Starting phenix.real_space_refine on Thu Sep 18 07:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_33467.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_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/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_33467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_33467.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_33467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuf_33467/09_2025/7xuf_33467.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'HIS:plan': 1, 'TYR:plan': 1} 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: {'ASP:plan': 6, 'HIS:plan': 1, 'TYR:plan': 1} 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: 3.67, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 681.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.62 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: 2.11 Time building geometry restraints manager: 1.65 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: 1.510 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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= 0.138 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG B 182 TYR 0.025 0.001 TYR C 319 PHE 0.014 0.001 PHE D 99 TRP 0.017 0.001 TRP A 237 HIS 0.006 0.001 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00282 (15406) covalent geometry : angle 0.58128 (20908) hydrogen bonds : bond 0.19534 ( 579) hydrogen bonds : angle 5.53069 ( 1668) *********************** 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 to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.544 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: 0.1257 time to fit residues: 36.8028 Evaluate side-chains 165 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.229653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177114 restraints weight = 16766.616| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.91 r_work: 0.3276 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15406 Z= 0.254 Angle : 0.678 9.215 20908 Z= 0.365 Chirality : 0.048 0.213 2372 Planarity : 0.005 0.050 2618 Dihedral : 4.844 21.612 2050 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.43 % Allowed : 9.10 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.19), residues: 1856 helix: -0.62 (0.16), residues: 982 sheet: -0.44 (0.53), residues: 104 loop : -1.61 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.024 0.002 TYR A 292 PHE 0.028 0.002 PHE A 66 TRP 0.020 0.002 TRP C 102 HIS 0.007 0.001 HIS D 203 Details of bonding type rmsd covalent geometry : bond 0.00620 (15406) covalent geometry : angle 0.67788 (20908) hydrogen bonds : bond 0.09099 ( 579) hydrogen bonds : angle 4.52454 ( 1668) *********************** 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 to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.589 Fit side-chains REVERT: A 122 ASP cc_start: 0.7832 (t70) cc_final: 0.7357 (t0) REVERT: C 408 LYS cc_start: 0.6717 (mttm) cc_final: 0.5370 (mtmm) REVERT: C 475 GLU cc_start: 0.7092 (tp30) cc_final: 0.6781 (tp30) REVERT: D 123 ASP cc_start: 0.5328 (t0) cc_final: 0.4514 (p0) REVERT: D 166 TRP cc_start: 0.7627 (t-100) cc_final: 0.7248 (t-100) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.1340 time to fit residues: 36.5821 Evaluate side-chains 182 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 B residue 92 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 293 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 304 ASP 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 93 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.236807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.180796 restraints weight = 17232.291| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.88 r_work: 0.3411 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15406 Z= 0.105 Angle : 0.504 8.779 20908 Z= 0.272 Chirality : 0.040 0.199 2372 Planarity : 0.004 0.044 2618 Dihedral : 4.327 18.148 2050 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.25 % Allowed : 11.85 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.20), residues: 1856 helix: -0.13 (0.17), residues: 972 sheet: -0.37 (0.52), residues: 104 loop : -1.43 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.014 0.001 TYR B 210 PHE 0.027 0.001 PHE A 66 TRP 0.015 0.001 TRP A 247 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00207 (15406) covalent geometry : angle 0.50412 (20908) hydrogen bonds : bond 0.04944 ( 579) hydrogen bonds : angle 3.94673 ( 1668) *********************** 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 205 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7490 (m110) REVERT: B 168 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 182 ARG cc_start: 0.6627 (mmm160) cc_final: 0.6205 (mmm160) REVERT: C 475 GLU cc_start: 0.7025 (tp30) cc_final: 0.6714 (tp30) REVERT: C 524 MET cc_start: 0.7440 (mmt) cc_final: 0.7132 (mmm) REVERT: D 166 TRP cc_start: 0.7476 (t-100) cc_final: 0.7090 (t-100) REVERT: D 485 MET cc_start: 0.6796 (mtm) cc_final: 0.6523 (mmm) outliers start: 20 outliers final: 10 residues processed: 193 average time/residue: 0.1356 time to fit residues: 38.2497 Evaluate side-chains 184 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 433 VAL 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 381 LEU 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 182 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.232561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177490 restraints weight = 16897.316| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.90 r_work: 0.3325 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15406 Z= 0.158 Angle : 0.549 8.983 20908 Z= 0.295 Chirality : 0.043 0.190 2372 Planarity : 0.004 0.046 2618 Dihedral : 4.349 18.311 2050 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.00 % Allowed : 12.41 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.19), residues: 1856 helix: -0.15 (0.17), residues: 972 sheet: -0.48 (0.52), residues: 106 loop : -1.47 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.020 0.002 TYR A 292 PHE 0.023 0.001 PHE A 66 TRP 0.013 0.001 TRP C 102 HIS 0.005 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00371 (15406) covalent geometry : angle 0.54933 (20908) hydrogen bonds : bond 0.06717 ( 579) hydrogen bonds : angle 3.94884 ( 1668) *********************** 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 to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 427 PHE cc_start: 0.8231 (m-80) cc_final: 0.7835 (m-80) REVERT: B 168 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7487 (mp) REVERT: C 475 GLU cc_start: 0.7076 (tp30) cc_final: 0.6784 (tp30) REVERT: C 524 MET cc_start: 0.7449 (mmt) cc_final: 0.7138 (mmm) REVERT: D 166 TRP cc_start: 0.7514 (t-100) cc_final: 0.7145 (t-100) REVERT: D 485 MET cc_start: 0.6816 (mtm) cc_final: 0.6542 (mmm) outliers start: 32 outliers final: 23 residues processed: 191 average time/residue: 0.1241 time to fit residues: 35.3272 Evaluate side-chains 191 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 71 THR 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 168 LEU Chi-restraints excluded: chain B residue 249 THR 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 B residue 495 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 142 LEU Chi-restraints excluded: chain C residue 381 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.227957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174420 restraints weight = 16914.423| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.86 r_work: 0.3260 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15406 Z= 0.282 Angle : 0.675 8.236 20908 Z= 0.364 Chirality : 0.048 0.194 2372 Planarity : 0.005 0.051 2618 Dihedral : 4.800 21.565 2050 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.31 % Allowed : 13.97 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.19), residues: 1856 helix: -0.50 (0.17), residues: 972 sheet: -0.54 (0.51), residues: 106 loop : -1.61 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.024 0.002 TYR A 292 PHE 0.023 0.002 PHE C 106 TRP 0.015 0.002 TRP C 102 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00691 (15406) covalent geometry : angle 0.67545 (20908) hydrogen bonds : bond 0.09341 ( 579) hydrogen bonds : angle 4.28525 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 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 205 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7868 (t70) cc_final: 0.7388 (t0) REVERT: A 518 MET cc_start: 0.7768 (mmm) cc_final: 0.6944 (mtp) REVERT: B 168 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7755 (mp) REVERT: C 475 GLU cc_start: 0.7262 (tp30) cc_final: 0.6833 (tp30) REVERT: D 123 ASP cc_start: 0.5169 (t0) cc_final: 0.4477 (p0) REVERT: D 166 TRP cc_start: 0.7642 (t-100) cc_final: 0.7316 (t-100) REVERT: D 485 MET cc_start: 0.6887 (mtm) cc_final: 0.6634 (mmm) outliers start: 37 outliers final: 28 residues processed: 190 average time/residue: 0.1279 time to fit residues: 36.4626 Evaluate side-chains 193 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 442 ASP 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 433 VAL Chi-restraints excluded: chain B residue 444 VAL 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 94 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.233513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173683 restraints weight = 17319.073| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.37 r_work: 0.3227 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15406 Z= 0.103 Angle : 0.509 8.971 20908 Z= 0.272 Chirality : 0.040 0.174 2372 Planarity : 0.004 0.046 2618 Dihedral : 4.244 16.977 2050 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.43 % Allowed : 15.84 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.20), residues: 1856 helix: 0.02 (0.17), residues: 964 sheet: -0.12 (0.55), residues: 86 loop : -1.46 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.014 0.001 TYR B 210 PHE 0.018 0.001 PHE A 178 TRP 0.017 0.001 TRP A 247 HIS 0.003 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00206 (15406) covalent geometry : angle 0.50893 (20908) hydrogen bonds : bond 0.04893 ( 579) hydrogen bonds : angle 3.78622 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 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 199 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.607 Fit side-chains REVERT: A 245 LEU cc_start: 0.8205 (tp) cc_final: 0.7972 (tp) REVERT: A 518 MET cc_start: 0.7663 (mmm) cc_final: 0.6806 (mtp) REVERT: B 168 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7278 (mp) REVERT: B 495 MET cc_start: 0.6266 (tmm) cc_final: 0.5314 (ptp) REVERT: C 475 GLU cc_start: 0.6961 (tp30) cc_final: 0.6465 (tp30) REVERT: C 524 MET cc_start: 0.7475 (mmt) cc_final: 0.7189 (mmm) REVERT: D 123 ASP cc_start: 0.4815 (t0) cc_final: 0.4098 (p0) REVERT: D 166 TRP cc_start: 0.7377 (t-100) cc_final: 0.7005 (t-100) REVERT: D 485 MET cc_start: 0.6871 (mtm) cc_final: 0.6623 (mmm) outliers start: 23 outliers final: 17 residues processed: 186 average time/residue: 0.1455 time to fit residues: 39.7906 Evaluate side-chains 187 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 442 ASP 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 433 VAL 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 C residue 451 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 164 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 154 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.229383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171218 restraints weight = 17109.198| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.51 r_work: 0.3138 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15406 Z= 0.173 Angle : 0.567 8.474 20908 Z= 0.302 Chirality : 0.043 0.170 2372 Planarity : 0.004 0.048 2618 Dihedral : 4.356 18.594 2050 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.93 % Allowed : 16.02 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.19), residues: 1856 helix: -0.13 (0.17), residues: 974 sheet: -0.55 (0.50), residues: 106 loop : -1.46 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 353 TYR 0.021 0.002 TYR A 292 PHE 0.023 0.001 PHE A 178 TRP 0.011 0.002 TRP C 102 HIS 0.005 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00411 (15406) covalent geometry : angle 0.56668 (20908) hydrogen bonds : bond 0.06961 ( 579) hydrogen bonds : angle 3.88073 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 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 203 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.618 Fit side-chains REVERT: A 152 ASP cc_start: 0.6515 (t0) cc_final: 0.6158 (t0) REVERT: A 518 MET cc_start: 0.7677 (mmm) cc_final: 0.6812 (mtp) REVERT: B 168 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 495 MET cc_start: 0.6361 (tmm) cc_final: 0.5306 (ptp) REVERT: C 475 GLU cc_start: 0.7056 (tp30) cc_final: 0.6598 (tp30) REVERT: C 524 MET cc_start: 0.7528 (mmt) cc_final: 0.7239 (mmm) REVERT: D 123 ASP cc_start: 0.4872 (t0) cc_final: 0.4152 (p0) REVERT: D 166 TRP cc_start: 0.7444 (t-100) cc_final: 0.7090 (t-100) REVERT: D 485 MET cc_start: 0.6849 (mtm) cc_final: 0.6633 (mmm) outliers start: 31 outliers final: 28 residues processed: 189 average time/residue: 0.1403 time to fit residues: 39.0949 Evaluate side-chains 194 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 68 VAL 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 433 VAL Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 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 227 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 451 VAL 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 Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 40 optimal weight: 0.0070 chunk 126 optimal weight: 0.0000 chunk 101 optimal weight: 0.0000 chunk 153 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.1164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.236423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173718 restraints weight = 17434.523| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.21 r_work: 0.3311 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15406 Z= 0.097 Angle : 0.492 8.873 20908 Z= 0.260 Chirality : 0.039 0.166 2372 Planarity : 0.004 0.048 2618 Dihedral : 3.995 16.387 2050 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.12 % Allowed : 16.83 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1856 helix: 0.32 (0.17), residues: 960 sheet: 0.09 (0.58), residues: 80 loop : -1.35 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 353 TYR 0.014 0.001 TYR B 210 PHE 0.021 0.001 PHE A 178 TRP 0.019 0.001 TRP A 237 HIS 0.003 0.000 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00194 (15406) covalent geometry : angle 0.49228 (20908) hydrogen bonds : bond 0.03778 ( 579) hydrogen bonds : angle 3.56317 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 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 to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.635 Fit side-chains REVERT: A 111 GLU cc_start: 0.8617 (tt0) cc_final: 0.8353 (tp30) REVERT: A 152 ASP cc_start: 0.6261 (t0) cc_final: 0.5938 (t0) REVERT: A 427 PHE cc_start: 0.7956 (m-80) cc_final: 0.7493 (m-80) REVERT: A 518 MET cc_start: 0.7646 (mmm) cc_final: 0.6773 (mtp) REVERT: B 495 MET cc_start: 0.6159 (tmm) cc_final: 0.5214 (ptp) REVERT: C 475 GLU cc_start: 0.6908 (tp30) cc_final: 0.6429 (tp30) REVERT: C 524 MET cc_start: 0.7504 (mmt) cc_final: 0.7223 (mmm) REVERT: D 123 ASP cc_start: 0.4890 (t0) cc_final: 0.4163 (p0) REVERT: D 166 TRP cc_start: 0.7316 (t-100) cc_final: 0.6956 (t-100) REVERT: D 485 MET cc_start: 0.6932 (mtm) cc_final: 0.6730 (mmm) outliers start: 18 outliers final: 16 residues processed: 192 average time/residue: 0.1342 time to fit residues: 38.0736 Evaluate side-chains 197 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 381 LEU 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 Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 168 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.231326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172308 restraints weight = 17222.970| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.50 r_work: 0.3162 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15406 Z= 0.143 Angle : 0.534 9.795 20908 Z= 0.284 Chirality : 0.042 0.166 2372 Planarity : 0.004 0.048 2618 Dihedral : 4.084 17.149 2050 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.18 % Allowed : 17.21 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1856 helix: 0.18 (0.17), residues: 974 sheet: 0.17 (0.58), residues: 80 loop : -1.38 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 353 TYR 0.021 0.001 TYR A 292 PHE 0.024 0.001 PHE A 178 TRP 0.010 0.001 TRP A 282 HIS 0.006 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00335 (15406) covalent geometry : angle 0.53441 (20908) hydrogen bonds : bond 0.06045 ( 579) hydrogen bonds : angle 3.65476 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 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 193 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 152 ASP cc_start: 0.6433 (t0) cc_final: 0.6084 (t0) REVERT: A 427 PHE cc_start: 0.7958 (m-80) cc_final: 0.7491 (m-80) REVERT: B 168 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7202 (mp) REVERT: B 495 MET cc_start: 0.6221 (tmm) cc_final: 0.5294 (ptp) REVERT: C 475 GLU cc_start: 0.6995 (tp30) cc_final: 0.6517 (tp30) REVERT: C 524 MET cc_start: 0.7532 (mmt) cc_final: 0.7247 (mmm) REVERT: D 150 MET cc_start: 0.4659 (mmm) cc_final: 0.4350 (mmm) REVERT: D 157 TYR cc_start: 0.7383 (t80) cc_final: 0.7162 (t80) REVERT: D 166 TRP cc_start: 0.7384 (t-100) cc_final: 0.7031 (t-100) outliers start: 19 outliers final: 16 residues processed: 183 average time/residue: 0.1327 time to fit residues: 35.9296 Evaluate side-chains 194 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 442 ASP 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 433 VAL Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 381 LEU 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 Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 104 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 138 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 41 optimal weight: 6.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.232156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173215 restraints weight = 17197.199| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.30 r_work: 0.3203 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15406 Z= 0.125 Angle : 0.528 9.943 20908 Z= 0.278 Chirality : 0.041 0.168 2372 Planarity : 0.004 0.048 2618 Dihedral : 4.064 16.640 2050 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.31 % Allowed : 17.46 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.20), residues: 1856 helix: 0.26 (0.17), residues: 972 sheet: 0.20 (0.58), residues: 80 loop : -1.41 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 353 TYR 0.018 0.001 TYR A 292 PHE 0.024 0.001 PHE A 178 TRP 0.011 0.001 TRP A 237 HIS 0.004 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00283 (15406) covalent geometry : angle 0.52841 (20908) hydrogen bonds : bond 0.05648 ( 579) hydrogen bonds : angle 3.61549 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 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 to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.608 Fit side-chains REVERT: A 152 ASP cc_start: 0.6474 (t0) cc_final: 0.6117 (t0) REVERT: A 427 PHE cc_start: 0.8041 (m-80) cc_final: 0.7575 (m-80) REVERT: A 518 MET cc_start: 0.7660 (mmm) cc_final: 0.6676 (mtp) REVERT: B 60 TRP cc_start: 0.6528 (OUTLIER) cc_final: 0.6088 (t60) REVERT: B 168 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 387 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7444 (tt0) REVERT: B 495 MET cc_start: 0.6155 (tmm) cc_final: 0.5292 (ptp) REVERT: C 475 GLU cc_start: 0.6997 (tp30) cc_final: 0.6521 (tp30) REVERT: C 524 MET cc_start: 0.7526 (mmt) cc_final: 0.7238 (mmm) REVERT: D 123 ASP cc_start: 0.4870 (t0) cc_final: 0.4188 (p0) REVERT: D 150 MET cc_start: 0.4706 (mmm) cc_final: 0.4415 (mmm) REVERT: D 157 TYR cc_start: 0.7420 (t80) cc_final: 0.7208 (t80) REVERT: D 166 TRP cc_start: 0.7415 (t-100) cc_final: 0.7072 (t-100) REVERT: D 485 MET cc_start: 0.7526 (mmm) cc_final: 0.7297 (mtm) outliers start: 21 outliers final: 17 residues processed: 186 average time/residue: 0.1346 time to fit residues: 37.1405 Evaluate side-chains 193 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain B residue 60 TRP 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 433 VAL Chi-restraints excluded: chain B residue 442 ILE 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 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 Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.234404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170982 restraints weight = 17199.118| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.12 r_work: 0.3259 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15406 Z= 0.103 Angle : 0.500 10.119 20908 Z= 0.262 Chirality : 0.040 0.173 2372 Planarity : 0.004 0.048 2618 Dihedral : 3.902 15.892 2050 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.25 % Allowed : 17.71 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.20), residues: 1856 helix: 0.39 (0.17), residues: 984 sheet: 0.25 (0.58), residues: 80 loop : -1.35 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 353 TYR 0.014 0.001 TYR A 292 PHE 0.023 0.001 PHE A 178 TRP 0.015 0.001 TRP A 237 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00223 (15406) covalent geometry : angle 0.50010 (20908) hydrogen bonds : bond 0.04656 ( 579) hydrogen bonds : angle 3.50268 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.93 seconds wall clock time: 75 minutes 24.32 seconds (4524.32 seconds total)