Starting phenix.real_space_refine on Sun Feb 18 05:53:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_31149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_31149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_31149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_31149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej2_31149/02_2024/7ej2_31149_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 11} 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: 11.02, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 8.89 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 136 helices and 16 sheets defined 49.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 97 through 106 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 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.786A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 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 303 through 313 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) removed outlier: 3.659A pdb=" N ARG A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 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) removed outlier: 4.061A pdb=" N ALA A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 345 through 355 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 124 removed outlier: 3.631A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 160 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 161 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 165 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 186 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 191 through 200 removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 231 through 254 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) Processing helix chain 'B' and resid 257 through 260 No H-bonds generated for 'chain 'B' and resid 257 through 260' Processing helix chain 'B' and resid 299 through 314 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) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 340 through 343 No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 360 through 378 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) removed outlier: 4.071A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 418 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 435 through 442 removed outlier: 3.590A pdb=" N MET B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 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 479 through 488 Processing helix chain 'B' and resid 494 through 501 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) Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 97 through 106 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 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.755A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.787A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 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 303 through 313 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) removed outlier: 3.659A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 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) removed outlier: 4.062A pdb=" N ALA C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 345 through 355 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 124 removed outlier: 3.631A pdb=" N GLN D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP D 157 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 158 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 186 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 191 through 200 removed outlier: 3.733A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 231 through 254 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) Processing helix chain 'D' and resid 257 through 260 No H-bonds generated for 'chain 'D' and resid 257 through 260' Processing helix chain 'D' and resid 299 through 314 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) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 327 through 330 No H-bonds generated for 'chain 'D' and resid 327 through 330' Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 340 through 343 No H-bonds generated for 'chain 'D' and resid 340 through 343' Processing helix chain 'D' and resid 360 through 378 removed outlier: 4.159A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 377 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 418 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 435 through 442 removed outlier: 3.590A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 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 479 through 488 Processing helix chain 'D' and resid 494 through 501 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) Processing helix chain 'E' and resid 66 through 77 removed outlier: 3.659A pdb=" N ALA E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 97 through 106 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 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 235 removed outlier: 3.785A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.662A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 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 303 through 313 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) removed outlier: 3.659A pdb=" N ARG E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 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) removed outlier: 4.061A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE E 337 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN E 338 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Proline residue: E 341 - end of helix Processing helix chain 'E' and resid 345 through 355 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 124 removed outlier: 3.630A pdb=" N GLN F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Processing helix chain 'F' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP F 157 " --> pdb=" O PRO F 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 158 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU F 160 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR F 161 " --> pdb=" O ALA F 158 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER F 165 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 186 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 191 through 200 removed outlier: 3.733A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 231 through 254 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) Processing helix chain 'F' and resid 257 through 260 No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 299 through 314 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) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 327 through 330 No H-bonds generated for 'chain 'F' and resid 327 through 330' Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 340 through 343 No H-bonds generated for 'chain 'F' and resid 340 through 343' Processing helix chain 'F' and resid 360 through 378 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) removed outlier: 4.071A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 418 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 435 through 442 removed outlier: 3.590A pdb=" N MET F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 472 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 479 through 488 Processing helix chain 'F' and resid 494 through 501 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) Processing helix chain 'G' and resid 66 through 77 removed outlier: 3.658A pdb=" N ALA G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 97 through 106 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 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 133 through 142 removed outlier: 3.517A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 200 removed outlier: 3.754A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 229 through 235 removed outlier: 3.786A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 removed outlier: 3.661A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 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 303 through 313 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) removed outlier: 3.659A pdb=" N ARG G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 342 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) removed outlier: 4.062A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE G 337 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) Proline residue: G 341 - end of helix Processing helix chain 'G' and resid 345 through 355 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 124 removed outlier: 3.629A pdb=" N GLN H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 139 Processing helix chain 'H' and resid 154 through 165 removed outlier: 3.592A pdb=" N ASP H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA H 158 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU H 160 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 161 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER H 165 " --> pdb=" O TYR H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 186 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 191 through 200 removed outlier: 3.734A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 221 Processing helix chain 'H' and resid 231 through 254 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) Processing helix chain 'H' and resid 257 through 260 No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 299 through 314 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) Processing helix chain 'H' and resid 322 through 324 No H-bonds generated for 'chain 'H' and resid 322 through 324' Processing helix chain 'H' and resid 327 through 330 No H-bonds generated for 'chain 'H' and resid 327 through 330' Processing helix chain 'H' and resid 333 through 335 No H-bonds generated for 'chain 'H' and resid 333 through 335' Processing helix chain 'H' and resid 340 through 343 No H-bonds generated for 'chain 'H' and resid 340 through 343' Processing helix chain 'H' and resid 360 through 378 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) removed outlier: 4.071A pdb=" N VAL H 371 " --> pdb=" O ARG H 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE H 372 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG H 373 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS H 376 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU H 377 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 392 removed outlier: 4.068A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 418 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 435 through 442 removed outlier: 3.590A pdb=" N MET H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 472 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 479 through 488 Processing helix chain 'H' and resid 494 through 501 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) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL A 320 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL A 154 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 156 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR A 184 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA A 157 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A 186 " --> pdb=" O ALA A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR B 147 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.216A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 113 through 118 removed outlier: 6.423A pdb=" N TYR D 147 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL E 320 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL E 154 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 119 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE E 156 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR E 184 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA E 157 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY E 186 " --> pdb=" O ALA E 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR F 147 " --> pdb=" O ASN F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 52 through 54 removed outlier: 6.217A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 116 through 119 removed outlier: 6.557A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 113 through 118 removed outlier: 6.424A pdb=" N TYR H 147 " --> pdb=" O ASN H 109 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1695 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: 5.82 Time building geometry restraints manager: 9.55 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: 98.26 - 105.47: 469 105.47 - 112.67: 10958 112.67 - 119.87: 7957 119.87 - 127.08: 9497 127.08 - 134.28: 255 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: 6946 2.81 - 3.33: 18448 3.33 - 3.86: 34021 3.86 - 4.38: 40506 4.38 - 4.90: 67767 Nonbonded interactions: 167688 Sorted by model distance: nonbonded pdb=" OH TYR A 184 " pdb=" OE2 GLU G 168 " model vdw 2.290 2.440 nonbonded pdb=" OE2 GLU A 168 " pdb=" OH TYR C 184 " model vdw 2.299 2.440 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR E 184 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR G 187 " pdb=" OE1 GLU G 213 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR E 187 " pdb=" OE1 GLU E 213 " model vdw 2.302 2.440 ... (remaining 167683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.260 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: 0.030 Extract box with map and model: 6.720 Check model and map are aligned: 0.320 Set scattering table: 0.220 Process input model: 55.760 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.460 ------------------------------------------------------------------------------- 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= 0.592 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 : 7.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP G 185 HIS 0.004 0.001 HIS E 218 PHE 0.010 0.001 PHE E 120 TYR 0.015 0.002 TYR E 270 ARG 0.003 0.000 ARG C 283 *********************** 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 fitting. rotamer outliers: 4 poor density : 551 time to evaluate : 2.562 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: 0.7769 (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: 0.7584 (tmm) REVERT: B 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8291 (tpt) REVERT: B 375 PHE cc_start: 0.8643 (m-80) cc_final: 0.8371 (m-80) REVERT: B 403 PHE cc_start: 0.8772 (t80) cc_final: 0.8548 (t80) REVERT: B 412 PHE cc_start: 0.9053 (m-80) cc_final: 0.8752 (m-80) REVERT: B 458 LYS cc_start: 0.8456 (mttt) cc_final: 0.7978 (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: 0.7777 (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: 0.8570 (t70) REVERT: D 194 MET cc_start: 0.8597 (tpp) cc_final: 0.8287 (tpt) REVERT: D 375 PHE cc_start: 0.8639 (m-80) cc_final: 0.8361 (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: 0.7923 (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: 0.7785 (mtm180) REVERT: E 204 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (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: 0.8563 (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: 0.8020 (mttm) REVERT: F 485 TYR cc_start: 0.7975 (t80) cc_final: 0.7743 (t80) REVERT: F 489 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7600 (mtp-110) REVERT: G 109 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7770 (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: 0.8564 (t70) REVERT: H 194 MET cc_start: 0.8589 (tpp) cc_final: 0.8318 (tpt) REVERT: H 375 PHE cc_start: 0.8665 (m-80) cc_final: 0.8390 (m-80) REVERT: H 412 PHE cc_start: 0.9055 (m-80) cc_final: 0.8838 (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: 0.4018 time to fit residues: 317.3233 Evaluate side-chains 447 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 443 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 226 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN C 314 ASN E 314 ASN G 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1782 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= 0.197 Angle : 0.549 6.219 29136 Z= 0.280 Chirality : 0.041 0.130 3304 Planarity : 0.005 0.051 3700 Dihedral : 10.112 59.110 3220 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.30 % Favored : 97.55 % Rotamer: Outliers : 3.82 % Allowed : 19.23 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.13), residues: 2696 helix: -3.22 (0.09), residues: 1476 sheet: -2.04 (0.40), residues: 176 loop : -1.98 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 221 HIS 0.002 0.001 HIS D 380 PHE 0.018 0.001 PHE F 403 TYR 0.014 0.001 TYR F 339 ARG 0.008 0.001 ARG F 214 *********************** 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 565 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 485 time to evaluate : 2.556 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: 0.7912 (mtm-85) cc_final: 0.7664 (mtm180) REVERT: B 118 GLN cc_start: 0.8735 (mt0) cc_final: 0.8485 (mm-40) REVERT: B 375 PHE cc_start: 0.8733 (m-80) cc_final: 0.8160 (m-80) REVERT: B 398 LEU cc_start: 0.9015 (mp) cc_final: 0.8731 (mp) REVERT: B 403 PHE cc_start: 0.8769 (t80) cc_final: 0.8436 (t80) REVERT: B 407 ILE cc_start: 0.8474 (mm) cc_final: 0.8089 (mm) REVERT: B 412 PHE cc_start: 0.9097 (m-80) cc_final: 0.8824 (m-80) REVERT: B 458 LYS cc_start: 0.8378 (mttt) cc_final: 0.7912 (mttm) REVERT: C 109 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7714 (mtm180) REVERT: D 118 GLN cc_start: 0.8727 (mt0) cc_final: 0.8475 (mm-40) REVERT: D 375 PHE cc_start: 0.8732 (m-80) cc_final: 0.8166 (m-80) REVERT: D 398 LEU cc_start: 0.9012 (mp) cc_final: 0.8729 (mp) REVERT: D 403 PHE cc_start: 0.8726 (t80) cc_final: 0.8406 (t80) REVERT: D 407 ILE cc_start: 0.8477 (mm) cc_final: 0.8095 (mm) REVERT: D 412 PHE cc_start: 0.9098 (m-80) cc_final: 0.8841 (m-80) REVERT: D 458 LYS cc_start: 0.8378 (mttt) cc_final: 0.7906 (mttm) REVERT: E 109 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7717 (mtm180) REVERT: F 118 GLN cc_start: 0.8742 (mt0) cc_final: 0.8489 (mm-40) REVERT: F 375 PHE cc_start: 0.8696 (m-80) cc_final: 0.8192 (m-80) REVERT: F 398 LEU cc_start: 0.9018 (mp) cc_final: 0.8745 (mp) REVERT: F 403 PHE cc_start: 0.8722 (t80) cc_final: 0.8466 (t80) REVERT: F 405 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8560 (tp) REVERT: F 407 ILE cc_start: 0.8540 (mm) cc_final: 0.8206 (mm) REVERT: F 412 PHE cc_start: 0.9131 (m-80) cc_final: 0.8887 (m-80) REVERT: F 458 LYS cc_start: 0.8355 (mttt) cc_final: 0.7893 (mttm) REVERT: F 489 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7096 (tpt90) REVERT: H 118 GLN cc_start: 0.8715 (mt0) cc_final: 0.8471 (mm-40) REVERT: H 375 PHE cc_start: 0.8749 (m-80) cc_final: 0.8183 (m-80) REVERT: H 398 LEU cc_start: 0.9016 (mp) cc_final: 0.8732 (mp) REVERT: H 403 PHE cc_start: 0.8816 (t80) cc_final: 0.8504 (t80) REVERT: H 407 ILE cc_start: 0.8555 (mm) cc_final: 0.8227 (mm) REVERT: H 412 PHE cc_start: 0.9100 (m-80) cc_final: 0.8865 (m-80) REVERT: H 458 LYS cc_start: 0.8408 (mttt) cc_final: 0.7947 (mttm) REVERT: H 489 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7577 (mtp-110) outliers start: 80 outliers final: 44 residues processed: 540 average time/residue: 0.3272 time to fit residues: 268.4885 Evaluate side-chains 483 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 438 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 A residue 328 ASP 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 460 VAL Chi-restraints excluded: chain C residue 58 VAL 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 C residue 328 ASP 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 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 E residue 328 ASP 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 381 SER Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain G residue 58 VAL 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 G residue 328 ASP 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 381 SER Chi-restraints excluded: chain H residue 405 LEU 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 135 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 243 optimal weight: 0.0270 chunk 263 optimal weight: 0.0040 chunk 217 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 overall best weight: 0.1768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS C 175 HIS E 175 HIS F 152 ASN G 175 HIS H 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21436 Z= 0.132 Angle : 0.529 8.598 29136 Z= 0.257 Chirality : 0.040 0.129 3304 Planarity : 0.004 0.036 3700 Dihedral : 7.542 53.939 3208 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.97 % Favored : 97.89 % Rotamer: Outliers : 1.86 % Allowed : 19.47 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.15), residues: 2696 helix: -2.10 (0.12), residues: 1444 sheet: -1.95 (0.39), residues: 176 loop : -1.81 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 221 HIS 0.003 0.001 HIS F 380 PHE 0.015 0.001 PHE D 259 TYR 0.018 0.001 TYR B 339 ARG 0.005 0.000 ARG F 214 *********************** 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 514 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 475 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 PHE cc_start: 0.8666 (m-80) cc_final: 0.8108 (m-10) REVERT: B 403 PHE cc_start: 0.8727 (t80) cc_final: 0.8201 (t80) REVERT: B 407 ILE cc_start: 0.8476 (mm) cc_final: 0.8008 (mm) REVERT: B 470 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7836 (tp) REVERT: D 144 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8064 (mtt90) REVERT: D 375 PHE cc_start: 0.8682 (m-80) cc_final: 0.8201 (m-80) REVERT: D 403 PHE cc_start: 0.8636 (t80) cc_final: 0.8341 (t80) REVERT: D 405 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8606 (tp) REVERT: D 407 ILE cc_start: 0.8465 (mm) cc_final: 0.8046 (mm) REVERT: D 470 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 270 TYR cc_start: 0.8270 (m-80) cc_final: 0.7777 (m-80) REVERT: F 118 GLN cc_start: 0.8678 (mt0) cc_final: 0.8310 (mt0) REVERT: F 375 PHE cc_start: 0.8689 (m-80) cc_final: 0.8197 (m-80) REVERT: F 470 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7855 (tp) REVERT: F 489 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7440 (mmm160) REVERT: H 144 ARG cc_start: 0.8268 (mtp85) cc_final: 0.8066 (mtt90) REVERT: H 375 PHE cc_start: 0.8694 (m-80) cc_final: 0.8198 (m-80) REVERT: H 405 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8562 (tp) REVERT: H 470 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7842 (tp) REVERT: H 489 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7036 (tpt90) outliers start: 39 outliers final: 19 residues processed: 497 average time/residue: 0.3384 time to fit residues: 257.0903 Evaluate side-chains 456 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 431 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 328 ASP 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 380 HIS Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21436 Z= 0.373 Angle : 0.609 6.634 29136 Z= 0.305 Chirality : 0.044 0.139 3304 Planarity : 0.004 0.037 3700 Dihedral : 7.464 54.771 3208 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.60 % Favored : 97.26 % Rotamer: Outliers : 3.20 % Allowed : 21.52 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2696 helix: -1.69 (0.13), residues: 1472 sheet: -2.15 (0.39), residues: 176 loop : -1.63 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 221 HIS 0.005 0.001 HIS D 380 PHE 0.017 0.001 PHE B 156 TYR 0.030 0.002 TYR E 270 ARG 0.005 0.000 ARG F 144 *********************** 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 520 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 453 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 137 MET cc_start: 0.8073 (tmm) cc_final: 0.7653 (tmm) REVERT: B 339 TYR cc_start: 0.6402 (t80) cc_final: 0.6148 (t80) REVERT: B 375 PHE cc_start: 0.8796 (m-80) cc_final: 0.8274 (m-80) REVERT: B 403 PHE cc_start: 0.8814 (t80) cc_final: 0.8468 (t80) REVERT: B 407 ILE cc_start: 0.8316 (mm) cc_final: 0.7920 (mm) REVERT: B 412 PHE cc_start: 0.9225 (m-80) cc_final: 0.8826 (m-80) REVERT: B 470 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8009 (tp) REVERT: D 118 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8539 (mm-40) REVERT: D 137 MET cc_start: 0.8083 (tmm) cc_final: 0.7659 (tmm) REVERT: D 339 TYR cc_start: 0.6385 (t80) cc_final: 0.6129 (t80) REVERT: D 375 PHE cc_start: 0.8807 (m-80) cc_final: 0.8360 (m-80) REVERT: D 403 PHE cc_start: 0.8777 (t80) cc_final: 0.8251 (t80) REVERT: D 407 ILE cc_start: 0.8368 (mm) cc_final: 0.7991 (mm) REVERT: D 412 PHE cc_start: 0.9231 (m-80) cc_final: 0.8865 (m-80) REVERT: D 470 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8003 (tp) REVERT: F 118 GLN cc_start: 0.8769 (mt0) cc_final: 0.8447 (mt0) REVERT: F 137 MET cc_start: 0.8077 (tmm) cc_final: 0.7652 (tmm) REVERT: F 339 TYR cc_start: 0.6342 (t80) cc_final: 0.6029 (t80) REVERT: F 375 PHE cc_start: 0.8783 (m-80) cc_final: 0.8339 (m-80) REVERT: F 412 PHE cc_start: 0.9243 (m-80) cc_final: 0.8857 (m-80) REVERT: F 470 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (tp) REVERT: F 489 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7114 (tpt90) REVERT: H 137 MET cc_start: 0.8081 (tmm) cc_final: 0.7656 (tmm) REVERT: H 339 TYR cc_start: 0.6380 (t80) cc_final: 0.6120 (t80) REVERT: H 375 PHE cc_start: 0.8863 (m-80) cc_final: 0.8393 (m-80) REVERT: H 412 PHE cc_start: 0.9207 (m-80) cc_final: 0.8842 (m-80) REVERT: H 470 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8010 (tp) REVERT: H 489 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7512 (mmm160) outliers start: 67 outliers final: 51 residues processed: 495 average time/residue: 0.3438 time to fit residues: 261.8848 Evaluate side-chains 495 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 440 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 A residue 328 ASP Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 58 VAL 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 C residue 328 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 470 LEU 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 328 ASP 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 390 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 58 VAL 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 G residue 328 ASP Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain H residue 470 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 132 optimal weight: 0.0370 chunk 232 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21436 Z= 0.180 Angle : 0.517 8.245 29136 Z= 0.255 Chirality : 0.040 0.131 3304 Planarity : 0.003 0.036 3700 Dihedral : 7.004 58.958 3208 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.82 % Favored : 98.03 % Rotamer: Outliers : 2.29 % Allowed : 22.23 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2696 helix: -1.35 (0.13), residues: 1452 sheet: -2.19 (0.39), residues: 176 loop : -1.45 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 221 HIS 0.003 0.001 HIS F 380 PHE 0.018 0.001 PHE B 216 TYR 0.021 0.001 TYR E 270 ARG 0.006 0.000 ARG F 144 *********************** 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 499 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 451 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 MET cc_start: 0.8031 (tmm) cc_final: 0.7616 (tmm) REVERT: B 339 TYR cc_start: 0.6370 (t80) cc_final: 0.6083 (t80) REVERT: B 375 PHE cc_start: 0.8757 (m-80) cc_final: 0.8272 (m-80) REVERT: B 403 PHE cc_start: 0.8779 (t80) cc_final: 0.8426 (t80) REVERT: B 407 ILE cc_start: 0.8520 (mm) cc_final: 0.8070 (mm) REVERT: B 412 PHE cc_start: 0.9248 (m-80) cc_final: 0.8752 (m-80) REVERT: B 442 MET cc_start: 0.8221 (mtm) cc_final: 0.7398 (mmt) REVERT: B 470 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7850 (tp) REVERT: D 137 MET cc_start: 0.8050 (tmm) cc_final: 0.7616 (tmm) REVERT: D 339 TYR cc_start: 0.6385 (t80) cc_final: 0.6119 (t80) REVERT: D 375 PHE cc_start: 0.8778 (m-80) cc_final: 0.8368 (m-80) REVERT: D 403 PHE cc_start: 0.8753 (t80) cc_final: 0.8393 (t80) REVERT: D 407 ILE cc_start: 0.8461 (mm) cc_final: 0.8046 (mm) REVERT: D 412 PHE cc_start: 0.9251 (m-80) cc_final: 0.8858 (m-80) REVERT: D 470 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7856 (tp) REVERT: F 137 MET cc_start: 0.8028 (tmm) cc_final: 0.7601 (tmm) REVERT: F 339 TYR cc_start: 0.6380 (t80) cc_final: 0.6069 (t80) REVERT: F 375 PHE cc_start: 0.8784 (m-80) cc_final: 0.8320 (m-80) REVERT: F 412 PHE cc_start: 0.9257 (m-80) cc_final: 0.8804 (m-80) REVERT: F 442 MET cc_start: 0.8230 (mtm) cc_final: 0.7286 (mmt) REVERT: F 458 LYS cc_start: 0.8412 (mttt) cc_final: 0.7962 (mttm) REVERT: F 470 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7887 (tp) REVERT: F 489 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7071 (tpt90) REVERT: H 137 MET cc_start: 0.8035 (tmm) cc_final: 0.7611 (tmm) REVERT: H 339 TYR cc_start: 0.6344 (t80) cc_final: 0.6067 (t80) REVERT: H 375 PHE cc_start: 0.8770 (m-80) cc_final: 0.8298 (m-80) REVERT: H 412 PHE cc_start: 0.9235 (m-80) cc_final: 0.8874 (m-80) REVERT: H 470 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7865 (tp) REVERT: H 489 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7078 (tpt90) outliers start: 48 outliers final: 37 residues processed: 483 average time/residue: 0.3158 time to fit residues: 232.7954 Evaluate side-chains 468 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 427 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 328 ASP 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 470 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 328 ASP 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 470 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 328 ASP 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 391 LEU Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 328 ASP 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 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN H 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21436 Z= 0.223 Angle : 0.523 7.027 29136 Z= 0.260 Chirality : 0.041 0.142 3304 Planarity : 0.003 0.035 3700 Dihedral : 7.003 58.336 3208 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.26 % Favored : 97.59 % Rotamer: Outliers : 3.20 % Allowed : 22.28 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2696 helix: -1.10 (0.14), residues: 1452 sheet: -2.16 (0.39), residues: 176 loop : -1.32 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 185 HIS 0.004 0.001 HIS F 380 PHE 0.018 0.001 PHE F 403 TYR 0.015 0.001 TYR E 270 ARG 0.005 0.000 ARG B 144 *********************** 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 522 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 455 time to evaluate : 2.593 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: B 137 MET cc_start: 0.8044 (tmm) cc_final: 0.7607 (tmm) REVERT: B 339 TYR cc_start: 0.6370 (t80) cc_final: 0.6091 (t80) REVERT: B 375 PHE cc_start: 0.8740 (m-80) cc_final: 0.8299 (m-80) REVERT: B 403 PHE cc_start: 0.8786 (t80) cc_final: 0.8425 (t80) REVERT: B 407 ILE cc_start: 0.8510 (mm) cc_final: 0.8050 (mm) REVERT: B 412 PHE cc_start: 0.9232 (m-80) cc_final: 0.8771 (m-80) REVERT: B 442 MET cc_start: 0.8224 (mtm) cc_final: 0.7360 (mmt) REVERT: B 470 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7911 (tp) REVERT: D 137 MET cc_start: 0.8048 (tmm) cc_final: 0.7619 (tmm) REVERT: D 339 TYR cc_start: 0.6376 (t80) cc_final: 0.6093 (t80) REVERT: D 375 PHE cc_start: 0.8757 (m-80) cc_final: 0.8396 (m-80) REVERT: D 403 PHE cc_start: 0.8754 (t80) cc_final: 0.8391 (t80) REVERT: D 407 ILE cc_start: 0.8503 (mm) cc_final: 0.8049 (mm) REVERT: D 412 PHE cc_start: 0.9229 (m-80) cc_final: 0.8777 (m-80) REVERT: D 442 MET cc_start: 0.8268 (mtm) cc_final: 0.7406 (mmt) REVERT: D 470 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7913 (tp) REVERT: F 137 MET cc_start: 0.8035 (tmm) cc_final: 0.7600 (tmm) REVERT: F 339 TYR cc_start: 0.6506 (t80) cc_final: 0.6189 (t80) REVERT: F 375 PHE cc_start: 0.8779 (m-80) cc_final: 0.8354 (m-80) REVERT: F 412 PHE cc_start: 0.9244 (m-80) cc_final: 0.8927 (m-80) REVERT: F 458 LYS cc_start: 0.8429 (mttt) cc_final: 0.7983 (mttm) REVERT: F 470 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7916 (tp) REVERT: F 489 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7051 (tpt90) REVERT: H 137 MET cc_start: 0.8041 (tmm) cc_final: 0.7617 (tmm) REVERT: H 339 TYR cc_start: 0.6373 (t80) cc_final: 0.6086 (t80) REVERT: H 375 PHE cc_start: 0.8736 (m-80) cc_final: 0.8292 (m-80) REVERT: H 412 PHE cc_start: 0.9217 (m-80) cc_final: 0.8889 (m-80) REVERT: H 470 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7916 (tp) REVERT: H 489 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7050 (tpt90) outliers start: 67 outliers final: 52 residues processed: 501 average time/residue: 0.3281 time to fit residues: 249.7933 Evaluate side-chains 507 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 451 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP 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 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 328 ASP 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 390 THR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 328 ASP Chi-restraints excluded: chain H residue 105 ARG 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 389 GLN Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 470 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 189 optimal weight: 6.9990 chunk 146 optimal weight: 0.4980 chunk 218 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 258 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3026 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= 0.167 Angle : 0.518 7.342 29136 Z= 0.254 Chirality : 0.040 0.213 3304 Planarity : 0.003 0.039 3700 Dihedral : 6.942 56.037 3208 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.78 % Favored : 98.07 % Rotamer: Outliers : 2.58 % Allowed : 22.61 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.16), residues: 2696 helix: -0.87 (0.14), residues: 1452 sheet: -2.03 (0.38), residues: 176 loop : -1.22 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 185 HIS 0.002 0.000 HIS E 218 PHE 0.022 0.001 PHE F 216 TYR 0.019 0.001 TYR E 270 ARG 0.008 0.000 ARG F 144 *********************** 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 518 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 464 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 MET cc_start: 0.8017 (tmm) cc_final: 0.7587 (tmm) REVERT: B 296 PHE cc_start: 0.7423 (t80) cc_final: 0.7058 (m-10) REVERT: B 339 TYR cc_start: 0.6532 (t80) cc_final: 0.6180 (t80) REVERT: B 375 PHE cc_start: 0.8712 (m-80) cc_final: 0.8283 (m-80) REVERT: B 403 PHE cc_start: 0.8827 (t80) cc_final: 0.8472 (t80) REVERT: B 407 ILE cc_start: 0.8532 (mm) cc_final: 0.8081 (mm) REVERT: B 412 PHE cc_start: 0.9237 (m-80) cc_final: 0.8880 (m-80) REVERT: B 470 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7930 (tp) REVERT: D 137 MET cc_start: 0.8030 (tmm) cc_final: 0.7599 (tmm) REVERT: D 296 PHE cc_start: 0.7425 (t80) cc_final: 0.7065 (m-10) REVERT: D 339 TYR cc_start: 0.6502 (t80) cc_final: 0.6146 (t80) REVERT: D 375 PHE cc_start: 0.8732 (m-80) cc_final: 0.8362 (m-80) REVERT: D 403 PHE cc_start: 0.8763 (t80) cc_final: 0.8418 (t80) REVERT: D 407 ILE cc_start: 0.8506 (mm) cc_final: 0.8057 (mm) REVERT: D 412 PHE cc_start: 0.9249 (m-80) cc_final: 0.8828 (m-80) REVERT: D 442 MET cc_start: 0.8232 (mtm) cc_final: 0.7406 (mmt) REVERT: D 470 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (tp) REVERT: F 137 MET cc_start: 0.8023 (tmm) cc_final: 0.7580 (tmm) REVERT: F 217 GLN cc_start: 0.5722 (tp-100) cc_final: 0.5355 (mm-40) REVERT: F 296 PHE cc_start: 0.7377 (t80) cc_final: 0.7051 (m-10) REVERT: F 339 TYR cc_start: 0.6340 (t80) cc_final: 0.5966 (t80) REVERT: F 375 PHE cc_start: 0.8748 (m-80) cc_final: 0.8324 (m-80) REVERT: F 412 PHE cc_start: 0.9249 (m-80) cc_final: 0.8919 (m-80) REVERT: F 470 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7910 (tp) REVERT: F 489 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7067 (tpt90) REVERT: H 137 MET cc_start: 0.8027 (tmm) cc_final: 0.7600 (tmm) REVERT: H 296 PHE cc_start: 0.7386 (t80) cc_final: 0.7044 (m-10) REVERT: H 339 TYR cc_start: 0.6494 (t80) cc_final: 0.6132 (t80) REVERT: H 375 PHE cc_start: 0.8672 (m-80) cc_final: 0.8197 (m-10) REVERT: H 403 PHE cc_start: 0.8730 (t80) cc_final: 0.8395 (t80) REVERT: H 407 ILE cc_start: 0.8540 (mm) cc_final: 0.8176 (mm) REVERT: H 412 PHE cc_start: 0.9243 (m-80) cc_final: 0.8887 (m-80) REVERT: H 470 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7927 (tp) REVERT: H 489 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7070 (tpt90) outliers start: 54 outliers final: 43 residues processed: 503 average time/residue: 0.3440 time to fit residues: 263.7340 Evaluate side-chains 495 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 448 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP 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 470 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 328 ASP 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 470 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 328 ASP 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 255 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 328 ASP 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 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS B 152 ASN C 135 HIS E 135 HIS G 135 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21436 Z= 0.293 Angle : 0.576 9.676 29136 Z= 0.284 Chirality : 0.043 0.194 3304 Planarity : 0.003 0.043 3700 Dihedral : 7.041 59.977 3208 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.01 % Allowed : 22.76 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2696 helix: -0.89 (0.14), residues: 1460 sheet: -2.23 (0.38), residues: 176 loop : -1.11 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 57 HIS 0.006 0.001 HIS D 380 PHE 0.029 0.001 PHE F 403 TYR 0.014 0.001 TYR A 270 ARG 0.010 0.000 ARG B 144 *********************** 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 504 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 441 time to evaluate : 2.694 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: B 137 MET cc_start: 0.8053 (tmm) cc_final: 0.7618 (tmm) REVERT: B 339 TYR cc_start: 0.6564 (t80) cc_final: 0.6274 (t80) REVERT: B 375 PHE cc_start: 0.8741 (m-80) cc_final: 0.8355 (m-80) REVERT: B 403 PHE cc_start: 0.8833 (t80) cc_final: 0.8443 (t80) REVERT: B 407 ILE cc_start: 0.8522 (mm) cc_final: 0.8091 (mm) REVERT: B 412 PHE cc_start: 0.9246 (m-80) cc_final: 0.8895 (m-80) REVERT: B 470 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7672 (tp) REVERT: D 137 MET cc_start: 0.8069 (tmm) cc_final: 0.7639 (tmm) REVERT: D 339 TYR cc_start: 0.6537 (t80) cc_final: 0.6247 (t80) REVERT: D 375 PHE cc_start: 0.8759 (m-80) cc_final: 0.8370 (m-80) REVERT: D 403 PHE cc_start: 0.8776 (t80) cc_final: 0.8409 (t80) REVERT: D 407 ILE cc_start: 0.8496 (mm) cc_final: 0.8051 (mm) REVERT: D 412 PHE cc_start: 0.9245 (m-80) cc_final: 0.8802 (m-80) REVERT: D 442 MET cc_start: 0.8292 (mtm) cc_final: 0.7383 (mmt) REVERT: F 137 MET cc_start: 0.8050 (tmm) cc_final: 0.7614 (tmm) REVERT: F 339 TYR cc_start: 0.6538 (t80) cc_final: 0.6210 (t80) REVERT: F 375 PHE cc_start: 0.8773 (m-80) cc_final: 0.8380 (m-80) REVERT: F 412 PHE cc_start: 0.9250 (m-80) cc_final: 0.8935 (m-80) REVERT: F 458 LYS cc_start: 0.8346 (mttt) cc_final: 0.7908 (mttm) REVERT: F 470 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7878 (tp) REVERT: F 489 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7090 (tpt90) REVERT: H 137 MET cc_start: 0.8066 (tmm) cc_final: 0.7636 (tmm) REVERT: H 339 TYR cc_start: 0.6531 (t80) cc_final: 0.6239 (t80) REVERT: H 403 PHE cc_start: 0.8781 (t80) cc_final: 0.8440 (t80) REVERT: H 407 ILE cc_start: 0.8548 (mm) cc_final: 0.8150 (mm) REVERT: H 412 PHE cc_start: 0.9245 (m-80) cc_final: 0.8827 (m-80) REVERT: H 442 MET cc_start: 0.8324 (mtm) cc_final: 0.7262 (mmt) REVERT: H 489 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7091 (tpt90) outliers start: 63 outliers final: 56 residues processed: 484 average time/residue: 0.3284 time to fit residues: 241.3836 Evaluate side-chains 493 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 435 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP 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 255 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 328 ASP 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 255 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 328 ASP 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 255 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 470 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 328 ASP 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 255 THR Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 380 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 240 optimal weight: 0.0770 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 227 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21436 Z= 0.174 Angle : 0.534 10.899 29136 Z= 0.263 Chirality : 0.040 0.193 3304 Planarity : 0.003 0.041 3700 Dihedral : 6.698 52.254 3208 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.19 % Allowed : 23.85 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2696 helix: -0.69 (0.14), residues: 1452 sheet: -2.10 (0.39), residues: 176 loop : -1.10 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 185 HIS 0.006 0.001 HIS D 380 PHE 0.018 0.001 PHE F 216 TYR 0.014 0.001 TYR E 270 ARG 0.009 0.000 ARG B 144 *********************** 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 494 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 448 time to evaluate : 2.447 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: B 137 MET cc_start: 0.8021 (tmm) cc_final: 0.7591 (tmm) REVERT: B 217 GLN cc_start: 0.5640 (tp-100) cc_final: 0.5206 (mm-40) REVERT: B 339 TYR cc_start: 0.6546 (t80) cc_final: 0.6264 (t80) REVERT: B 375 PHE cc_start: 0.8706 (m-80) cc_final: 0.8318 (m-80) REVERT: B 403 PHE cc_start: 0.8822 (t80) cc_final: 0.8421 (t80) REVERT: B 407 ILE cc_start: 0.8377 (mm) cc_final: 0.7903 (mm) REVERT: B 412 PHE cc_start: 0.9233 (m-80) cc_final: 0.8889 (m-80) REVERT: B 471 THR cc_start: 0.8175 (m) cc_final: 0.7654 (t) REVERT: D 137 MET cc_start: 0.8043 (tmm) cc_final: 0.7613 (tmm) REVERT: D 217 GLN cc_start: 0.5804 (tp-100) cc_final: 0.5440 (mm-40) REVERT: D 339 TYR cc_start: 0.6541 (t80) cc_final: 0.6260 (t80) REVERT: D 375 PHE cc_start: 0.8685 (m-80) cc_final: 0.8294 (m-10) REVERT: D 403 PHE cc_start: 0.8778 (t80) cc_final: 0.8433 (t80) REVERT: D 407 ILE cc_start: 0.8336 (mm) cc_final: 0.7874 (mm) REVERT: D 412 PHE cc_start: 0.9234 (m-80) cc_final: 0.8824 (m-80) REVERT: D 442 MET cc_start: 0.8319 (mtm) cc_final: 0.7385 (mmt) REVERT: F 137 MET cc_start: 0.8022 (tmm) cc_final: 0.7586 (tmm) REVERT: F 168 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7460 (mtp-110) REVERT: F 217 GLN cc_start: 0.5732 (tp-100) cc_final: 0.5395 (mm-40) REVERT: F 339 TYR cc_start: 0.6501 (t80) cc_final: 0.6191 (t80) REVERT: F 375 PHE cc_start: 0.8706 (m-80) cc_final: 0.8288 (m-80) REVERT: F 412 PHE cc_start: 0.9232 (m-80) cc_final: 0.8917 (m-80) REVERT: F 489 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7162 (tpt90) REVERT: H 137 MET cc_start: 0.8038 (tmm) cc_final: 0.7615 (tmm) REVERT: H 217 GLN cc_start: 0.5654 (tp-100) cc_final: 0.5194 (mm-40) REVERT: H 339 TYR cc_start: 0.6531 (t80) cc_final: 0.6237 (t80) REVERT: H 403 PHE cc_start: 0.8789 (t80) cc_final: 0.8414 (t80) REVERT: H 407 ILE cc_start: 0.8530 (mm) cc_final: 0.8103 (mm) REVERT: H 412 PHE cc_start: 0.9238 (m-80) cc_final: 0.8848 (m-80) REVERT: H 442 MET cc_start: 0.8336 (mtm) cc_final: 0.7244 (mmt) REVERT: H 489 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7174 (tpt90) outliers start: 46 outliers final: 44 residues processed: 477 average time/residue: 0.3425 time to fit residues: 248.8615 Evaluate side-chains 480 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 436 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP 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 C residue 58 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 328 ASP 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 E residue 111 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 328 ASP 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 255 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 328 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 9.9990 chunk 155 optimal weight: 0.0770 chunk 120 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 266 optimal weight: 0.0770 chunk 245 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21436 Z= 0.147 Angle : 0.528 10.768 29136 Z= 0.258 Chirality : 0.040 0.188 3304 Planarity : 0.003 0.040 3700 Dihedral : 6.389 50.550 3208 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.86 % Allowed : 24.33 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2696 helix: -0.49 (0.14), residues: 1452 sheet: -1.94 (0.39), residues: 176 loop : -1.09 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.005 0.001 HIS B 380 PHE 0.030 0.001 PHE F 403 TYR 0.009 0.001 TYR A 199 ARG 0.009 0.000 ARG B 144 ********************** 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 499 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 460 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 MET cc_start: 0.7994 (tmm) cc_final: 0.7560 (tmm) REVERT: B 192 GLU cc_start: 0.7498 (tp30) cc_final: 0.7274 (tp30) REVERT: B 217 GLN cc_start: 0.5678 (tp-100) cc_final: 0.5288 (mm-40) REVERT: B 339 TYR cc_start: 0.6513 (t80) cc_final: 0.6242 (t80) REVERT: B 375 PHE cc_start: 0.8679 (m-80) cc_final: 0.8312 (m-80) REVERT: B 403 PHE cc_start: 0.8827 (t80) cc_final: 0.8406 (t80) REVERT: B 407 ILE cc_start: 0.8354 (mm) cc_final: 0.7877 (mm) REVERT: B 412 PHE cc_start: 0.9212 (m-80) cc_final: 0.8865 (m-80) REVERT: D 137 MET cc_start: 0.8024 (tmm) cc_final: 0.7591 (tmm) REVERT: D 217 GLN cc_start: 0.5776 (tp-100) cc_final: 0.5431 (mm-40) REVERT: D 339 TYR cc_start: 0.6518 (t80) cc_final: 0.6248 (t80) REVERT: D 412 PHE cc_start: 0.9196 (m-80) cc_final: 0.8861 (m-80) REVERT: F 137 MET cc_start: 0.7993 (tmm) cc_final: 0.7554 (tmm) REVERT: F 168 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7469 (mtp-110) REVERT: F 217 GLN cc_start: 0.5719 (tp-100) cc_final: 0.5390 (mm-40) REVERT: F 339 TYR cc_start: 0.6512 (t80) cc_final: 0.6199 (t80) REVERT: F 403 PHE cc_start: 0.8666 (t80) cc_final: 0.8451 (t80) REVERT: F 407 ILE cc_start: 0.8407 (mm) cc_final: 0.8098 (mm) REVERT: F 412 PHE cc_start: 0.9194 (m-80) cc_final: 0.8844 (m-80) REVERT: F 489 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7164 (tpt90) REVERT: G 109 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7838 (mtm180) REVERT: H 137 MET cc_start: 0.8018 (tmm) cc_final: 0.7586 (tmm) REVERT: H 217 GLN cc_start: 0.5672 (tp-100) cc_final: 0.5286 (mm-40) REVERT: H 339 TYR cc_start: 0.6512 (t80) cc_final: 0.6222 (t80) REVERT: H 403 PHE cc_start: 0.8797 (t80) cc_final: 0.8434 (t80) REVERT: H 407 ILE cc_start: 0.8551 (mm) cc_final: 0.8139 (mm) REVERT: H 412 PHE cc_start: 0.9212 (m-80) cc_final: 0.8878 (m-80) REVERT: H 489 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7165 (tpt90) outliers start: 39 outliers final: 39 residues processed: 485 average time/residue: 0.3390 time to fit residues: 247.9825 Evaluate side-chains 488 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 449 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP 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 255 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 328 ASP 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 E residue 111 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 328 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 186 optimal weight: 0.0010 overall best weight: 0.2964 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.155888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107749 restraints weight = 30205.722| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.42 r_work: 0.3126 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21436 Z= 0.149 Angle : 0.552 10.826 29136 Z= 0.264 Chirality : 0.040 0.186 3304 Planarity : 0.003 0.050 3700 Dihedral : 6.216 49.516 3208 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.86 % Allowed : 24.76 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2696 helix: -0.38 (0.14), residues: 1456 sheet: -1.77 (0.39), residues: 176 loop : -1.11 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 221 HIS 0.005 0.001 HIS B 380 PHE 0.035 0.001 PHE D 403 TYR 0.010 0.001 TYR A 199 ARG 0.013 0.000 ARG E 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5726.06 seconds wall clock time: 103 minutes 26.78 seconds (6206.78 seconds total)