Starting phenix.real_space_refine on Sun Oct 13 12:16:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuf_33467/10_2024/7xuf_33467.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuf_33467/10_2024/7xuf_33467.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/7xuf_33467/10_2024/7xuf_33467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuf_33467/10_2024/7xuf_33467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuf_33467/10_2024/7xuf_33467.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuf_33467/10_2024/7xuf_33467.cif" } 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= 0.012 sd= 0.183 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 K 3 8.98 5 S 76 5.16 5 C 9822 2.51 5 N 2524 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 15041 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3849 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 460} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3670 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 440} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3849 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 460} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3670 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 440} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.30, per 1000 atoms: 0.62 Number of scatterers: 15041 At special positions: 0 Unit cell: (132.44, 122.12, 129.86, 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) K 3 19.00 S 76 16.00 O 2616 8.00 N 2524 7.00 C 9822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3548 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 10 sheets defined 59.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.852A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.778A pdb=" N LEU A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 removed outlier: 3.907A pdb=" N THR A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 removed outlier: 4.037A pdb=" N LYS A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 removed outlier: 4.454A pdb=" N VAL A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.557A pdb=" N LYS A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.748A pdb=" N ARG A 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 202 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 203 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.753A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 removed outlier: 3.778A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.548A pdb=" N GLY A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 320 through 330 removed outlier: 4.217A pdb=" N ASN A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.878A pdb=" N TYR A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 377 removed outlier: 3.826A pdb=" N ARG A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 369 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 403 removed outlier: 3.641A pdb=" N ARG A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 401 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 removed outlier: 3.500A pdb=" N VAL A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.515A pdb=" N VAL A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.800A pdb=" N VAL A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 removed outlier: 3.907A pdb=" N GLY A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.785A pdb=" N ILE B 59 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Proline residue: B 76 - end of helix removed outlier: 3.616A pdb=" N LEU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.521A pdb=" N ILE B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 142 removed outlier: 3.660A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.649A pdb=" N ALA B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 removed outlier: 5.974A pdb=" N SER B 154 " --> pdb=" O ARG B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 155 through 161 removed outlier: 4.154A pdb=" N LEU B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.738A pdb=" N LEU B 165 " --> pdb=" O MET B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.728A pdb=" N GLY B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 Processing helix chain 'B' and resid 238 through 252 removed outlier: 4.066A pdb=" N THR B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 294 removed outlier: 3.876A pdb=" N LEU B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE B 276 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.522A pdb=" N GLN B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 removed outlier: 3.804A pdb=" N GLU B 345 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 347 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 349 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 350 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.872A pdb=" N SER B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 removed outlier: 4.384A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 removed outlier: 3.808A pdb=" N GLN B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 removed outlier: 3.561A pdb=" N VAL B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.767A pdb=" N ILE B 484 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 491 " --> pdb=" O ASN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'C' and resid 89 through 101 removed outlier: 3.503A pdb=" N LEU C 93 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 removed outlier: 3.990A pdb=" N LEU C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 removed outlier: 4.003A pdb=" N THR C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 129 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 removed outlier: 3.699A pdb=" N LYS C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 160 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 4.051A pdb=" N VAL C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.801A pdb=" N ILE C 179 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 removed outlier: 3.851A pdb=" N ARG C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG C 203 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.821A pdb=" N LYS C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.640A pdb=" N HIS C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 removed outlier: 3.703A pdb=" N GLY C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 302 through 313 removed outlier: 3.643A pdb=" N ASN C 313 " --> pdb=" O TYR C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.755A pdb=" N TYR C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 328 " --> pdb=" O MET C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 352 removed outlier: 4.056A pdb=" N TYR C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 352 " --> pdb=" O TYR C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 377 removed outlier: 3.527A pdb=" N ARG C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS C 369 " --> pdb=" O HIS C 365 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 403 removed outlier: 3.515A pdb=" N ARG C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 401 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 420 removed outlier: 3.963A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.994A pdb=" N VAL C 478 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE C 480 " --> pdb=" O ILE C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 510 removed outlier: 3.855A pdb=" N GLU C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 508 " --> pdb=" O PHE C 504 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 529 removed outlier: 3.544A pdb=" N GLY C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 3.676A pdb=" N ILE D 59 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 64 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.927A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 91 through 106 removed outlier: 3.602A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.503A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.631A pdb=" N LEU D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.737A pdb=" N ASN D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.504A pdb=" N TRP D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.851A pdb=" N GLY D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 216 removed outlier: 3.932A pdb=" N ASN D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 252 removed outlier: 4.033A pdb=" N THR D 242 " --> pdb=" O MET D 238 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET D 244 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 281 removed outlier: 3.892A pdb=" N LEU D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE D 276 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 277 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.688A pdb=" N MET D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 316 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 336 removed outlier: 4.241A pdb=" N MET D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 348 Processing helix chain 'D' and resid 351 through 359 removed outlier: 3.629A pdb=" N ARG D 355 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 359 " --> pdb=" O ARG D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.614A pdb=" N TYR D 364 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 467 through 477 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.108A pdb=" N MET D 485 " --> pdb=" O GLY D 481 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 508 removed outlier: 3.538A pdb=" N LEU D 504 " --> pdb=" O MET D 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.957A pdb=" N TYR A 141 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.657A pdb=" N VAL A 496 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 494 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 473 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 432 through 434 removed outlier: 6.752A pdb=" N GLU A 432 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A 490 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 434 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 393 removed outlier: 3.686A pdb=" N LYS B 389 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 393 " --> pdb=" O CYS B 460 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS B 460 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 465 " --> pdb=" O PHE B 409 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 409 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 431 through 434 removed outlier: 3.701A pdb=" N ARG B 431 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.516A pdb=" N TYR C 141 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 432 through 434 removed outlier: 7.033A pdb=" N GLU C 432 " --> pdb=" O THR C 490 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 490 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 434 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 472 through 473 removed outlier: 3.511A pdb=" N TYR C 444 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 389 through 393 removed outlier: 3.663A pdb=" N LYS D 389 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET D 465 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 409 " --> pdb=" O MET D 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 398 through 400 removed outlier: 6.717A pdb=" N VAL D 454 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 455 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 418 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 417 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP D 421 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE D 429 " --> pdb=" O ASP D 421 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4724 1.34 - 1.46: 2561 1.46 - 1.57: 7987 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 15406 Sorted by residual: bond pdb=" CA ILE C 183 " pdb=" CB ILE C 183 " ideal model delta sigma weight residual 1.545 1.531 0.014 1.05e-02 9.07e+03 1.77e+00 bond pdb=" N GLN C 421 " pdb=" CA GLN C 421 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.37e+00 bond pdb=" CA GLY C 185 " pdb=" C GLY C 185 " ideal model delta sigma weight residual 1.516 1.527 -0.011 1.07e-02 8.73e+03 1.04e+00 bond pdb=" CA VAL D 254 " pdb=" CB VAL D 254 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.34e-02 5.57e+03 1.04e+00 bond pdb=" N LYS A 112 " pdb=" CA LYS A 112 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.77e-02 3.19e+03 1.03e+00 ... (remaining 15401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 20443 1.63 - 3.26: 392 3.26 - 4.89: 50 4.89 - 6.52: 18 6.52 - 8.15: 5 Bond angle restraints: 20908 Sorted by residual: angle pdb=" C GLU A 111 " pdb=" N LYS A 112 " pdb=" CA LYS A 112 " ideal model delta sigma weight residual 125.66 133.14 -7.48 1.85e+00 2.92e-01 1.64e+01 angle pdb=" C SER A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta sigma weight residual 120.58 125.83 -5.25 1.32e+00 5.74e-01 1.58e+01 angle pdb=" C ASN C 71 " pdb=" N PRO C 72 " pdb=" CA PRO C 72 " ideal model delta sigma weight residual 121.65 117.74 3.91 1.01e+00 9.80e-01 1.50e+01 angle pdb=" N ILE C 260 " pdb=" CA ILE C 260 " pdb=" C ILE C 260 " ideal model delta sigma weight residual 112.96 109.41 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N VAL A 419 " pdb=" CA VAL A 419 " pdb=" C VAL A 419 " ideal model delta sigma weight residual 112.98 109.31 3.67 1.25e+00 6.40e-01 8.63e+00 ... (remaining 20903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8132 17.89 - 35.78: 781 35.78 - 53.67: 135 53.67 - 71.57: 18 71.57 - 89.46: 16 Dihedral angle restraints: 9082 sinusoidal: 3594 harmonic: 5488 Sorted by residual: dihedral pdb=" CA ASP A 442 " pdb=" C ASP A 442 " pdb=" N PHE A 443 " pdb=" CA PHE A 443 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA SER A 74 " pdb=" C SER A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR A 180 " pdb=" C TYR A 180 " pdb=" N LYS A 181 " pdb=" CA LYS A 181 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1683 0.040 - 0.081: 543 0.081 - 0.121: 119 0.121 - 0.162: 25 0.162 - 0.202: 2 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA ASN C 71 " pdb=" N ASN C 71 " pdb=" C ASN C 71 " pdb=" CB ASN C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE D 429 " pdb=" CA ILE D 429 " pdb=" CG1 ILE D 429 " pdb=" CG2 ILE D 429 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA SER B 75 " pdb=" N SER B 75 " pdb=" C SER B 75 " pdb=" CB SER B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2369 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 86 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 87 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 482 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO C 483 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 483 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 483 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 385 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " 0.026 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 999 2.74 - 3.34: 16824 3.34 - 3.94: 24809 3.94 - 4.54: 32636 4.54 - 5.14: 50962 Nonbonded interactions: 126230 Sorted by model distance: nonbonded pdb=" OE2 GLU D 78 " pdb=" OH TYR D 157 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR B 70 " pdb=" OG1 THR B 92 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR D 70 " pdb=" OG1 THR D 92 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP C 442 " pdb=" NH2 ARG C 498 " model vdw 2.271 3.120 nonbonded pdb=" O GLN D 343 " pdb=" OG1 THR D 346 " model vdw 2.274 3.040 ... (remaining 126225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 54 through 529) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 54 through 509) selection = chain 'D' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.000 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.003 0.038 15406 Z= 0.183 Angle : 0.581 8.154 20908 Z= 0.323 Chirality : 0.042 0.202 2372 Planarity : 0.004 0.051 2618 Dihedral : 14.567 89.456 5534 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -1.36 (0.19), residues: 1856 helix: -0.48 (0.17), residues: 962 sheet: -0.62 (0.57), residues: 92 loop : -1.34 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 237 HIS 0.006 0.001 HIS B 491 PHE 0.014 0.001 PHE D 99 TYR 0.025 0.001 TYR C 319 ARG 0.006 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: B 387 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7646 (tt0) REVERT: B 402 GLN cc_start: 0.5512 (mm110) cc_final: 0.4996 (mm-40) REVERT: C 475 GLU cc_start: 0.7108 (tp30) cc_final: 0.6837 (tp30) REVERT: D 166 TRP cc_start: 0.7371 (t-100) cc_final: 0.7098 (t-100) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3053 time to fit residues: 88.0536 Evaluate side-chains 165 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.0030 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 294 HIS D 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15406 Z= 0.288 Angle : 0.608 8.847 20908 Z= 0.327 Chirality : 0.044 0.212 2372 Planarity : 0.004 0.048 2618 Dihedral : 4.621 20.377 2050 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.25 % Allowed : 8.29 % Favored : 90.46 % 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: -1.33 (0.19), residues: 1856 helix: -0.39 (0.17), residues: 978 sheet: -0.34 (0.52), residues: 104 loop : -1.50 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 102 HIS 0.006 0.001 HIS B 203 PHE 0.028 0.001 PHE A 66 TYR 0.020 0.002 TYR A 292 ARG 0.004 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: C 475 GLU cc_start: 0.7119 (tp30) cc_final: 0.6841 (tp30) REVERT: D 166 TRP cc_start: 0.7407 (t-100) cc_final: 0.7120 (t-100) outliers start: 20 outliers final: 16 residues processed: 187 average time/residue: 0.3556 time to fit residues: 97.7912 Evaluate side-chains 179 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 379 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 15406 Z= 0.511 Angle : 0.732 9.546 20908 Z= 0.395 Chirality : 0.050 0.220 2372 Planarity : 0.005 0.052 2618 Dihedral : 5.088 22.356 2050 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.24 % Allowed : 11.72 % Favored : 86.03 % 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: -1.80 (0.19), residues: 1856 helix: -0.78 (0.16), residues: 974 sheet: -0.59 (0.52), residues: 106 loop : -1.72 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 102 HIS 0.008 0.002 HIS A 239 PHE 0.028 0.002 PHE A 66 TYR 0.026 0.002 TYR A 292 ARG 0.004 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 1.929 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7913 (t70) cc_final: 0.7607 (t0) REVERT: B 168 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7848 (mp) REVERT: D 166 TRP cc_start: 0.7466 (t-100) cc_final: 0.7230 (t-100) outliers start: 36 outliers final: 27 residues processed: 191 average time/residue: 0.3079 time to fit residues: 86.6595 Evaluate side-chains 195 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 379 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 0.0170 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15406 Z= 0.141 Angle : 0.510 8.886 20908 Z= 0.274 Chirality : 0.040 0.188 2372 Planarity : 0.004 0.046 2618 Dihedral : 4.386 17.714 2050 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % Favored : 84.48 % 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: -1.20 (0.19), residues: 1856 helix: -0.25 (0.17), residues: 992 sheet: -0.58 (0.51), residues: 106 loop : -1.47 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.002 0.001 HIS D 260 PHE 0.023 0.001 PHE A 66 TYR 0.014 0.001 TYR B 210 ARG 0.006 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 518 MET cc_start: 0.7370 (mmm) cc_final: 0.6890 (mtp) REVERT: C 155 LEU cc_start: 0.7513 (mt) cc_final: 0.7267 (mt) REVERT: C 475 GLU cc_start: 0.7111 (tp30) cc_final: 0.6803 (tp30) REVERT: D 166 TRP cc_start: 0.7337 (t-100) cc_final: 0.7096 (t-100) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.3100 time to fit residues: 84.9037 Evaluate side-chains 187 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 379 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 73 optimal weight: 0.0370 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 159 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: