00121 ( 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 238 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 169 time to evaluate : 2.281 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: 0.7608 (mmp) cc_final: 0.6323 (mmm) REVERT: B 218 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5603 (tt) REVERT: B 236 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 131 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7816 (tt) REVERT: A 145 MET cc_start: 0.8271 (tpp) cc_final: 0.8010 (tpp) REVERT: A 165 LEU cc_start: 0.8893 (tp) cc_final: 0.8600 (pp) REVERT: A 217 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7098 (mmm-85) REVERT: A 260 ASP cc_start: 0.8330 (m-30) cc_final: 0.7983 (t70) REVERT: A 344 MET cc_start: 0.7308 (pmm) cc_final: 0.5679 (mmt) REVERT: A 393 LEU cc_start: 0.7468 (tp) cc_final: 0.6895 (pp) REVERT: A 404 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 445 HIS cc_start: 0.4458 (m90) cc_final: 0.3688 (t70) REVERT: D 87 MET cc_start: 0.7677 (mmp) cc_final: 0.6384 (mmm) REVERT: D 218 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5332 (tt) REVERT: D 222 ILE cc_start: 0.8096 (tt) cc_final: 0.7763 (tt) REVERT: D 432 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7273 (tp30) REVERT: C 217 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7228 (mmm-85) REVERT: C 322 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.6911 (m-40) REVERT: C 329 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7840 (tttm) REVERT: C 340 MET cc_start: 0.3886 (mmt) cc_final: 0.3582 (ptp) REVERT: C 398 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6782 (mm) REVERT: C 404 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6990 (t80) REVERT: C 445 HIS cc_start: 0.4016 (m90) cc_final: 0.3401 (t70) outliers start: 69 outliers final: 50 residues processed: 223 average time/residue: 0.3137 time to fit residues: 108.1661 Evaluate side-chains 224 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER 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 256 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 ARG 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 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 380 ASP 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 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 344 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 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 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 329 LYS Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 380 ASP 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 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 132 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS A 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.256685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.4209 r_free = 0.4209 target = 0.184992 restraints weight = 19210.891| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.04 r_work: 0.3727 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4183 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= 0.139 Angle : 0.635 12.303 21134 Z= 0.321 Chirality : 0.044 0.172 2328 Planarity : 0.005 0.069 2592 Dihedral : 8.311 58.841 2280 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.97 % Favored : 94.59 % Rotamer: Outliers : 3.74 % Allowed : 28.10 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1810 helix: 0.19 (0.16), residues: 1070 sheet: -1.06 (0.58), residues: 80 loop : -0.22 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 92 HIS 0.003 0.001 HIS B 363 PHE 0.022 0.001 PHE D 411 TYR 0.034 0.001 TYR C 368 ARG 0.012 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 837) hydrogen bonds : angle 4.95940 ( 2355) covalent geometry : bond 0.00307 (15694) covalent geometry : angle 0.63500 (21134) Misc. bond : bond 0.00067 ( 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 245 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 1.667 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: 0.7478 (mmp) cc_final: 0.6370 (mmm) REVERT: B 89 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6219 (tp) REVERT: B 202 PHE cc_start: 0.7273 (m-80) cc_final: 0.7022 (m-80) REVERT: B 236 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 347 MET cc_start: 0.3669 (OUTLIER) cc_final: 0.3396 (mtm) REVERT: A 131 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8007 (tt) REVERT: A 217 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6956 (mmm-85) REVERT: A 260 ASP cc_start: 0.8031 (m-30) cc_final: 0.7705 (t70) REVERT: A 322 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6716 (m-40) REVERT: A 344 MET cc_start: 0.7295 (pmm) cc_final: 0.5698 (mmt) REVERT: A 393 LEU cc_start: 0.7425 (tp) cc_final: 0.6858 (pp) REVERT: A 404 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6889 (t80) REVERT: A 445 HIS cc_start: 0.4388 (m90) cc_final: 0.3635 (t70) REVERT: D 87 MET cc_start: 0.7555 (mmp) cc_final: 0.6387 (mmm) REVERT: D 90 LEU cc_start: 0.7326 (tp) cc_final: 0.6484 (tt) REVERT: D 218 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.4752 (tt) REVERT: D 222 ILE cc_start: 0.8173 (tt) cc_final: 0.7889 (tt) REVERT: D 421 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6501 (tm-30) REVERT: C 78 ASP cc_start: 0.8677 (t0) cc_final: 0.8464 (t0) REVERT: C 217 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6896 (mmm-85) REVERT: C 279 MET cc_start: 0.8386 (mmm) cc_final: 0.8172 (tpt) REVERT: C 306 MET cc_start: 0.7698 (mmt) cc_final: 0.7350 (mmp) REVERT: C 322 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.6880 (m-40) REVERT: C 344 MET cc_start: 0.4882 (mmt) cc_final: 0.4201 (pmm) REVERT: C 404 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6855 (t80) REVERT: C 445 HIS cc_start: 0.4063 (m90) cc_final: 0.3411 (t70) outliers start: 61 outliers final: 44 residues processed: 232 average time/residue: 0.2361 time to fit residues: 84.6241 Evaluate side-chains 235 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 310 SER Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 366 LEU 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 217 ARG 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 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 380 ASP 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 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 178 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS A 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.256815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.187494 restraints weight = 19031.286| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.03 r_work: 0.3740 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4300 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= 0.140 Angle : 0.628 12.169 21134 Z= 0.317 Chirality : 0.044 0.162 2328 Planarity : 0.005 0.072 2592 Dihedral : 8.120 57.712 2280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.19 % Favored : 94.36 % Rotamer: Outliers : 3.68 % Allowed : 28.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1810 helix: 0.30 (0.16), residues: 1074 sheet: -1.16 (0.57), residues: 80 loop : -0.15 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 92 HIS 0.004 0.001 HIS A 295 PHE 0.022 0.001 PHE D 411 TYR 0.020 0.001 TYR A 368 ARG 0.011 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 837) hydrogen bonds : angle 4.89531 ( 2355) covalent geometry : bond 0.00313 (15694) covalent geometry : angle 0.62798 (21134) Misc. bond : bond 0.00070 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11071.12 seconds wall clock time: 195 minutes 30.07 seconds (11730.07 seconds total)