Starting phenix.real_space_refine on Thu Sep 26 17:45:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yae_10747/09_2024/6yae_10747.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.151 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8767 2.51 5 N 2336 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4737 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4578 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 552} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3192 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain breaks: 3 Chain: "S" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1200 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'TRANS': 141} Time building chain proxies: 7.71, per 1000 atoms: 0.56 Number of scatterers: 13707 At special positions: 0 Unit cell: (97.37, 109.14, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2532 8.00 N 2336 7.00 C 8767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 8 sheets defined 62.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.578A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.589A pdb=" N VAL A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.347A pdb=" N LYS A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.689A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.507A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.950A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.649A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.964A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.582A pdb=" N THR A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 removed outlier: 3.776A pdb=" N ARG A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 417 through 436 removed outlier: 3.757A pdb=" N ARG A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.318A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.670A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.508A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.718A pdb=" N GLN A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.550A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 4.199A pdb=" N GLN A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 62 through 78 removed outlier: 3.659A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.565A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.701A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.677A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.520A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.646A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.152A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 190 removed outlier: 3.569A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 removed outlier: 4.266A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 229 removed outlier: 3.966A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 251 through 266 removed outlier: 3.844A pdb=" N VAL B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 295 through 313 removed outlier: 4.002A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.363A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 4.029A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 Processing helix chain 'B' and resid 382 through 383 No H-bonds generated for 'chain 'B' and resid 382 through 383' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.654A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.512A pdb=" N CYS B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.923A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.593A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 removed outlier: 3.528A pdb=" N ASP B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 removed outlier: 4.536A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.347A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 575' Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.909A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL M 36 " --> pdb=" O PHE M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.595A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 129 Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 40 Processing helix chain 'S' and resid 77 through 95 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 removed outlier: 4.136A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 5.620A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER M 387 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL M 322 " --> pdb=" O SER M 387 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN M 389 " --> pdb=" O ILE M 320 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE M 320 " --> pdb=" O ASN M 389 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 263 through 265 Processing sheet with id=AA6, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.552A pdb=" N GLU M 371 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.488A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 118 through 119 789 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 3.60 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: 4482 1.34 - 1.46: 2500 1.46 - 1.57: 6858 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 13951 Sorted by residual: bond pdb=" CA ALA B 178 " pdb=" C ALA B 178 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.41e-02 5.03e+03 1.60e+01 bond pdb=" C ALA B 178 " pdb=" N ASN B 179 " ideal model delta sigma weight residual 1.332 1.289 0.043 1.35e-02 5.49e+03 1.01e+01 bond pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.07e+00 bond pdb=" CB TRP M 64 " pdb=" CG TRP M 64 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.87e+00 bond pdb=" C PRO A 604 " pdb=" N PHE A 605 " ideal model delta sigma weight residual 1.326 1.299 0.027 1.84e-02 2.95e+03 2.17e+00 ... (remaining 13946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 18686 2.95 - 5.91: 175 5.91 - 8.86: 23 8.86 - 11.82: 1 11.82 - 14.77: 1 Bond angle restraints: 18886 Sorted by residual: angle pdb=" C GLN A 488 " pdb=" N ALA A 489 " pdb=" CA ALA A 489 " ideal model delta sigma weight residual 120.69 105.92 14.77 2.95e+00 1.15e-01 2.51e+01 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.85e+01 angle pdb=" C VAL S 39 " pdb=" N THR S 40 " pdb=" CA THR S 40 " ideal model delta sigma weight residual 122.31 115.93 6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N HIS B 191 " pdb=" CA HIS B 191 " pdb=" C HIS B 191 " ideal model delta sigma weight residual 108.59 114.68 -6.09 1.96e+00 2.60e-01 9.64e+00 angle pdb=" C PHE S 49 " pdb=" N VAL S 50 " pdb=" CA VAL S 50 " ideal model delta sigma weight residual 123.14 119.23 3.91 1.31e+00 5.83e-01 8.89e+00 ... (remaining 18881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 7681 17.40 - 34.80: 748 34.80 - 52.20: 114 52.20 - 69.60: 22 69.60 - 86.99: 15 Dihedral angle restraints: 8580 sinusoidal: 3488 harmonic: 5092 Sorted by residual: dihedral pdb=" CA SER B 190 " pdb=" C SER B 190 " pdb=" N HIS B 191 " pdb=" CA HIS B 191 " ideal model delta harmonic sigma weight residual -180.00 -144.22 -35.78 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" CA HIS B 191 " pdb=" C HIS B 191 " pdb=" N PRO B 192 " pdb=" CA PRO B 192 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1232 0.034 - 0.068: 659 0.068 - 0.102: 233 0.102 - 0.137: 61 0.137 - 0.171: 13 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CA TRP A 462 " pdb=" N TRP A 462 " pdb=" C TRP A 462 " pdb=" CB TRP A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ASP A 474 " pdb=" N ASP A 474 " pdb=" C ASP A 474 " pdb=" CB ASP A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ILE M 263 " pdb=" N ILE M 263 " pdb=" C ILE M 263 " pdb=" CB ILE M 263 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2195 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 295 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 296 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE M 290 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ILE M 290 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE M 290 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO M 291 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 556 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 557 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 557 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 557 " -0.024 5.00e-02 4.00e+02 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 339 2.65 - 3.22: 14575 3.22 - 3.78: 20637 3.78 - 4.34: 27703 4.34 - 4.90: 44080 Nonbonded interactions: 107334 Sorted by model distance: nonbonded pdb=" OH TYR B 229 " pdb=" OE2 GLU B 236 " model vdw 2.093 3.040 nonbonded pdb=" O MET B 155 " pdb=" N ASP B 158 " model vdw 2.105 3.120 nonbonded pdb=" OG SER A 322 " pdb=" OE2 GLU A 323 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASP A 444 " pdb=" OH TYR A 478 " model vdw 2.127 3.040 nonbonded pdb=" O HIS A 369 " pdb=" OG1 THR A 372 " model vdw 2.146 3.040 ... (remaining 107329 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 30.480 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 13951 Z= 0.563 Angle : 0.820 14.773 18886 Z= 0.450 Chirality : 0.046 0.171 2198 Planarity : 0.004 0.045 2403 Dihedral : 14.185 86.995 5262 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.49 % Rotamer: Outliers : 0.13 % Allowed : 8.78 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.17), residues: 1703 helix: -1.83 (0.13), residues: 958 sheet: -1.48 (0.34), residues: 190 loop : -2.89 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 462 HIS 0.010 0.002 HIS S 85 PHE 0.026 0.002 PHE A 523 TYR 0.024 0.002 TYR B 524 ARG 0.009 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8457 (t0) cc_final: 0.8076 (t0) REVERT: A 77 MET cc_start: 0.8085 (tpp) cc_final: 0.7738 (tpp) REVERT: A 161 MET cc_start: 0.7078 (ttt) cc_final: 0.6607 (ttt) REVERT: A 162 ASP cc_start: 0.8466 (p0) cc_final: 0.8235 (p0) REVERT: A 396 MET cc_start: 0.9039 (ptt) cc_final: 0.8716 (ptp) REVERT: A 401 ASN cc_start: 0.8672 (t0) cc_final: 0.8334 (t0) REVERT: A 578 GLN cc_start: 0.8676 (tp40) cc_final: 0.8457 (tt0) REVERT: B 32 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 86 MET cc_start: 0.9175 (mtm) cc_final: 0.8607 (mpp) REVERT: B 297 GLU cc_start: 0.8389 (mp0) cc_final: 0.7982 (mp0) REVERT: B 322 LYS cc_start: 0.9368 (mttt) cc_final: 0.9118 (mttp) REVERT: B 330 ASP cc_start: 0.8540 (m-30) cc_final: 0.8281 (m-30) REVERT: B 366 ASP cc_start: 0.8272 (t0) cc_final: 0.7816 (t70) REVERT: B 385 GLU cc_start: 0.8159 (tt0) cc_final: 0.7801 (mm-30) REVERT: B 485 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 509 LEU cc_start: 0.9187 (tp) cc_final: 0.8742 (tp) REVERT: M 118 PHE cc_start: 0.8110 (t80) cc_final: 0.7410 (t80) REVERT: M 277 TYR cc_start: 0.8195 (p90) cc_final: 0.7257 (p90) REVERT: M 361 MET cc_start: 0.9007 (mmt) cc_final: 0.8660 (mmm) REVERT: S 74 ASN cc_start: 0.8727 (p0) cc_final: 0.8503 (p0) REVERT: S 93 GLU cc_start: 0.9147 (tp30) cc_final: 0.8576 (tm-30) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.2922 time to fit residues: 120.7245 Evaluate side-chains 209 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 320 HIS A 339 GLN A 344 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN B 195 ASN B 238 GLN B 252 ASN B 311 GLN B 575 HIS M 27 ASN M 35 ASN M 38 HIS M 72 ASN M 135 GLN M 188 GLN M 195 HIS M 310 ASN S 46 HIS S 48 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13951 Z= 0.193 Angle : 0.634 10.784 18886 Z= 0.332 Chirality : 0.043 0.230 2198 Planarity : 0.004 0.036 2403 Dihedral : 5.301 50.523 1870 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 1.97 % Allowed : 12.71 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1703 helix: 0.09 (0.16), residues: 954 sheet: -0.76 (0.36), residues: 191 loop : -2.05 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.006 0.001 HIS S 85 PHE 0.020 0.002 PHE B 492 TYR 0.017 0.001 TYR A 583 ARG 0.005 0.001 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 290 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8539 (t0) cc_final: 0.8239 (t0) REVERT: A 71 ASP cc_start: 0.8136 (t0) cc_final: 0.7864 (t0) REVERT: A 77 MET cc_start: 0.7981 (tpp) cc_final: 0.7720 (tpp) REVERT: A 92 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8420 (tp-100) REVERT: A 142 GLU cc_start: 0.8935 (mp0) cc_final: 0.8658 (mp0) REVERT: A 341 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7555 (ttm170) REVERT: A 372 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8559 (t) REVERT: A 396 MET cc_start: 0.8936 (ptt) cc_final: 0.8671 (ptp) REVERT: A 401 ASN cc_start: 0.8509 (t0) cc_final: 0.8254 (t0) REVERT: A 492 CYS cc_start: 0.7650 (t) cc_final: 0.7433 (t) REVERT: B 110 MET cc_start: 0.8448 (mtm) cc_final: 0.8166 (ptp) REVERT: B 330 ASP cc_start: 0.8340 (m-30) cc_final: 0.8058 (m-30) REVERT: B 385 GLU cc_start: 0.7911 (tt0) cc_final: 0.7489 (tm-30) REVERT: B 406 VAL cc_start: 0.9374 (t) cc_final: 0.9170 (p) REVERT: B 441 GLU cc_start: 0.7694 (mp0) cc_final: 0.7489 (mp0) REVERT: B 448 MET cc_start: 0.8656 (tpt) cc_final: 0.8170 (tpt) REVERT: B 509 LEU cc_start: 0.9057 (tp) cc_final: 0.8553 (tp) REVERT: B 524 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: B 536 THR cc_start: 0.8871 (p) cc_final: 0.8639 (t) REVERT: M 35 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8321 (t0) REVERT: M 41 GLN cc_start: 0.8310 (mp10) cc_final: 0.8082 (mp10) REVERT: M 118 PHE cc_start: 0.7949 (t80) cc_final: 0.7736 (t80) REVERT: M 277 TYR cc_start: 0.8473 (p90) cc_final: 0.7779 (p90) REVERT: S 15 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8483 (mmt90) REVERT: S 74 ASN cc_start: 0.9016 (p0) cc_final: 0.8738 (p0) REVERT: S 93 GLU cc_start: 0.9102 (tp30) cc_final: 0.8828 (tm-30) REVERT: S 112 THR cc_start: 0.8987 (m) cc_final: 0.8716 (p) outliers start: 30 outliers final: 11 residues processed: 304 average time/residue: 0.2498 time to fit residues: 111.2747 Evaluate side-chains 249 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.0000 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 566 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13951 Z= 0.173 Angle : 0.588 10.892 18886 Z= 0.307 Chirality : 0.042 0.243 2198 Planarity : 0.004 0.082 2403 Dihedral : 4.950 32.317 1868 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 2.23 % Allowed : 15.53 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1703 helix: 0.59 (0.16), residues: 971 sheet: -0.48 (0.36), residues: 193 loop : -1.71 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.005 0.001 HIS S 85 PHE 0.015 0.001 PHE S 87 TYR 0.030 0.001 TYR A 583 ARG 0.003 0.000 ARG S 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8549 (t0) cc_final: 0.8253 (t0) REVERT: A 71 ASP cc_start: 0.8205 (t0) cc_final: 0.7868 (t0) REVERT: A 77 MET cc_start: 0.7950 (tpp) cc_final: 0.7632 (tpp) REVERT: A 142 GLU cc_start: 0.8844 (mp0) cc_final: 0.8604 (mp0) REVERT: A 323 GLU cc_start: 0.8750 (mp0) cc_final: 0.8546 (mp0) REVERT: A 372 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8580 (t) REVERT: A 396 MET cc_start: 0.8892 (ptt) cc_final: 0.8612 (ptp) REVERT: A 401 ASN cc_start: 0.8498 (t0) cc_final: 0.8250 (t0) REVERT: A 427 LYS cc_start: 0.9383 (mttt) cc_final: 0.8934 (mttm) REVERT: B 74 MET cc_start: 0.8963 (mmt) cc_final: 0.8511 (mmm) REVERT: B 330 ASP cc_start: 0.8343 (m-30) cc_final: 0.8099 (m-30) REVERT: B 385 GLU cc_start: 0.7935 (tt0) cc_final: 0.7522 (tm-30) REVERT: B 448 MET cc_start: 0.8672 (tpt) cc_final: 0.8470 (tpt) REVERT: B 536 THR cc_start: 0.8904 (p) cc_final: 0.8656 (t) REVERT: M 41 GLN cc_start: 0.8240 (mp10) cc_final: 0.7936 (mp10) REVERT: M 277 TYR cc_start: 0.8403 (p90) cc_final: 0.7765 (p90) REVERT: S 89 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8413 (mm-30) REVERT: S 93 GLU cc_start: 0.9055 (tp30) cc_final: 0.8767 (tm-30) outliers start: 34 outliers final: 18 residues processed: 301 average time/residue: 0.2500 time to fit residues: 110.7948 Evaluate side-chains 259 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN B 24 ASN B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13951 Z= 0.198 Angle : 0.578 11.176 18886 Z= 0.303 Chirality : 0.042 0.260 2198 Planarity : 0.004 0.055 2403 Dihedral : 4.816 30.623 1868 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 3.28 % Allowed : 17.10 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1703 helix: 0.81 (0.17), residues: 975 sheet: -0.14 (0.37), residues: 188 loop : -1.51 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 PHE 0.018 0.001 PHE A 97 TYR 0.023 0.001 TYR A 247 ARG 0.003 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 258 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.7565 (mpp) cc_final: 0.7078 (mmt) REVERT: A 19 ASP cc_start: 0.8555 (t0) cc_final: 0.8285 (t0) REVERT: A 77 MET cc_start: 0.7990 (tpp) cc_final: 0.7723 (tpp) REVERT: A 372 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8582 (t) REVERT: A 396 MET cc_start: 0.8902 (ptt) cc_final: 0.8586 (ptm) REVERT: A 401 ASN cc_start: 0.8512 (t0) cc_final: 0.8279 (t0) REVERT: A 427 LYS cc_start: 0.9390 (mttt) cc_final: 0.9034 (mttm) REVERT: A 561 ASP cc_start: 0.7858 (t0) cc_final: 0.7557 (t70) REVERT: A 583 TYR cc_start: 0.8718 (m-80) cc_final: 0.8507 (m-80) REVERT: B 74 MET cc_start: 0.8958 (mmt) cc_final: 0.8508 (mmm) REVERT: B 330 ASP cc_start: 0.8370 (m-30) cc_final: 0.8103 (m-30) REVERT: B 385 GLU cc_start: 0.7780 (tt0) cc_final: 0.7448 (tm-30) REVERT: B 441 GLU cc_start: 0.7684 (mp0) cc_final: 0.7388 (mp0) REVERT: B 509 LEU cc_start: 0.9027 (tp) cc_final: 0.8650 (tp) REVERT: B 524 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: B 536 THR cc_start: 0.8931 (p) cc_final: 0.8640 (t) REVERT: M 41 GLN cc_start: 0.8250 (mp10) cc_final: 0.7892 (mp10) REVERT: M 277 TYR cc_start: 0.8384 (p90) cc_final: 0.7792 (p90) REVERT: S 60 ARG cc_start: 0.8561 (ttm170) cc_final: 0.8220 (ttm-80) REVERT: S 89 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8674 (mm-30) REVERT: S 93 GLU cc_start: 0.9015 (tp30) cc_final: 0.8694 (tp30) outliers start: 50 outliers final: 30 residues processed: 281 average time/residue: 0.2368 time to fit residues: 98.7536 Evaluate side-chains 271 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 488 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN M 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13951 Z= 0.200 Angle : 0.592 11.396 18886 Z= 0.306 Chirality : 0.042 0.274 2198 Planarity : 0.004 0.045 2403 Dihedral : 4.745 30.059 1868 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 3.21 % Allowed : 18.41 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1703 helix: 0.93 (0.17), residues: 974 sheet: 0.03 (0.37), residues: 188 loop : -1.37 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS A 527 PHE 0.025 0.001 PHE A 523 TYR 0.013 0.001 TYR B 405 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 261 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8558 (t0) cc_final: 0.8284 (t0) REVERT: A 77 MET cc_start: 0.7980 (tpp) cc_final: 0.7707 (tpp) REVERT: A 92 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8442 (tp-100) REVERT: A 372 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8593 (t) REVERT: A 396 MET cc_start: 0.8910 (ptt) cc_final: 0.8264 (ptm) REVERT: A 401 ASN cc_start: 0.8507 (t0) cc_final: 0.8265 (t0) REVERT: A 427 LYS cc_start: 0.9381 (mttt) cc_final: 0.9049 (mttm) REVERT: A 561 ASP cc_start: 0.7891 (t0) cc_final: 0.7613 (t70) REVERT: B 74 MET cc_start: 0.8872 (mmt) cc_final: 0.8442 (mmm) REVERT: B 83 MET cc_start: 0.9220 (mtp) cc_final: 0.8555 (mpp) REVERT: B 86 MET cc_start: 0.8820 (mtm) cc_final: 0.8272 (mpp) REVERT: B 330 ASP cc_start: 0.8370 (m-30) cc_final: 0.8144 (m-30) REVERT: B 385 GLU cc_start: 0.7805 (tt0) cc_final: 0.7467 (tm-30) REVERT: B 509 LEU cc_start: 0.9013 (tp) cc_final: 0.8657 (tp) REVERT: B 524 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: B 536 THR cc_start: 0.8929 (p) cc_final: 0.8643 (t) REVERT: M 41 GLN cc_start: 0.8277 (mp10) cc_final: 0.7973 (mp10) REVERT: M 277 TYR cc_start: 0.8374 (p90) cc_final: 0.7715 (p90) REVERT: S 13 LYS cc_start: 0.8996 (tttt) cc_final: 0.8475 (tttm) REVERT: S 60 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8189 (ttm-80) REVERT: S 89 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8663 (mm-30) REVERT: S 93 GLU cc_start: 0.8937 (tp30) cc_final: 0.8603 (tp30) outliers start: 49 outliers final: 32 residues processed: 283 average time/residue: 0.2404 time to fit residues: 102.0252 Evaluate side-chains 270 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.0370 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 488 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13951 Z= 0.184 Angle : 0.598 11.380 18886 Z= 0.306 Chirality : 0.042 0.239 2198 Planarity : 0.004 0.051 2403 Dihedral : 4.676 29.853 1868 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 3.28 % Allowed : 18.81 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1703 helix: 1.01 (0.17), residues: 981 sheet: 0.17 (0.38), residues: 189 loop : -1.31 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS A 527 PHE 0.023 0.001 PHE A 523 TYR 0.020 0.001 TYR A 583 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8569 (t0) cc_final: 0.8269 (t0) REVERT: A 77 MET cc_start: 0.7965 (tpp) cc_final: 0.7688 (tpp) REVERT: A 372 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8596 (t) REVERT: A 396 MET cc_start: 0.8890 (ptt) cc_final: 0.8265 (ptm) REVERT: A 401 ASN cc_start: 0.8457 (t0) cc_final: 0.8254 (t0) REVERT: A 427 LYS cc_start: 0.9391 (mttt) cc_final: 0.9088 (mttm) REVERT: A 533 CYS cc_start: 0.9308 (m) cc_final: 0.8888 (m) REVERT: A 561 ASP cc_start: 0.8070 (t0) cc_final: 0.7820 (t70) REVERT: A 583 TYR cc_start: 0.8772 (m-80) cc_final: 0.8569 (m-80) REVERT: B 74 MET cc_start: 0.8857 (mmt) cc_final: 0.8430 (mmm) REVERT: B 83 MET cc_start: 0.9209 (mtp) cc_final: 0.8529 (mpp) REVERT: B 86 MET cc_start: 0.8840 (mtm) cc_final: 0.8290 (mpp) REVERT: B 297 GLU cc_start: 0.8349 (mp0) cc_final: 0.7932 (mp0) REVERT: B 330 ASP cc_start: 0.8394 (m-30) cc_final: 0.8178 (m-30) REVERT: B 385 GLU cc_start: 0.7784 (tt0) cc_final: 0.7474 (tm-30) REVERT: B 448 MET cc_start: 0.8724 (tpt) cc_final: 0.8344 (tpt) REVERT: B 509 LEU cc_start: 0.8987 (tp) cc_final: 0.8641 (tp) REVERT: B 524 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: B 536 THR cc_start: 0.8928 (p) cc_final: 0.8637 (t) REVERT: M 26 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7021 (ptp90) REVERT: M 41 GLN cc_start: 0.8271 (mp10) cc_final: 0.7951 (mp10) REVERT: M 277 TYR cc_start: 0.8387 (p90) cc_final: 0.7809 (p90) REVERT: S 34 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8751 (mt-10) REVERT: S 53 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8112 (mtp85) REVERT: S 60 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8197 (ttm-80) REVERT: S 89 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8655 (mm-30) REVERT: S 93 GLU cc_start: 0.8934 (tp30) cc_final: 0.8598 (tp30) REVERT: S 104 VAL cc_start: 0.9205 (t) cc_final: 0.8945 (p) outliers start: 50 outliers final: 33 residues processed: 275 average time/residue: 0.2342 time to fit residues: 96.5352 Evaluate side-chains 277 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Chi-restraints excluded: chain S residue 138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 488 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13951 Z= 0.261 Angle : 0.619 11.235 18886 Z= 0.317 Chirality : 0.043 0.228 2198 Planarity : 0.004 0.084 2403 Dihedral : 4.690 30.111 1868 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 3.60 % Allowed : 19.72 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1703 helix: 1.00 (0.17), residues: 982 sheet: 0.21 (0.38), residues: 188 loop : -1.28 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 PHE 0.038 0.001 PHE A 523 TYR 0.018 0.001 TYR A 439 ARG 0.011 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7989 (tpp) cc_final: 0.7718 (tpp) REVERT: A 92 GLN cc_start: 0.8943 (tp40) cc_final: 0.8604 (tp40) REVERT: A 372 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8609 (t) REVERT: A 396 MET cc_start: 0.8923 (ptt) cc_final: 0.8251 (ptm) REVERT: A 401 ASN cc_start: 0.8541 (t0) cc_final: 0.8295 (t0) REVERT: A 427 LYS cc_start: 0.9401 (mttt) cc_final: 0.8994 (mttm) REVERT: A 533 CYS cc_start: 0.9303 (m) cc_final: 0.8780 (m) REVERT: A 561 ASP cc_start: 0.8126 (t0) cc_final: 0.7892 (t70) REVERT: B 74 MET cc_start: 0.8866 (mmt) cc_final: 0.8461 (mmm) REVERT: B 83 MET cc_start: 0.9219 (mtp) cc_final: 0.8532 (mpp) REVERT: B 86 MET cc_start: 0.8904 (mtm) cc_final: 0.8345 (mpp) REVERT: B 261 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8709 (tppt) REVERT: B 297 GLU cc_start: 0.8421 (mp0) cc_final: 0.7979 (mp0) REVERT: B 330 ASP cc_start: 0.8450 (m-30) cc_final: 0.8221 (m-30) REVERT: B 342 MET cc_start: 0.8241 (mtt) cc_final: 0.7978 (mtt) REVERT: B 385 GLU cc_start: 0.7855 (tt0) cc_final: 0.7509 (tm-30) REVERT: B 448 MET cc_start: 0.8741 (tpt) cc_final: 0.8350 (tpt) REVERT: B 509 LEU cc_start: 0.9022 (tp) cc_final: 0.8688 (tp) REVERT: B 524 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: B 536 THR cc_start: 0.8983 (p) cc_final: 0.8708 (t) REVERT: M 41 GLN cc_start: 0.8301 (mp10) cc_final: 0.7988 (mp10) REVERT: M 277 TYR cc_start: 0.8424 (p90) cc_final: 0.7792 (p90) REVERT: S 13 LYS cc_start: 0.8985 (tttt) cc_final: 0.8571 (tttm) REVERT: S 53 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8133 (mtp85) REVERT: S 60 ARG cc_start: 0.8629 (ttm170) cc_final: 0.8381 (ttm-80) REVERT: S 89 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8667 (mm-30) REVERT: S 93 GLU cc_start: 0.8998 (tp30) cc_final: 0.8653 (tp30) outliers start: 55 outliers final: 40 residues processed: 270 average time/residue: 0.2296 time to fit residues: 92.7079 Evaluate side-chains 275 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 232 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 169 ARG Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 24 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13951 Z= 0.176 Angle : 0.605 11.373 18886 Z= 0.308 Chirality : 0.042 0.237 2198 Planarity : 0.004 0.043 2403 Dihedral : 4.564 29.417 1868 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 2.69 % Allowed : 20.71 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1703 helix: 1.11 (0.17), residues: 982 sheet: 0.28 (0.38), residues: 189 loop : -1.14 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.005 0.001 HIS A 320 PHE 0.033 0.001 PHE A 523 TYR 0.016 0.001 TYR A 583 ARG 0.009 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 266 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.6319 (mtm-85) REVERT: A 77 MET cc_start: 0.7932 (tpp) cc_final: 0.7668 (tpp) REVERT: A 92 GLN cc_start: 0.8857 (tp40) cc_final: 0.8515 (tp40) REVERT: A 119 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: A 372 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8599 (t) REVERT: A 396 MET cc_start: 0.8846 (ptt) cc_final: 0.8242 (ptm) REVERT: A 401 ASN cc_start: 0.8449 (t0) cc_final: 0.8249 (t0) REVERT: A 427 LYS cc_start: 0.9377 (mttt) cc_final: 0.9039 (mttm) REVERT: A 533 CYS cc_start: 0.9248 (m) cc_final: 0.8737 (m) REVERT: B 83 MET cc_start: 0.9189 (mtp) cc_final: 0.8432 (mpp) REVERT: B 86 MET cc_start: 0.8869 (mtm) cc_final: 0.8376 (mpp) REVERT: B 297 GLU cc_start: 0.8346 (mp0) cc_final: 0.7889 (mp0) REVERT: B 385 GLU cc_start: 0.7901 (tt0) cc_final: 0.7525 (tm-30) REVERT: B 448 MET cc_start: 0.8748 (tpt) cc_final: 0.8393 (tpt) REVERT: B 508 SER cc_start: 0.9162 (m) cc_final: 0.8816 (p) REVERT: B 509 LEU cc_start: 0.8935 (tp) cc_final: 0.8669 (tp) REVERT: B 536 THR cc_start: 0.8957 (p) cc_final: 0.8679 (t) REVERT: M 41 GLN cc_start: 0.8255 (mp10) cc_final: 0.7959 (mp10) REVERT: M 277 TYR cc_start: 0.8399 (p90) cc_final: 0.7815 (p90) REVERT: S 13 LYS cc_start: 0.8978 (tttt) cc_final: 0.8554 (tttm) REVERT: S 53 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8087 (mtp85) REVERT: S 60 ARG cc_start: 0.8673 (ttm170) cc_final: 0.8361 (ttm-80) REVERT: S 89 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8660 (mm-30) REVERT: S 93 GLU cc_start: 0.8966 (tp30) cc_final: 0.8613 (tp30) REVERT: S 104 VAL cc_start: 0.9168 (t) cc_final: 0.8878 (p) outliers start: 41 outliers final: 29 residues processed: 289 average time/residue: 0.2399 time to fit residues: 102.8148 Evaluate side-chains 272 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13951 Z= 0.182 Angle : 0.642 13.528 18886 Z= 0.320 Chirality : 0.043 0.384 2198 Planarity : 0.004 0.042 2403 Dihedral : 4.516 29.294 1868 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 2.42 % Allowed : 21.95 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1703 helix: 1.08 (0.17), residues: 983 sheet: 0.32 (0.38), residues: 189 loop : -1.11 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.006 0.001 HIS A 200 PHE 0.028 0.001 PHE A 523 TYR 0.013 0.001 TYR B 405 ARG 0.008 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.6282 (mtm-85) REVERT: A 77 MET cc_start: 0.7898 (tpp) cc_final: 0.7587 (tpp) REVERT: A 92 GLN cc_start: 0.8827 (tp40) cc_final: 0.8527 (tp40) REVERT: A 119 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8361 (t70) REVERT: A 372 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (t) REVERT: A 396 MET cc_start: 0.8819 (ptt) cc_final: 0.8241 (ptm) REVERT: A 533 CYS cc_start: 0.9238 (m) cc_final: 0.8750 (m) REVERT: B 74 MET cc_start: 0.9168 (tpp) cc_final: 0.8943 (mmm) REVERT: B 83 MET cc_start: 0.8984 (mtp) cc_final: 0.8423 (mpp) REVERT: B 86 MET cc_start: 0.8864 (mtm) cc_final: 0.8388 (mpp) REVERT: B 297 GLU cc_start: 0.8345 (mp0) cc_final: 0.7892 (mp0) REVERT: B 342 MET cc_start: 0.8094 (mtt) cc_final: 0.7691 (mtt) REVERT: B 385 GLU cc_start: 0.7883 (tt0) cc_final: 0.7564 (tm-30) REVERT: B 448 MET cc_start: 0.8747 (tpt) cc_final: 0.8475 (tpt) REVERT: B 508 SER cc_start: 0.9145 (m) cc_final: 0.8799 (p) REVERT: B 509 LEU cc_start: 0.8939 (tp) cc_final: 0.8682 (tp) REVERT: B 536 THR cc_start: 0.8968 (p) cc_final: 0.8694 (t) REVERT: M 41 GLN cc_start: 0.8255 (mp10) cc_final: 0.7936 (mp10) REVERT: M 277 TYR cc_start: 0.8408 (p90) cc_final: 0.7819 (p90) REVERT: S 13 LYS cc_start: 0.8989 (tttt) cc_final: 0.8433 (tttm) REVERT: S 60 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8475 (ttm-80) REVERT: S 89 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8674 (mm-30) REVERT: S 93 GLU cc_start: 0.8950 (tp30) cc_final: 0.8510 (tp30) REVERT: S 104 VAL cc_start: 0.9204 (t) cc_final: 0.8887 (p) outliers start: 37 outliers final: 28 residues processed: 277 average time/residue: 0.2421 time to fit residues: 99.6852 Evaluate side-chains 271 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13951 Z= 0.193 Angle : 0.676 14.781 18886 Z= 0.331 Chirality : 0.043 0.315 2198 Planarity : 0.004 0.044 2403 Dihedral : 4.497 29.207 1868 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.29 % Allowed : 22.61 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1703 helix: 1.05 (0.17), residues: 984 sheet: 0.35 (0.38), residues: 189 loop : -1.12 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 PHE 0.029 0.001 PHE A 523 TYR 0.013 0.001 TYR M 120 ARG 0.010 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.6265 (mtm-85) REVERT: A 77 MET cc_start: 0.7894 (tpp) cc_final: 0.7582 (tpp) REVERT: A 92 GLN cc_start: 0.8801 (tp40) cc_final: 0.8499 (tp40) REVERT: A 119 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8334 (t70) REVERT: A 128 MET cc_start: 0.8496 (mmt) cc_final: 0.7951 (mmt) REVERT: A 372 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8567 (t) REVERT: A 396 MET cc_start: 0.8844 (ptt) cc_final: 0.8458 (ptm) REVERT: A 533 CYS cc_start: 0.9191 (m) cc_final: 0.8782 (m) REVERT: B 83 MET cc_start: 0.8960 (mtp) cc_final: 0.8429 (mpp) REVERT: B 86 MET cc_start: 0.8866 (mtm) cc_final: 0.8399 (mpp) REVERT: B 297 GLU cc_start: 0.8365 (mp0) cc_final: 0.7905 (mp0) REVERT: B 342 MET cc_start: 0.8242 (mtt) cc_final: 0.7848 (mtt) REVERT: B 385 GLU cc_start: 0.7897 (tt0) cc_final: 0.7571 (tm-30) REVERT: B 448 MET cc_start: 0.8675 (tpt) cc_final: 0.8303 (tpt) REVERT: B 508 SER cc_start: 0.9126 (m) cc_final: 0.8783 (p) REVERT: B 509 LEU cc_start: 0.8922 (tp) cc_final: 0.8660 (tp) REVERT: B 536 THR cc_start: 0.8941 (p) cc_final: 0.8664 (t) REVERT: M 41 GLN cc_start: 0.8242 (mp10) cc_final: 0.7949 (mp10) REVERT: M 277 TYR cc_start: 0.8417 (p90) cc_final: 0.7800 (p90) REVERT: S 13 LYS cc_start: 0.8933 (tttt) cc_final: 0.8490 (tttm) REVERT: S 60 ARG cc_start: 0.8802 (ttm170) cc_final: 0.8503 (ttm-80) REVERT: S 89 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8682 (mm-30) REVERT: S 93 GLU cc_start: 0.8964 (tp30) cc_final: 0.8513 (tp30) outliers start: 35 outliers final: 28 residues processed: 270 average time/residue: 0.2434 time to fit residues: 97.8579 Evaluate side-chains 268 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 26 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 207 SER Chi-restraints excluded: chain M residue 338 MET Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0970 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.101181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083595 restraints weight = 30577.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086729 restraints weight = 16477.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088869 restraints weight = 10594.316| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13951 Z= 0.175 Angle : 0.678 14.906 18886 Z= 0.330 Chirality : 0.044 0.374 2198 Planarity : 0.004 0.043 2403 Dihedral : 4.406 28.354 1868 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 1.77 % Allowed : 23.59 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1703 helix: 1.07 (0.17), residues: 983 sheet: 0.39 (0.38), residues: 189 loop : -1.11 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 462 HIS 0.004 0.001 HIS A 320 PHE 0.027 0.001 PHE A 523 TYR 0.013 0.001 TYR M 120 ARG 0.008 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.00 seconds wall clock time: 50 minutes 55.23 seconds (3055.23 seconds total)