Starting phenix.real_space_refine on Thu Mar 5 09:35:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ej2_31149/03_2026/7ej2_31149.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 12 5.49 5 S 96 5.16 5 C 13488 2.51 5 N 3548 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20968 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "E" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "F" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "G" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "H" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2640 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 10, 'ASP:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 20968 At special positions: 0 Unit cell: (128.778, 128.778, 157.17, 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 96 16.00 P 12 15.00 O 3824 8.00 N 3548 7.00 C 13488 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=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 57.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 140 " --> pdb=" O MET B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 344' Processing helix chain 'B' and resid 360 through 370 removed outlier: 3.501A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 removed outlier: 4.011A pdb=" N ILE C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.755A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER C 353 " --> pdb=" O HIS C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG D 138 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 140 " --> pdb=" O MET D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 339 through 344' Processing helix chain 'D' and resid 360 through 370 removed outlier: 4.159A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 500 " --> pdb=" O GLN D 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.662A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA E 309 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 4.146A pdb=" N GLU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 335 " --> pdb=" O MET E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 343 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG F 138 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 140 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 166 removed outlier: 3.653A pdb=" N ILE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 187 removed outlier: 4.138A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 185 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.733A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 255 removed outlier: 3.500A pdb=" N ILE F 236 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 Processing helix chain 'F' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS F 302 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.869A pdb=" N ILE F 331 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 336 Processing helix chain 'F' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY F 344 " --> pdb=" O PHE F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 360 through 370 removed outlier: 3.501A pdb=" N ILE F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.683A pdb=" N ARG F 379 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 removed outlier: 4.321A pdb=" N GLN F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 419 removed outlier: 3.749A pdb=" N LEU F 400 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 405 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 406 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 472 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE F 479 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET F 500 " --> pdb=" O GLN F 496 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 removed outlier: 3.530A pdb=" N ALA G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 107 removed outlier: 4.012A pdb=" N ILE G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 132 through 143 removed outlier: 3.517A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.595A pdb=" N THR G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.754A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'G' and resid 228 through 236 removed outlier: 3.502A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 278 removed outlier: 3.661A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 299 removed outlier: 3.546A pdb=" N LYS G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 312 removed outlier: 3.715A pdb=" N ALA G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 4.145A pdb=" N GLU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.725A pdb=" N SER G 353 " --> pdb=" O HIS G 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 135 through 140 removed outlier: 4.058A pdb=" N ARG H 138 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE H 140 " --> pdb=" O MET H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 166 removed outlier: 3.652A pdb=" N ILE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 187 removed outlier: 4.137A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 199 removed outlier: 3.734A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 222 removed outlier: 3.538A pdb=" N GLN H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 255 removed outlier: 3.501A pdb=" N ILE H 236 " --> pdb=" O PRO H 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 238 " --> pdb=" O ARG H 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 298 through 315 removed outlier: 3.991A pdb=" N CYS H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.868A pdb=" N ILE H 331 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 336 Processing helix chain 'H' and resid 339 through 344 removed outlier: 3.803A pdb=" N LEU H 343 " --> pdb=" O TYR H 339 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY H 344 " --> pdb=" O PHE H 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 339 through 344' Processing helix chain 'H' and resid 360 through 370 removed outlier: 3.500A pdb=" N ILE H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 379 removed outlier: 3.682A pdb=" N ARG H 379 " --> pdb=" O LYS H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 4.320A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 419 removed outlier: 3.750A pdb=" N LEU H 400 " --> pdb=" O ARG H 396 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 405 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE H 406 " --> pdb=" O ILE H 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 443 removed outlier: 3.590A pdb=" N MET H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 473 removed outlier: 3.502A pdb=" N ILE H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 472 " --> pdb=" O GLY H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 489 removed outlier: 4.152A pdb=" N ILE H 479 " --> pdb=" O PRO H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 502 removed outlier: 4.223A pdb=" N TYR H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET H 500 " --> pdb=" O GLN H 496 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY A 53 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 242 " --> pdb=" O LEU A 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.669A pdb=" N ILE A 115 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE A 156 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 117 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN A 214 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR A 187 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY C 53 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 242 " --> pdb=" O LEU C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.669A pdb=" N ILE C 115 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 117 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN C 214 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR C 187 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 113 through 118 Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.806A pdb=" N GLY E 53 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR E 242 " --> pdb=" O LEU E 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.668A pdb=" N ILE E 115 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE E 156 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR E 117 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN E 214 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR E 187 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'G' and resid 52 through 54 removed outlier: 6.805A pdb=" N GLY G 53 " --> pdb=" O LEU G 322 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR G 242 " --> pdb=" O LEU G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.668A pdb=" N ILE G 115 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE G 156 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR G 117 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN G 214 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR G 187 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 113 through 118 821 hydrogen bonds defined for protein. 2271 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: 3.14 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3392 1.31 - 1.43: 5730 1.43 - 1.56: 12134 1.56 - 1.68: 20 1.68 - 1.80: 160 Bond restraints: 21436 Sorted by residual: bond pdb=" C1B NAP C 401 " pdb=" C2B NAP C 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP E 401 " pdb=" C2B NAP E 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C1B NAP A 401 " pdb=" C2B NAP A 401 " ideal model delta sigma weight residual 1.528 1.312 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4D NAP C 401 " pdb=" O4D NAP C 401 " ideal model delta sigma weight residual 1.447 1.307 0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 21431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 28569 2.77 - 5.54: 467 5.54 - 8.31: 68 8.31 - 11.08: 16 11.08 - 13.85: 16 Bond angle restraints: 29136 Sorted by residual: angle pdb=" N LEU F 330 " pdb=" CA LEU F 330 " pdb=" C LEU F 330 " ideal model delta sigma weight residual 112.54 120.93 -8.39 1.22e+00 6.72e-01 4.73e+01 angle pdb=" N LEU H 330 " pdb=" CA LEU H 330 " pdb=" C LEU H 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU D 330 " pdb=" CA LEU D 330 " pdb=" C LEU D 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N LEU B 330 " pdb=" CA LEU B 330 " pdb=" C LEU B 330 " ideal model delta sigma weight residual 112.54 120.90 -8.36 1.22e+00 6.72e-01 4.69e+01 angle pdb=" N1A NAP A 401 " pdb=" C6A NAP A 401 " pdb=" N6A NAP A 401 " ideal model delta sigma weight residual 119.30 105.45 13.85 3.00e+00 1.11e-01 2.13e+01 ... (remaining 29131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 11183 16.93 - 33.85: 1257 33.85 - 50.78: 272 50.78 - 67.71: 104 67.71 - 84.63: 52 Dihedral angle restraints: 12868 sinusoidal: 5020 harmonic: 7848 Sorted by residual: dihedral pdb=" N PHE E 120 " pdb=" C PHE E 120 " pdb=" CA PHE E 120 " pdb=" CB PHE E 120 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE A 120 " pdb=" C PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N PHE C 120 " pdb=" C PHE C 120 " pdb=" CA PHE C 120 " pdb=" CB PHE C 120 " ideal model delta harmonic sigma weight residual 122.80 132.03 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 12865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3065 0.091 - 0.182: 211 0.182 - 0.273: 12 0.273 - 0.364: 8 0.364 - 0.455: 8 Chirality restraints: 3304 Sorted by residual: chirality pdb=" C2B NAP C 401 " pdb=" C1B NAP C 401 " pdb=" C3B NAP C 401 " pdb=" O2B NAP C 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C2B NAP E 401 " pdb=" C1B NAP E 401 " pdb=" C3B NAP E 401 " pdb=" O2B NAP E 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C2B NAP A 401 " pdb=" C1B NAP A 401 " pdb=" C3B NAP A 401 " pdb=" O2B NAP A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.30 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3301 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 337 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO D 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " 0.051 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO B 338 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 337 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.67e+00 pdb=" N PRO H 338 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 338 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 338 " -0.042 5.00e-02 4.00e+02 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6930 2.81 - 3.33: 18292 3.33 - 3.86: 33805 3.86 - 4.38: 40026 4.38 - 4.90: 67707 Nonbonded interactions: 166760 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OE2 GLU G 168 " model vdw 2.290 3.040 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR C 184 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR E 184 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR G 187 " pdb=" OE1 GLU G 213 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR E 187 " pdb=" OE1 GLU E 213 " model vdw 2.302 3.040 ... (remaining 166755 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 1.860 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.009 0.217 21436 Z= 0.418 Angle : 0.938 13.854 29136 Z= 0.498 Chirality : 0.058 0.455 3304 Planarity : 0.006 0.086 3700 Dihedral : 16.550 84.632 7820 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 0.19 % Allowed : 18.23 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.99 (0.11), residues: 2696 helix: -4.61 (0.05), residues: 1508 sheet: -2.47 (0.38), residues: 180 loop : -2.81 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 283 TYR 0.015 0.002 TYR E 270 PHE 0.010 0.001 PHE E 120 TRP 0.015 0.002 TRP G 185 HIS 0.004 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00895 (21436) covalent geometry : angle 0.93790 (29136) hydrogen bonds : bond 0.31943 ( 821) hydrogen bonds : angle 9.75420 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 551 time to evaluate : 0.807 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: A 109 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7768 (mtm180) REVERT: A 204 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: B 137 MET cc_start: 0.7836 (ttp) cc_final: 0.7585 (tmm) REVERT: B 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8292 (tpt) REVERT: B 375 PHE cc_start: 0.8643 (m-80) cc_final: 0.8372 (m-80) REVERT: B 403 PHE cc_start: 0.8772 (t80) cc_final: 0.8547 (t80) REVERT: B 412 PHE cc_start: 0.9053 (m-80) cc_final: 0.8751 (m-80) REVERT: B 458 LYS cc_start: 0.8456 (mttt) cc_final: 0.7979 (mttm) REVERT: B 484 ASN cc_start: 0.8380 (t0) cc_final: 0.8091 (t0) REVERT: B 489 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7174 (tpt90) REVERT: C 109 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7776 (mtm180) REVERT: C 204 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: D 137 MET cc_start: 0.7836 (ttp) cc_final: 0.7575 (tmm) REVERT: D 141 ASP cc_start: 0.8777 (t0) cc_final: 0.8569 (t70) REVERT: D 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8288 (tpt) REVERT: D 375 PHE cc_start: 0.8639 (m-80) cc_final: 0.8362 (m-80) REVERT: D 403 PHE cc_start: 0.8770 (t80) cc_final: 0.8521 (t80) REVERT: D 412 PHE cc_start: 0.9056 (m-80) cc_final: 0.8746 (m-80) REVERT: D 458 LYS cc_start: 0.8453 (mttt) cc_final: 0.7953 (mttm) REVERT: D 484 ASN cc_start: 0.8377 (t0) cc_final: 0.8088 (t0) REVERT: D 489 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7173 (tpt90) REVERT: E 109 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7784 (mtm180) REVERT: E 204 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: F 137 MET cc_start: 0.7831 (ttp) cc_final: 0.7582 (tmm) REVERT: F 141 ASP cc_start: 0.8771 (t0) cc_final: 0.8562 (t70) REVERT: F 151 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8411 (mtt-85) REVERT: F 194 MET cc_start: 0.8587 (tpp) cc_final: 0.8341 (tpt) REVERT: F 375 PHE cc_start: 0.8637 (m-80) cc_final: 0.8358 (m-80) REVERT: F 412 PHE cc_start: 0.9067 (m-80) cc_final: 0.8739 (m-80) REVERT: F 458 LYS cc_start: 0.8510 (mttt) cc_final: 0.8021 (mttm) REVERT: F 485 TYR cc_start: 0.7975 (t80) cc_final: 0.7742 (t80) REVERT: F 489 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7601 (mtp-110) REVERT: G 109 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7769 (mtm180) REVERT: G 204 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: H 137 MET cc_start: 0.7829 (ttp) cc_final: 0.7570 (tmm) REVERT: H 141 ASP cc_start: 0.8773 (t0) cc_final: 0.8563 (t70) REVERT: H 194 MET cc_start: 0.8589 (tpp) cc_final: 0.8319 (tpt) REVERT: H 375 PHE cc_start: 0.8665 (m-80) cc_final: 0.8391 (m-80) REVERT: H 412 PHE cc_start: 0.9055 (m-80) cc_final: 0.8837 (m-80) REVERT: H 458 LYS cc_start: 0.8528 (mttt) cc_final: 0.8024 (mttm) REVERT: H 489 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7177 (tpt90) outliers start: 4 outliers final: 0 residues processed: 555 average time/residue: 0.1823 time to fit residues: 145.3017 Evaluate side-chains 443 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 439 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain G residue 204 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 152 ASN C 314 ASN D 152 ASN E 314 ASN F 152 ASN G 314 ASN H 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103549 restraints weight = 31005.496| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.03 r_work: 0.3113 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21436 Z= 0.129 Angle : 0.590 6.335 29136 Z= 0.308 Chirality : 0.042 0.146 3304 Planarity : 0.005 0.051 3700 Dihedral : 10.255 57.919 3220 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.63 % Rotamer: Outliers : 3.15 % Allowed : 18.03 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.13), residues: 2696 helix: -3.03 (0.09), residues: 1500 sheet: -2.02 (0.38), residues: 176 loop : -2.10 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 214 TYR 0.029 0.001 TYR E 270 PHE 0.017 0.001 PHE F 403 TRP 0.014 0.001 TRP B 221 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00274 (21436) covalent geometry : angle 0.58985 (29136) hydrogen bonds : bond 0.05327 ( 821) hydrogen bonds : angle 5.34190 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 506 time to evaluate : 0.778 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: A 78 ASP cc_start: 0.9101 (m-30) cc_final: 0.8852 (m-30) REVERT: B 118 GLN cc_start: 0.9023 (mt0) cc_final: 0.8821 (mm-40) REVERT: B 137 MET cc_start: 0.8785 (ttp) cc_final: 0.8470 (tmm) REVERT: B 256 LEU cc_start: 0.7866 (tt) cc_final: 0.7609 (tt) REVERT: B 375 PHE cc_start: 0.8814 (m-80) cc_final: 0.8275 (m-80) REVERT: B 391 LEU cc_start: 0.9039 (mt) cc_final: 0.8837 (mp) REVERT: B 398 LEU cc_start: 0.9071 (mp) cc_final: 0.8787 (mp) REVERT: B 403 PHE cc_start: 0.8872 (t80) cc_final: 0.8572 (t80) REVERT: B 407 ILE cc_start: 0.8580 (mm) cc_final: 0.8201 (mm) REVERT: B 412 PHE cc_start: 0.9047 (m-80) cc_final: 0.8790 (m-80) REVERT: B 489 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7287 (tpt90) REVERT: C 78 ASP cc_start: 0.9079 (m-30) cc_final: 0.8829 (m-30) REVERT: D 118 GLN cc_start: 0.9027 (mt0) cc_final: 0.8816 (mm-40) REVERT: D 137 MET cc_start: 0.8750 (ttp) cc_final: 0.8439 (tmm) REVERT: D 375 PHE cc_start: 0.8810 (m-80) cc_final: 0.8291 (m-80) REVERT: D 398 LEU cc_start: 0.9071 (mp) cc_final: 0.8790 (mp) REVERT: D 403 PHE cc_start: 0.8834 (t80) cc_final: 0.8575 (t80) REVERT: D 407 ILE cc_start: 0.8590 (mm) cc_final: 0.8213 (mm) REVERT: D 412 PHE cc_start: 0.9056 (m-80) cc_final: 0.8810 (m-80) REVERT: D 489 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7286 (tpt90) REVERT: E 78 ASP cc_start: 0.9090 (m-30) cc_final: 0.8835 (m-30) REVERT: F 137 MET cc_start: 0.8742 (ttp) cc_final: 0.8442 (tmm) REVERT: F 339 TYR cc_start: 0.6330 (t80) cc_final: 0.6126 (t80) REVERT: F 375 PHE cc_start: 0.8814 (m-80) cc_final: 0.8346 (m-80) REVERT: F 391 LEU cc_start: 0.8981 (mt) cc_final: 0.8774 (mp) REVERT: F 403 PHE cc_start: 0.8799 (t80) cc_final: 0.8577 (t80) REVERT: F 405 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8567 (tp) REVERT: F 407 ILE cc_start: 0.8643 (mm) cc_final: 0.8298 (mm) REVERT: F 412 PHE cc_start: 0.9075 (m-80) cc_final: 0.8841 (m-80) REVERT: F 484 ASN cc_start: 0.8571 (m-40) cc_final: 0.8314 (t0) REVERT: F 489 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7284 (tpt90) REVERT: G 78 ASP cc_start: 0.9078 (m-30) cc_final: 0.8828 (m-30) REVERT: H 137 MET cc_start: 0.8740 (ttp) cc_final: 0.8441 (tmm) REVERT: H 375 PHE cc_start: 0.8807 (m-80) cc_final: 0.8311 (m-80) REVERT: H 398 LEU cc_start: 0.9078 (mp) cc_final: 0.8799 (mp) REVERT: H 403 PHE cc_start: 0.8913 (t80) cc_final: 0.8626 (t80) REVERT: H 407 ILE cc_start: 0.8659 (mm) cc_final: 0.8327 (mm) REVERT: H 412 PHE cc_start: 0.9064 (m-80) cc_final: 0.8814 (m-80) REVERT: H 484 ASN cc_start: 0.8593 (m-40) cc_final: 0.8322 (t0) REVERT: H 489 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7287 (tpt90) outliers start: 66 outliers final: 32 residues processed: 553 average time/residue: 0.1438 time to fit residues: 122.7189 Evaluate side-chains 480 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 447 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 118 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 215 optimal weight: 0.0040 chunk 68 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101027 restraints weight = 30365.947| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.98 r_work: 0.3074 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 21436 Z= 0.216 Angle : 0.624 8.240 29136 Z= 0.315 Chirality : 0.044 0.137 3304 Planarity : 0.004 0.043 3700 Dihedral : 8.369 56.586 3208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.18 % Rotamer: Outliers : 3.34 % Allowed : 18.65 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.15), residues: 2696 helix: -1.90 (0.12), residues: 1512 sheet: -1.93 (0.38), residues: 180 loop : -1.78 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 284 TYR 0.015 0.002 TYR B 339 PHE 0.013 0.001 PHE D 156 TRP 0.018 0.002 TRP D 221 HIS 0.005 0.002 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00504 (21436) covalent geometry : angle 0.62440 (29136) hydrogen bonds : bond 0.04852 ( 821) hydrogen bonds : angle 4.75383 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 0.764 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: B 137 MET cc_start: 0.8798 (ttp) cc_final: 0.8470 (tmm) REVERT: B 375 PHE cc_start: 0.8778 (m-80) cc_final: 0.8322 (m-80) REVERT: B 403 PHE cc_start: 0.8870 (t80) cc_final: 0.8424 (t80) REVERT: B 407 ILE cc_start: 0.8651 (mm) cc_final: 0.8225 (mm) REVERT: B 489 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7368 (tpt90) REVERT: D 137 MET cc_start: 0.8806 (ttp) cc_final: 0.8469 (tmm) REVERT: D 375 PHE cc_start: 0.8784 (m-80) cc_final: 0.8342 (m-80) REVERT: D 403 PHE cc_start: 0.8865 (t80) cc_final: 0.8426 (t80) REVERT: D 407 ILE cc_start: 0.8651 (mm) cc_final: 0.8237 (mm) REVERT: D 489 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7353 (tpt90) REVERT: F 137 MET cc_start: 0.8790 (ttp) cc_final: 0.8454 (tmm) REVERT: F 339 TYR cc_start: 0.6336 (t80) cc_final: 0.6019 (t80) REVERT: F 375 PHE cc_start: 0.8781 (m-80) cc_final: 0.8410 (m-80) REVERT: F 405 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8657 (tp) REVERT: F 484 ASN cc_start: 0.8625 (m-40) cc_final: 0.8418 (t0) REVERT: F 489 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7317 (tpt90) REVERT: H 118 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8795 (mt0) REVERT: H 137 MET cc_start: 0.8790 (ttp) cc_final: 0.8464 (tmm) REVERT: H 375 PHE cc_start: 0.8783 (m-80) cc_final: 0.8333 (m-80) REVERT: H 484 ASN cc_start: 0.8621 (m-40) cc_final: 0.8357 (t0) REVERT: H 489 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7335 (tpt90) outliers start: 70 outliers final: 53 residues processed: 503 average time/residue: 0.1404 time to fit residues: 110.1509 Evaluate side-chains 479 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 425 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 167 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105357 restraints weight = 30419.881| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.20 r_work: 0.3093 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21436 Z= 0.122 Angle : 0.557 8.527 29136 Z= 0.280 Chirality : 0.041 0.133 3304 Planarity : 0.004 0.041 3700 Dihedral : 7.165 59.994 3208 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.08 % Favored : 97.77 % Rotamer: Outliers : 3.91 % Allowed : 19.47 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.16), residues: 2696 helix: -1.35 (0.13), residues: 1508 sheet: -1.78 (0.37), residues: 176 loop : -1.50 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 284 TYR 0.015 0.001 TYR B 339 PHE 0.017 0.001 PHE D 259 TRP 0.014 0.001 TRP F 221 HIS 0.005 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00279 (21436) covalent geometry : angle 0.55741 (29136) hydrogen bonds : bond 0.03974 ( 821) hydrogen bonds : angle 4.42454 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 449 time to evaluate : 0.767 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: A 128 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 118 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8753 (mt0) REVERT: B 137 MET cc_start: 0.8861 (ttp) cc_final: 0.8518 (tmm) REVERT: B 258 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6354 (tm-30) REVERT: B 296 PHE cc_start: 0.7292 (t80) cc_final: 0.7041 (m-10) REVERT: B 339 TYR cc_start: 0.6157 (t80) cc_final: 0.5754 (t80) REVERT: B 375 PHE cc_start: 0.8818 (m-80) cc_final: 0.8428 (m-80) REVERT: B 403 PHE cc_start: 0.8875 (t80) cc_final: 0.8629 (t80) REVERT: B 405 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8675 (tp) REVERT: B 407 ILE cc_start: 0.8624 (mm) cc_final: 0.8312 (pt) REVERT: B 412 PHE cc_start: 0.9145 (m-80) cc_final: 0.8738 (m-80) REVERT: B 489 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7402 (tpt90) REVERT: C 109 ARG cc_start: 0.8511 (mtm180) cc_final: 0.8254 (mtm180) REVERT: C 128 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8031 (mt-10) REVERT: D 118 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8761 (mt0) REVERT: D 137 MET cc_start: 0.8846 (ttp) cc_final: 0.8530 (tmm) REVERT: D 339 TYR cc_start: 0.6110 (t80) cc_final: 0.5723 (t80) REVERT: D 375 PHE cc_start: 0.8820 (m-80) cc_final: 0.8447 (m-80) REVERT: D 403 PHE cc_start: 0.8880 (t80) cc_final: 0.8644 (t80) REVERT: D 405 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8668 (tp) REVERT: D 407 ILE cc_start: 0.8592 (mm) cc_final: 0.8220 (pt) REVERT: D 412 PHE cc_start: 0.9149 (m-80) cc_final: 0.8733 (m-80) REVERT: D 489 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7421 (tpt90) REVERT: E 109 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8229 (mtm180) REVERT: E 128 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8028 (mt-10) REVERT: F 137 MET cc_start: 0.8865 (ttp) cc_final: 0.8518 (tmm) REVERT: F 296 PHE cc_start: 0.7236 (t80) cc_final: 0.7032 (m-10) REVERT: F 339 TYR cc_start: 0.6287 (t80) cc_final: 0.5861 (t80) REVERT: F 375 PHE cc_start: 0.8822 (m-80) cc_final: 0.8456 (m-80) REVERT: F 412 PHE cc_start: 0.9194 (m-80) cc_final: 0.8795 (m-80) REVERT: F 484 ASN cc_start: 0.8589 (m-40) cc_final: 0.8383 (t0) REVERT: F 489 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7373 (tpt90) REVERT: G 109 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8261 (mtm180) REVERT: G 128 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8254 (mt-10) REVERT: H 137 MET cc_start: 0.8839 (ttp) cc_final: 0.8492 (tmm) REVERT: H 339 TYR cc_start: 0.6094 (t80) cc_final: 0.5709 (t80) REVERT: H 375 PHE cc_start: 0.8791 (m-80) cc_final: 0.8399 (m-80) REVERT: H 405 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8629 (tp) REVERT: H 412 PHE cc_start: 0.9153 (m-80) cc_final: 0.8715 (m-80) REVERT: H 484 ASN cc_start: 0.8603 (m-40) cc_final: 0.8396 (t0) REVERT: H 489 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7393 (tpt90) outliers start: 82 outliers final: 41 residues processed: 513 average time/residue: 0.1436 time to fit residues: 115.6488 Evaluate side-chains 468 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 424 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 245 optimal weight: 0.2980 chunk 221 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN E 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103358 restraints weight = 30211.068| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21436 Z= 0.147 Angle : 0.563 8.466 29136 Z= 0.283 Chirality : 0.042 0.193 3304 Planarity : 0.004 0.039 3700 Dihedral : 6.864 55.786 3208 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.15 % Favored : 97.70 % Rotamer: Outliers : 3.20 % Allowed : 19.47 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2696 helix: -0.96 (0.14), residues: 1504 sheet: -1.74 (0.37), residues: 176 loop : -1.39 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 284 TYR 0.014 0.001 TYR G 270 PHE 0.020 0.001 PHE F 403 TRP 0.011 0.001 TRP D 221 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00341 (21436) covalent geometry : angle 0.56295 (29136) hydrogen bonds : bond 0.03930 ( 821) hydrogen bonds : angle 4.25559 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 448 time to evaluate : 0.814 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: A 128 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 137 MET cc_start: 0.8782 (ttp) cc_final: 0.8464 (tmm) REVERT: B 245 LEU cc_start: 0.8663 (mt) cc_final: 0.8436 (mt) REVERT: B 339 TYR cc_start: 0.6248 (t80) cc_final: 0.5823 (t80) REVERT: B 375 PHE cc_start: 0.8793 (m-80) cc_final: 0.8484 (m-80) REVERT: B 403 PHE cc_start: 0.8864 (t80) cc_final: 0.8434 (t80) REVERT: B 407 ILE cc_start: 0.8621 (mm) cc_final: 0.8187 (mm) REVERT: B 412 PHE cc_start: 0.9160 (m-80) cc_final: 0.8781 (m-80) REVERT: B 489 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7387 (tpt90) REVERT: C 109 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8115 (mtm180) REVERT: C 128 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8100 (mt-10) REVERT: D 137 MET cc_start: 0.8792 (ttp) cc_final: 0.8469 (tmm) REVERT: D 245 LEU cc_start: 0.8670 (mt) cc_final: 0.8426 (mt) REVERT: D 339 TYR cc_start: 0.6149 (t80) cc_final: 0.5741 (t80) REVERT: D 375 PHE cc_start: 0.8822 (m-80) cc_final: 0.8578 (m-80) REVERT: D 412 PHE cc_start: 0.9156 (m-80) cc_final: 0.8772 (m-80) REVERT: D 489 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7366 (tpt90) REVERT: E 109 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8147 (mtm180) REVERT: E 128 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8106 (mt-10) REVERT: F 137 MET cc_start: 0.8775 (ttp) cc_final: 0.8466 (tmm) REVERT: F 339 TYR cc_start: 0.6351 (t80) cc_final: 0.5919 (t80) REVERT: F 375 PHE cc_start: 0.8763 (m-80) cc_final: 0.8552 (m-80) REVERT: F 412 PHE cc_start: 0.9154 (m-80) cc_final: 0.8786 (m-80) REVERT: F 484 ASN cc_start: 0.8575 (m-40) cc_final: 0.8366 (t0) REVERT: F 489 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7332 (tpt90) REVERT: G 109 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8150 (mtm180) REVERT: G 128 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8287 (mt-10) REVERT: H 137 MET cc_start: 0.8776 (ttp) cc_final: 0.8461 (tmm) REVERT: H 245 LEU cc_start: 0.8665 (mt) cc_final: 0.8432 (mt) REVERT: H 339 TYR cc_start: 0.6142 (t80) cc_final: 0.5742 (t80) REVERT: H 375 PHE cc_start: 0.8756 (m-80) cc_final: 0.8526 (m-80) REVERT: H 412 PHE cc_start: 0.9166 (m-80) cc_final: 0.8784 (m-80) REVERT: H 484 ASN cc_start: 0.8615 (m-40) cc_final: 0.8413 (t0) REVERT: H 489 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7350 (tpt90) outliers start: 67 outliers final: 52 residues processed: 498 average time/residue: 0.1410 time to fit residues: 109.0093 Evaluate side-chains 484 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 248 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 156 optimal weight: 0.0570 chunk 213 optimal weight: 0.0980 chunk 242 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 135 HIS E 135 HIS G 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104050 restraints weight = 30425.628| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.29 r_work: 0.3078 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21436 Z= 0.175 Angle : 0.592 9.669 29136 Z= 0.297 Chirality : 0.043 0.170 3304 Planarity : 0.004 0.041 3700 Dihedral : 6.920 52.723 3208 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.15 % Allowed : 20.47 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2696 helix: -0.76 (0.14), residues: 1484 sheet: -1.81 (0.38), residues: 176 loop : -1.35 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 144 TYR 0.014 0.001 TYR C 270 PHE 0.021 0.001 PHE B 216 TRP 0.011 0.001 TRP G 185 HIS 0.003 0.001 HIS F 380 Details of bonding type rmsd covalent geometry : bond 0.00416 (21436) covalent geometry : angle 0.59170 (29136) hydrogen bonds : bond 0.03895 ( 821) hydrogen bonds : angle 4.22817 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 444 time to evaluate : 0.798 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: A 128 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 137 MET cc_start: 0.8852 (ttp) cc_final: 0.8501 (tmm) REVERT: B 245 LEU cc_start: 0.8625 (mt) cc_final: 0.8411 (mt) REVERT: B 339 TYR cc_start: 0.6250 (t80) cc_final: 0.5884 (t80) REVERT: B 375 PHE cc_start: 0.8789 (m-80) cc_final: 0.8515 (m-80) REVERT: B 403 PHE cc_start: 0.8918 (t80) cc_final: 0.8698 (t80) REVERT: B 412 PHE cc_start: 0.9181 (m-80) cc_final: 0.8754 (m-80) REVERT: B 442 MET cc_start: 0.8842 (mtm) cc_final: 0.7961 (mmt) REVERT: B 489 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7420 (tpt170) REVERT: C 109 ARG cc_start: 0.8526 (mtm180) cc_final: 0.8182 (mtm180) REVERT: C 128 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 137 MET cc_start: 0.8871 (ttp) cc_final: 0.8514 (tmm) REVERT: D 245 LEU cc_start: 0.8628 (mt) cc_final: 0.8411 (mt) REVERT: D 339 TYR cc_start: 0.6222 (t80) cc_final: 0.5850 (t80) REVERT: D 412 PHE cc_start: 0.9171 (m-80) cc_final: 0.8807 (m-80) REVERT: D 489 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7430 (tpt170) REVERT: E 109 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8234 (mtm180) REVERT: E 128 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8209 (mt-10) REVERT: F 137 MET cc_start: 0.8881 (ttp) cc_final: 0.8528 (tmm) REVERT: F 339 TYR cc_start: 0.6310 (t80) cc_final: 0.5916 (t80) REVERT: F 375 PHE cc_start: 0.8808 (m-80) cc_final: 0.8454 (m-80) REVERT: F 412 PHE cc_start: 0.9171 (m-80) cc_final: 0.8815 (m-80) REVERT: F 484 ASN cc_start: 0.8639 (m-40) cc_final: 0.8425 (t0) REVERT: F 489 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7393 (tpt170) REVERT: G 109 ARG cc_start: 0.8523 (mtm180) cc_final: 0.8201 (mtm180) REVERT: G 128 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8298 (mt-10) REVERT: H 137 MET cc_start: 0.8860 (ttp) cc_final: 0.8508 (tmm) REVERT: H 245 LEU cc_start: 0.8627 (mt) cc_final: 0.8408 (mt) REVERT: H 339 TYR cc_start: 0.6203 (t80) cc_final: 0.5839 (t80) REVERT: H 375 PHE cc_start: 0.8780 (m-80) cc_final: 0.8423 (m-80) REVERT: H 412 PHE cc_start: 0.9161 (m-80) cc_final: 0.8811 (m-80) REVERT: H 484 ASN cc_start: 0.8635 (m-40) cc_final: 0.8420 (t0) REVERT: H 489 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7424 (tpt170) outliers start: 66 outliers final: 59 residues processed: 500 average time/residue: 0.1437 time to fit residues: 111.2519 Evaluate side-chains 490 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 431 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 12 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 285 GLN C 175 HIS E 175 HIS E 285 GLN G 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105773 restraints weight = 30432.361| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.33 r_work: 0.3095 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21436 Z= 0.130 Angle : 0.573 10.000 29136 Z= 0.286 Chirality : 0.042 0.175 3304 Planarity : 0.004 0.039 3700 Dihedral : 6.833 59.411 3208 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 21.09 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2696 helix: -0.56 (0.14), residues: 1464 sheet: -1.67 (0.38), residues: 176 loop : -1.39 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 144 TYR 0.012 0.001 TYR E 270 PHE 0.028 0.001 PHE D 403 TRP 0.009 0.001 TRP E 185 HIS 0.002 0.000 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00309 (21436) covalent geometry : angle 0.57335 (29136) hydrogen bonds : bond 0.03694 ( 821) hydrogen bonds : angle 4.10159 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 469 time to evaluate : 0.738 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: A 109 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8360 (mtp-110) REVERT: A 128 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 285 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7918 (mm-40) REVERT: B 137 MET cc_start: 0.8917 (ttp) cc_final: 0.8564 (tmm) REVERT: B 245 LEU cc_start: 0.8646 (mt) cc_final: 0.8432 (mt) REVERT: B 339 TYR cc_start: 0.6357 (t80) cc_final: 0.5994 (t80) REVERT: B 375 PHE cc_start: 0.8762 (m-80) cc_final: 0.8510 (m-80) REVERT: B 403 PHE cc_start: 0.8909 (t80) cc_final: 0.8665 (t80) REVERT: B 412 PHE cc_start: 0.9149 (m-80) cc_final: 0.8705 (m-80) REVERT: B 442 MET cc_start: 0.8844 (mtm) cc_final: 0.7990 (mmt) REVERT: B 489 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7419 (tpt170) REVERT: C 109 ARG cc_start: 0.8542 (mtm180) cc_final: 0.8158 (mtm180) REVERT: C 128 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 137 MET cc_start: 0.8900 (ttp) cc_final: 0.8545 (tmm) REVERT: D 245 LEU cc_start: 0.8642 (mt) cc_final: 0.8425 (mt) REVERT: D 339 TYR cc_start: 0.6333 (t80) cc_final: 0.5960 (t80) REVERT: D 375 PHE cc_start: 0.8750 (m-80) cc_final: 0.8452 (m-80) REVERT: D 412 PHE cc_start: 0.9161 (m-80) cc_final: 0.8830 (m-80) REVERT: D 489 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7430 (tpt170) REVERT: E 109 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8186 (mtm180) REVERT: E 128 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 285 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (mm-40) REVERT: F 137 MET cc_start: 0.8891 (ttp) cc_final: 0.8540 (tmm) REVERT: F 217 GLN cc_start: 0.5924 (tp-100) cc_final: 0.5473 (mm-40) REVERT: F 339 TYR cc_start: 0.6424 (t80) cc_final: 0.5997 (t80) REVERT: F 375 PHE cc_start: 0.8776 (m-80) cc_final: 0.8446 (m-80) REVERT: F 412 PHE cc_start: 0.9176 (m-80) cc_final: 0.8759 (m-80) REVERT: F 442 MET cc_start: 0.8895 (mtm) cc_final: 0.7943 (mmt) REVERT: F 484 ASN cc_start: 0.8624 (m-40) cc_final: 0.8336 (t0) REVERT: F 489 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7369 (tpt170) REVERT: G 109 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8209 (mtm180) REVERT: H 137 MET cc_start: 0.8892 (ttp) cc_final: 0.8539 (tmm) REVERT: H 245 LEU cc_start: 0.8650 (mt) cc_final: 0.8431 (mt) REVERT: H 339 TYR cc_start: 0.6374 (t80) cc_final: 0.5968 (t80) REVERT: H 375 PHE cc_start: 0.8779 (m-80) cc_final: 0.8469 (m-80) REVERT: H 412 PHE cc_start: 0.9134 (m-80) cc_final: 0.8788 (m-80) REVERT: H 484 ASN cc_start: 0.8621 (m-40) cc_final: 0.8329 (t0) REVERT: H 489 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7418 (tpt170) outliers start: 62 outliers final: 57 residues processed: 520 average time/residue: 0.1382 time to fit residues: 111.6311 Evaluate side-chains 500 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 441 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 223 optimal weight: 0.0370 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105676 restraints weight = 30047.938| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.98 r_work: 0.3141 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21436 Z= 0.113 Angle : 0.574 10.166 29136 Z= 0.286 Chirality : 0.041 0.153 3304 Planarity : 0.004 0.037 3700 Dihedral : 6.626 55.937 3208 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.53 % Allowed : 22.52 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2696 helix: -0.39 (0.14), residues: 1460 sheet: -1.63 (0.45), residues: 136 loop : -1.40 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 144 TYR 0.011 0.001 TYR E 270 PHE 0.019 0.001 PHE D 216 TRP 0.007 0.001 TRP G 185 HIS 0.002 0.000 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00267 (21436) covalent geometry : angle 0.57415 (29136) hydrogen bonds : bond 0.03589 ( 821) hydrogen bonds : angle 4.04153 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 456 time to evaluate : 0.817 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: A 128 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 137 MET cc_start: 0.8786 (ttp) cc_final: 0.8436 (tmm) REVERT: B 328 MET cc_start: 0.6420 (mmm) cc_final: 0.6177 (tpt) REVERT: B 339 TYR cc_start: 0.6397 (t80) cc_final: 0.6015 (t80) REVERT: B 375 PHE cc_start: 0.8785 (m-80) cc_final: 0.8442 (m-80) REVERT: B 412 PHE cc_start: 0.9173 (m-80) cc_final: 0.8747 (m-80) REVERT: B 442 MET cc_start: 0.8762 (mtm) cc_final: 0.7871 (mmt) REVERT: B 489 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7392 (tpt170) REVERT: C 109 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8164 (mtm180) REVERT: C 128 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8060 (mt-10) REVERT: D 137 MET cc_start: 0.8790 (ttp) cc_final: 0.8435 (tmm) REVERT: D 245 LEU cc_start: 0.8601 (mt) cc_final: 0.8396 (mt) REVERT: D 339 TYR cc_start: 0.6424 (t80) cc_final: 0.6020 (t80) REVERT: D 375 PHE cc_start: 0.8757 (m-80) cc_final: 0.8403 (m-80) REVERT: D 412 PHE cc_start: 0.9148 (m-80) cc_final: 0.8812 (m-80) REVERT: D 489 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7397 (tpt170) REVERT: E 109 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8160 (mtm180) REVERT: E 128 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8090 (mt-10) REVERT: F 137 MET cc_start: 0.8795 (ttp) cc_final: 0.8447 (tmm) REVERT: F 217 GLN cc_start: 0.5844 (tp-100) cc_final: 0.5407 (mm-40) REVERT: F 339 TYR cc_start: 0.6430 (t80) cc_final: 0.5978 (t80) REVERT: F 375 PHE cc_start: 0.8785 (m-80) cc_final: 0.8377 (m-80) REVERT: F 412 PHE cc_start: 0.9188 (m-80) cc_final: 0.8766 (m-80) REVERT: F 442 MET cc_start: 0.8814 (mtm) cc_final: 0.7819 (mmt) REVERT: F 484 ASN cc_start: 0.8615 (m-40) cc_final: 0.8335 (t0) REVERT: F 489 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7346 (tpt170) REVERT: G 109 ARG cc_start: 0.8494 (mtm180) cc_final: 0.8175 (mtm180) REVERT: H 137 MET cc_start: 0.8794 (ttp) cc_final: 0.8442 (tmm) REVERT: H 245 LEU cc_start: 0.8615 (mt) cc_final: 0.8406 (mt) REVERT: H 339 TYR cc_start: 0.6399 (t80) cc_final: 0.5997 (t80) REVERT: H 375 PHE cc_start: 0.8804 (m-80) cc_final: 0.8413 (m-10) REVERT: H 412 PHE cc_start: 0.9135 (m-80) cc_final: 0.8809 (m-80) REVERT: H 484 ASN cc_start: 0.8615 (m-40) cc_final: 0.8333 (t0) REVERT: H 489 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7376 (tpt170) outliers start: 53 outliers final: 43 residues processed: 502 average time/residue: 0.1387 time to fit residues: 108.2021 Evaluate side-chains 491 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 448 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 90 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 239 optimal weight: 0.7980 chunk 254 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN E 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106760 restraints weight = 30227.921| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.34 r_work: 0.3098 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21436 Z= 0.124 Angle : 0.596 12.270 29136 Z= 0.295 Chirality : 0.042 0.142 3304 Planarity : 0.004 0.045 3700 Dihedral : 6.411 48.097 3208 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.86 % Allowed : 22.71 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2696 helix: -0.17 (0.14), residues: 1440 sheet: -1.71 (0.45), residues: 140 loop : -1.29 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 284 TYR 0.017 0.001 TYR G 270 PHE 0.035 0.001 PHE D 403 TRP 0.008 0.001 TRP A 185 HIS 0.002 0.000 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00296 (21436) covalent geometry : angle 0.59622 (29136) hydrogen bonds : bond 0.03558 ( 821) hydrogen bonds : angle 4.00495 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 460 time to evaluate : 0.795 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: A 109 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8200 (mtp-110) REVERT: A 128 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 137 MET cc_start: 0.8926 (ttp) cc_final: 0.8694 (tmm) REVERT: B 328 MET cc_start: 0.6374 (mmm) cc_final: 0.6147 (tpt) REVERT: B 339 TYR cc_start: 0.6442 (t80) cc_final: 0.6058 (t80) REVERT: B 375 PHE cc_start: 0.8789 (m-80) cc_final: 0.8430 (m-10) REVERT: B 412 PHE cc_start: 0.9136 (m-80) cc_final: 0.8728 (m-80) REVERT: B 442 MET cc_start: 0.8844 (mtm) cc_final: 0.7938 (mmt) REVERT: B 489 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7405 (tpt170) REVERT: C 109 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8182 (mtm180) REVERT: C 128 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 137 MET cc_start: 0.8948 (ttp) cc_final: 0.8719 (tmm) REVERT: D 328 MET cc_start: 0.6380 (mmm) cc_final: 0.6158 (tpt) REVERT: D 339 TYR cc_start: 0.6463 (t80) cc_final: 0.6058 (t80) REVERT: D 375 PHE cc_start: 0.8763 (m-80) cc_final: 0.8334 (m-80) REVERT: D 412 PHE cc_start: 0.9149 (m-80) cc_final: 0.8760 (m-80) REVERT: D 442 MET cc_start: 0.8871 (mtm) cc_final: 0.7882 (mmt) REVERT: D 489 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7399 (tpt170) REVERT: E 109 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8173 (mtm180) REVERT: E 128 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8137 (mt-10) REVERT: F 137 MET cc_start: 0.8951 (ttp) cc_final: 0.8581 (tmm) REVERT: F 217 GLN cc_start: 0.5804 (tp-100) cc_final: 0.5375 (mm-40) REVERT: F 339 TYR cc_start: 0.6549 (t80) cc_final: 0.6131 (t80) REVERT: F 412 PHE cc_start: 0.9164 (m-80) cc_final: 0.8744 (m-80) REVERT: F 442 MET cc_start: 0.8902 (mtm) cc_final: 0.8078 (mmt) REVERT: F 484 ASN cc_start: 0.8630 (m-40) cc_final: 0.8343 (t0) REVERT: F 489 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7380 (tpt170) REVERT: G 109 ARG cc_start: 0.8546 (mtm180) cc_final: 0.8209 (mtm180) REVERT: H 137 MET cc_start: 0.8910 (ttp) cc_final: 0.8548 (tmm) REVERT: H 339 TYR cc_start: 0.6453 (t80) cc_final: 0.6054 (t80) REVERT: H 375 PHE cc_start: 0.8780 (m-80) cc_final: 0.8308 (m-10) REVERT: H 412 PHE cc_start: 0.9128 (m-80) cc_final: 0.8688 (m-80) REVERT: H 442 MET cc_start: 0.8926 (mtm) cc_final: 0.7928 (mmt) REVERT: H 484 ASN cc_start: 0.8636 (m-40) cc_final: 0.8338 (t0) REVERT: H 489 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7332 (tpt170) outliers start: 60 outliers final: 49 residues processed: 504 average time/residue: 0.1422 time to fit residues: 110.9103 Evaluate side-chains 500 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 451 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 28 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 126 optimal weight: 0.0870 chunk 121 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN E 285 GLN G 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.155068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106983 restraints weight = 30430.457| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.41 r_work: 0.3086 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21436 Z= 0.116 Angle : 0.600 11.207 29136 Z= 0.297 Chirality : 0.041 0.144 3304 Planarity : 0.004 0.051 3700 Dihedral : 6.272 45.995 3208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.34 % Allowed : 23.57 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2696 helix: -0.06 (0.14), residues: 1436 sheet: -1.64 (0.45), residues: 140 loop : -1.23 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 284 TYR 0.014 0.001 TYR C 270 PHE 0.036 0.001 PHE B 403 TRP 0.007 0.001 TRP C 185 HIS 0.003 0.001 HIS F 380 Details of bonding type rmsd covalent geometry : bond 0.00277 (21436) covalent geometry : angle 0.60013 (29136) hydrogen bonds : bond 0.03512 ( 821) hydrogen bonds : angle 3.98758 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 456 time to evaluate : 0.807 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: A 109 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8022 (mtp-110) REVERT: A 285 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7840 (mm110) REVERT: B 137 MET cc_start: 0.8651 (ttp) cc_final: 0.8436 (tmm) REVERT: B 339 TYR cc_start: 0.6415 (t80) cc_final: 0.6024 (t80) REVERT: B 375 PHE cc_start: 0.8731 (m-80) cc_final: 0.8330 (m-10) REVERT: B 412 PHE cc_start: 0.9063 (m-80) cc_final: 0.8649 (m-80) REVERT: B 442 MET cc_start: 0.8626 (mtm) cc_final: 0.7790 (mmt) REVERT: B 489 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7354 (tpt170) REVERT: D 137 MET cc_start: 0.8634 (ttp) cc_final: 0.8426 (tmm) REVERT: D 217 GLN cc_start: 0.6043 (tp-100) cc_final: 0.5629 (mm-40) REVERT: D 339 TYR cc_start: 0.6399 (t80) cc_final: 0.6006 (t80) REVERT: D 375 PHE cc_start: 0.8689 (m-80) cc_final: 0.8290 (m-80) REVERT: D 412 PHE cc_start: 0.9063 (m-80) cc_final: 0.8656 (m-80) REVERT: D 442 MET cc_start: 0.8655 (mtm) cc_final: 0.7906 (mmt) REVERT: D 488 HIS cc_start: 0.7022 (m-70) cc_final: 0.6735 (m-70) REVERT: E 285 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7851 (mm110) REVERT: F 217 GLN cc_start: 0.6013 (tp-100) cc_final: 0.5576 (mm-40) REVERT: F 339 TYR cc_start: 0.6473 (t80) cc_final: 0.6063 (t80) REVERT: F 375 PHE cc_start: 0.8743 (m-80) cc_final: 0.8322 (m-80) REVERT: F 412 PHE cc_start: 0.9098 (m-80) cc_final: 0.8696 (m-80) REVERT: F 442 MET cc_start: 0.8618 (mtm) cc_final: 0.7868 (mmt) REVERT: F 484 ASN cc_start: 0.8580 (m-40) cc_final: 0.8286 (t0) REVERT: F 489 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7301 (tpt170) REVERT: G 285 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7836 (mm110) REVERT: H 217 GLN cc_start: 0.5866 (tp-100) cc_final: 0.5476 (mm-40) REVERT: H 339 TYR cc_start: 0.6403 (t80) cc_final: 0.6009 (t80) REVERT: H 412 PHE cc_start: 0.9039 (m-80) cc_final: 0.8707 (m-80) REVERT: H 484 ASN cc_start: 0.8602 (m-40) cc_final: 0.8259 (t0) outliers start: 49 outliers final: 43 residues processed: 495 average time/residue: 0.1427 time to fit residues: 109.5913 Evaluate side-chains 493 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 447 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 144 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104672 restraints weight = 30298.743| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.01 r_work: 0.3125 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21436 Z= 0.159 Angle : 0.626 10.464 29136 Z= 0.312 Chirality : 0.043 0.149 3304 Planarity : 0.004 0.056 3700 Dihedral : 6.286 45.775 3208 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.29 % Allowed : 23.57 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2696 helix: -0.09 (0.14), residues: 1436 sheet: -1.68 (0.45), residues: 140 loop : -1.18 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 168 TYR 0.014 0.001 TYR C 270 PHE 0.035 0.001 PHE D 403 TRP 0.015 0.001 TRP B 221 HIS 0.009 0.001 HIS H 380 Details of bonding type rmsd covalent geometry : bond 0.00385 (21436) covalent geometry : angle 0.62649 (29136) hydrogen bonds : bond 0.03639 ( 821) hydrogen bonds : angle 4.04680 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6784.82 seconds wall clock time: 115 minutes 57.49 seconds (6957.49 seconds total)