Starting phenix.real_space_refine on Sat Jul 4 18:15:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.map" model { file = "/net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cui_45934/07_2026/9cui_45934.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.103 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 12 5.49 5 S 161 5.16 5 C 14943 2.51 5 N 3657 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4916 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4991 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "C" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5286 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 26, 'TRANS': 626} Chain breaks: 1 Chain: "D" Number of atoms: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4972 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 26, 'TRANS': 590} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'CLR': 1, 'PCW': 12, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain breaks: 2 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PCW:plan-1': 9, 'PCW:plan-3': 9, 'PCW:plan-4': 9, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 357 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 1, 'PCW': 9, 'Y01': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PCW:plan-1': 6, 'PCW:plan-3': 6, 'PCW:plan-4': 6, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 338 Unusual residues: {'CLR': 1, 'PCW': 10, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PCW:plan-1': 7, 'PCW:plan-3': 7, 'PCW:plan-4': 7, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 327 Unusual residues: {'CLR': 1, 'PCW': 12, 'Y01': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PCW:plan-1': 9, 'PCW:plan-3': 9, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Time building chain proxies: 4.84, per 1000 atoms: 0.21 Number of scatterers: 22713 At special positions: 0 Unit cell: (137.643, 139.777, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 161 16.00 P 12 15.00 O 3933 8.00 N 3657 7.00 C 14943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 937.3 milliseconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 7 sheets defined 61.4% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.118A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.963A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.527A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 93 through 102 removed outlier: 3.504A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.698A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.777A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.595A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.658A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.866A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.702A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 removed outlier: 3.594A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.737A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.545A pdb=" N ILE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.707A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 402 removed outlier: 3.567A pdb=" N ASP A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.836A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.536A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.745A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.777A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.511A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.516A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 4.102A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.588A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.691A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 608 removed outlier: 3.752A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 38 removed outlier: 3.623A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.821A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.552A pdb=" N ILE B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.653A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.754A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.793A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.582A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.667A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.678A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.638A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 4.086A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.692A pdb=" N SER B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 349 removed outlier: 4.065A pdb=" N MET B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 removed outlier: 3.545A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 4.286A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.736A pdb=" N GLY B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.587A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.837A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.819A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 512 removed outlier: 4.080A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 498 " --> pdb=" O CYS B 494 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.614A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.916A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.568A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.865A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 608 removed outlier: 3.847A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 645 Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.610A pdb=" N GLN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.553A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.919A pdb=" N ASN C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.544A pdb=" N ILE C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.787A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.699A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.606A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.531A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.953A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.638A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.986A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.818A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 313 through 322 Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.530A pdb=" N MET C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.632A pdb=" N ILE C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 400 removed outlier: 3.764A pdb=" N ASP C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.513A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 423 Processing helix chain 'C' and resid 423 through 445 removed outlier: 4.216A pdb=" N VAL C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 463 removed outlier: 3.621A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 465 No H-bonds generated for 'chain 'C' and resid 464 through 465' Processing helix chain 'C' and resid 466 through 470 removed outlier: 3.645A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 466 through 470' Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.660A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 512 removed outlier: 4.160A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.553A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 3.881A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 removed outlier: 4.263A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.734A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 652 removed outlier: 3.548A pdb=" N ILE C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 646 " --> pdb=" O GLN C 642 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 647 " --> pdb=" O ARG C 643 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.514A pdb=" N GLU C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 701 " --> pdb=" O ARG C 697 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 704 " --> pdb=" O GLN C 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 46 removed outlier: 3.671A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.760A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.600A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.821A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.634A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.625A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.711A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.069A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.690A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.581A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.672A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.899A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 4.084A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 310 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.866A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.902A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS D 347 " --> pdb=" O PHE D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.762A pdb=" N THR D 366 " --> pdb=" O ARG D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 400 removed outlier: 3.581A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.629A pdb=" N ILE D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.601A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 438 " --> pdb=" O PHE D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.542A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.827A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.544A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 496 removed outlier: 3.711A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 512 removed outlier: 3.652A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.575A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 4.251A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 4.225A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 removed outlier: 3.615A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.849A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D 600 " --> pdb=" O GLN D 596 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.662A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.794A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 53 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.562A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.681A pdb=" N VAL E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 146 removed outlier: 3.587A pdb=" N MET E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.648A pdb=" N THR A 274 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 618 through 619 Processing sheet with id=AA4, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.908A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'D' and resid 266 through 269 removed outlier: 7.075A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 352 through 354 796 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3493 1.31 - 1.43: 5851 1.43 - 1.56: 13184 1.56 - 1.68: 351 1.68 - 1.81: 294 Bond restraints: 23173 Sorted by residual: bond pdb=" C19 PCW C 810 " pdb=" C20 PCW C 810 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C19 PCW A 809 " pdb=" C20 PCW A 809 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C19 PCW D 809 " pdb=" C20 PCW D 809 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW D 810 " pdb=" C20 PCW D 810 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW D 814 " pdb=" C20 PCW D 814 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 23168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 30228 3.33 - 6.66: 745 6.66 - 10.00: 175 10.00 - 13.33: 47 13.33 - 16.66: 15 Bond angle restraints: 31210 Sorted by residual: angle pdb=" C GLU D 515 " pdb=" N ASP D 516 " pdb=" CA ASP D 516 " ideal model delta sigma weight residual 121.17 132.74 -11.57 1.62e+00 3.81e-01 5.10e+01 angle pdb=" N LEU D 571 " pdb=" CA LEU D 571 " pdb=" C LEU D 571 " ideal model delta sigma weight residual 114.75 106.90 7.85 1.26e+00 6.30e-01 3.89e+01 angle pdb=" N ASP A 406 " pdb=" CA ASP A 406 " pdb=" C ASP A 406 " ideal model delta sigma weight residual 114.56 106.69 7.87 1.27e+00 6.20e-01 3.84e+01 angle pdb=" N ILE B 540 " pdb=" CA ILE B 540 " pdb=" C ILE B 540 " ideal model delta sigma weight residual 112.43 106.78 5.65 9.20e-01 1.18e+00 3.78e+01 angle pdb=" C19 PCW A 809 " pdb=" C20 PCW A 809 " pdb=" C21 PCW A 809 " ideal model delta sigma weight residual 127.82 111.16 16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 31205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 14143 35.18 - 70.37: 483 70.37 - 105.55: 28 105.55 - 140.73: 7 140.73 - 175.92: 3 Dihedral angle restraints: 14664 sinusoidal: 6921 harmonic: 7743 Sorted by residual: dihedral pdb=" CA SER B 361 " pdb=" C SER B 361 " pdb=" N PRO B 362 " pdb=" CA PRO B 362 " ideal model delta harmonic sigma weight residual -180.00 -128.64 -51.36 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta harmonic sigma weight residual -180.00 -134.12 -45.88 0 5.00e+00 4.00e-02 8.42e+01 dihedral pdb=" CA SER D 361 " pdb=" C SER D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta harmonic sigma weight residual -180.00 -136.40 -43.60 0 5.00e+00 4.00e-02 7.60e+01 ... (remaining 14661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3157 0.092 - 0.184: 250 0.184 - 0.276: 27 0.276 - 0.368: 6 0.368 - 0.459: 3 Chirality restraints: 3443 Sorted by residual: chirality pdb=" CG LEU D 367 " pdb=" CB LEU D 367 " pdb=" CD1 LEU D 367 " pdb=" CD2 LEU D 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB THR A 311 " pdb=" CA THR A 311 " pdb=" OG1 THR A 311 " pdb=" CG2 THR A 311 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 3440 not shown) Planarity restraints: 3850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW D 805 " 0.281 2.00e-02 2.50e+03 2.87e-01 8.24e+02 pdb=" C19 PCW D 805 " -0.476 2.00e-02 2.50e+03 pdb=" C20 PCW D 805 " 0.147 2.00e-02 2.50e+03 pdb=" C21 PCW D 805 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 810 " -0.299 2.00e-02 2.50e+03 2.83e-01 7.99e+02 pdb=" C19 PCW B 810 " 0.465 2.00e-02 2.50e+03 pdb=" C20 PCW B 810 " -0.069 2.00e-02 2.50e+03 pdb=" C21 PCW B 810 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW C 802 " -0.289 2.00e-02 2.50e+03 2.60e-01 6.77e+02 pdb=" C19 PCW C 802 " 0.407 2.00e-02 2.50e+03 pdb=" C20 PCW C 802 " 0.027 2.00e-02 2.50e+03 pdb=" C21 PCW C 802 " -0.145 2.00e-02 2.50e+03 ... (remaining 3847 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1607 2.73 - 3.27: 20823 3.27 - 3.81: 34268 3.81 - 4.36: 43882 4.36 - 4.90: 73771 Nonbonded interactions: 174351 Sorted by model distance: nonbonded pdb="CA CA A 816 " pdb="CA CA A 817 " model vdw 2.183 3.460 nonbonded pdb=" O LEU C 295 " pdb=" OG1 THR C 299 " model vdw 2.276 3.040 nonbonded pdb=" OG SER D 285 " pdb=" OG SER D 291 " model vdw 2.296 3.040 nonbonded pdb=" O GLN B 370 " pdb=" OG1 THR C 514 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR B 623 " pdb=" OE1 GLU C 35 " model vdw 2.310 3.040 ... (remaining 174346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 638 or (resid 805 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 810 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 811 a \ nd (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 813)) selection = (chain 'B' and (resid 27 through 638 or (resid 802 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 807 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26)) or resid 808 or \ (resid 810 and (name C12 or name C13 or name C14 or name C15 or name C16 or nam \ e C17 or name C18 or name C19)))) selection = (chain 'C' and (resid 27 through 638 or (resid 801 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 806 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 807 a \ nd (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 809)) selection = (chain 'D' and (resid 27 through 638 or (resid 805 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26)) or (resid 810 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26)) or resid 811 or \ resid 813)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.370 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.011 0.215 23173 Z= 0.561 Angle : 1.429 16.659 31210 Z= 0.744 Chirality : 0.056 0.459 3443 Planarity : 0.012 0.287 3850 Dihedral : 15.901 175.916 9660 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.30 % Favored : 88.17 % Rotamer: Outliers : 0.39 % Allowed : 5.87 % Favored : 93.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.40 (0.11), residues: 2638 helix: -4.43 (0.06), residues: 1476 sheet: -4.36 (0.38), residues: 79 loop : -3.75 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 350 TYR 0.022 0.002 TYR C 547 PHE 0.033 0.002 PHE D 508 TRP 0.034 0.002 TRP C 45 HIS 0.014 0.002 HIS B 522 Details of bonding type rmsd/Z covalent geometry : bond 0.01128 / 0.56 (23173) covalent geometry : angle 1.42850 / 0.74 (31210) hydrogen bonds : bond 0.33788 / 22.69 ( 796) hydrogen bonds : angle 10.41366 / 7.24 ( 2307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 594 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8442 (tp) cc_final: 0.8157 (mp) REVERT: A 195 LEU cc_start: 0.8392 (mm) cc_final: 0.8058 (mt) REVERT: A 257 GLN cc_start: 0.8276 (mt0) cc_final: 0.7380 (mt0) REVERT: A 328 TYR cc_start: 0.8211 (m-10) cc_final: 0.7959 (m-80) REVERT: A 528 MET cc_start: 0.7424 (tpp) cc_final: 0.7054 (tpp) REVERT: A 565 ILE cc_start: 0.8879 (pp) cc_final: 0.8569 (mp) REVERT: B 55 ASP cc_start: 0.8134 (t0) cc_final: 0.7889 (p0) REVERT: B 181 LEU cc_start: 0.9221 (tt) cc_final: 0.8709 (tt) REVERT: B 442 MET cc_start: 0.8296 (mtt) cc_final: 0.7957 (mtt) REVERT: C 35 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7722 (tm-30) REVERT: C 45 TRP cc_start: 0.8134 (m-90) cc_final: 0.7909 (m100) REVERT: C 255 MET cc_start: 0.8580 (mmm) cc_final: 0.8132 (mmp) REVERT: C 265 HIS cc_start: 0.7227 (t70) cc_final: 0.6793 (t-90) REVERT: C 319 LEU cc_start: 0.8568 (mp) cc_final: 0.8299 (mp) REVERT: C 368 LEU cc_start: 0.8318 (pt) cc_final: 0.8040 (mt) REVERT: C 394 ILE cc_start: 0.8770 (mt) cc_final: 0.8508 (mm) REVERT: C 410 MET cc_start: 0.4268 (mtt) cc_final: 0.3949 (mtp) REVERT: C 694 ASN cc_start: 0.7434 (m-40) cc_final: 0.7170 (m110) REVERT: D 96 MET cc_start: 0.8776 (mmt) cc_final: 0.8121 (mmm) REVERT: D 210 THR cc_start: 0.8828 (m) cc_final: 0.8610 (p) REVERT: D 233 ASP cc_start: 0.7582 (p0) cc_final: 0.7279 (p0) REVERT: D 295 LEU cc_start: 0.8177 (mm) cc_final: 0.7904 (mt) REVERT: D 319 LEU cc_start: 0.8695 (mm) cc_final: 0.8460 (mt) REVERT: D 456 PHE cc_start: 0.8471 (m-80) cc_final: 0.8056 (m-80) REVERT: D 481 MET cc_start: 0.7528 (mmm) cc_final: 0.7271 (mmm) REVERT: D 594 ARG cc_start: 0.7875 (mpp80) cc_final: 0.7659 (mpp80) REVERT: E 37 ARG cc_start: 0.6957 (mtm180) cc_final: 0.6518 (mtm-85) REVERT: E 131 ASP cc_start: 0.6397 (p0) cc_final: 0.6161 (m-30) outliers start: 9 outliers final: 3 residues processed: 600 average time/residue: 0.1518 time to fit residues: 138.1395 Evaluate side-chains 349 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain C residue 367 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 84 HIS A 129 ASN A 174 ASN A 206 GLN A 225 HIS A 230 GLN A 267 GLN A 572 ASN B 56 ASN B 74 GLN B 84 HIS B 91 ASN B 118 GLN B 128 GLN B 131 ASN B 174 ASN B 185 HIS B 252 ASN B 267 GLN B 365 ASN B 418 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS B 572 ASN B 587 HIS C 74 GLN C 118 GLN C 158 ASN C 214 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 267 GLN C 358 ASN C 370 GLN C 572 ASN C 637 GLN D 31 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN D 257 GLN D 365 ASN D 464 ASN D 522 HIS D 572 ASN D 587 HIS E 49 GLN E 53 ASN E 107 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127682 restraints weight = 33909.055| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.71 r_work: 0.3375 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23173 Z= 0.204 Angle : 0.767 11.113 31210 Z= 0.394 Chirality : 0.044 0.203 3443 Planarity : 0.006 0.067 3850 Dihedral : 16.389 178.631 4506 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.49 % Favored : 88.17 % Rotamer: Outliers : 2.70 % Allowed : 11.91 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.63 (0.13), residues: 2638 helix: -2.70 (0.10), residues: 1525 sheet: -4.19 (0.37), residues: 95 loop : -3.37 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 492 TYR 0.016 0.002 TYR B 623 PHE 0.026 0.002 PHE A 531 TRP 0.020 0.001 TRP A 29 HIS 0.010 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (23173) covalent geometry : angle 0.76744 / 0.39 (31210) hydrogen bonds : bond 0.05388 / 3.58 ( 796) hydrogen bonds : angle 5.14764 / 3.56 ( 2307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 380 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8311 (mm) cc_final: 0.8071 (mt) REVERT: A 549 VAL cc_start: 0.9226 (t) cc_final: 0.8843 (p) REVERT: A 565 ILE cc_start: 0.9196 (pp) cc_final: 0.8889 (mp) REVERT: B 410 MET cc_start: 0.6040 (mpp) cc_final: 0.5220 (ppp) REVERT: B 613 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.7348 (t60) REVERT: C 63 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8565 (tppt) REVERT: C 78 MET cc_start: 0.7506 (mmt) cc_final: 0.6948 (mmt) REVERT: C 80 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: C 265 HIS cc_start: 0.7667 (t70) cc_final: 0.7129 (t-170) REVERT: C 270 TYR cc_start: 0.8434 (t80) cc_final: 0.8119 (t80) REVERT: C 368 LEU cc_start: 0.8488 (pt) cc_final: 0.8077 (mt) REVERT: C 410 MET cc_start: 0.3964 (mtt) cc_final: 0.3657 (mtp) REVERT: C 432 TYR cc_start: 0.8950 (t80) cc_final: 0.8058 (t80) REVERT: C 485 MET cc_start: 0.8248 (mmt) cc_final: 0.8021 (mmt) REVERT: D 96 MET cc_start: 0.9181 (mmt) cc_final: 0.8938 (mmm) REVERT: D 210 THR cc_start: 0.8975 (m) cc_final: 0.8741 (p) REVERT: D 319 LEU cc_start: 0.8799 (mm) cc_final: 0.8524 (mt) REVERT: D 456 PHE cc_start: 0.8948 (m-80) cc_final: 0.8689 (m-80) REVERT: D 458 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8283 (mm) REVERT: D 546 ASN cc_start: 0.8206 (t0) cc_final: 0.8005 (t0) REVERT: D 594 ARG cc_start: 0.8443 (mpp80) cc_final: 0.8110 (mpp80) REVERT: D 611 CYS cc_start: 0.7905 (t) cc_final: 0.7605 (m) REVERT: E 49 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8141 (tp40) REVERT: E 86 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7686 (ttm-80) REVERT: E 144 MET cc_start: 0.7604 (mmm) cc_final: 0.6835 (tpp) outliers start: 62 outliers final: 35 residues processed: 421 average time/residue: 0.1538 time to fit residues: 101.5218 Evaluate side-chains 352 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 164 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 ASN B 206 GLN B 258 HIS B 426 HIS B 637 GLN C 158 ASN C 694 ASN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 53 ASN E 107 HIS E 111 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129888 restraints weight = 33896.675| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.59 r_work: 0.3411 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23173 Z= 0.131 Angle : 0.666 10.105 31210 Z= 0.339 Chirality : 0.041 0.184 3443 Planarity : 0.005 0.058 3850 Dihedral : 14.959 163.329 4506 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.99 % Favored : 88.82 % Rotamer: Outliers : 3.09 % Allowed : 13.35 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.83 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.15), residues: 2638 helix: -1.54 (0.12), residues: 1538 sheet: -4.11 (0.40), residues: 84 loop : -3.22 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 140 TYR 0.013 0.001 TYR A 555 PHE 0.019 0.001 PHE A 531 TRP 0.022 0.001 TRP A 29 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (23173) covalent geometry : angle 0.66619 / 0.34 (31210) hydrogen bonds : bond 0.04062 / 2.70 ( 796) hydrogen bonds : angle 4.44882 / 3.05 ( 2307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 374 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8314 (mm) cc_final: 0.8091 (mt) REVERT: A 502 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8869 (mt) REVERT: A 549 VAL cc_start: 0.9170 (t) cc_final: 0.8757 (p) REVERT: A 565 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8890 (pt) REVERT: B 128 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 211 PHE cc_start: 0.8524 (m-80) cc_final: 0.8310 (m-10) REVERT: B 410 MET cc_start: 0.6043 (mpp) cc_final: 0.5331 (ppp) REVERT: B 574 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 621 ARG cc_start: 0.7399 (ttm110) cc_final: 0.6673 (mtm-85) REVERT: B 637 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: C 78 MET cc_start: 0.7386 (mmt) cc_final: 0.6820 (mmt) REVERT: C 265 HIS cc_start: 0.7568 (t70) cc_final: 0.6549 (t-170) REVERT: C 368 LEU cc_start: 0.8592 (pt) cc_final: 0.8107 (mp) REVERT: C 410 MET cc_start: 0.4004 (mtt) cc_final: 0.3739 (mtp) REVERT: C 473 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 26 ARG cc_start: 0.5687 (mtm180) cc_final: 0.5445 (mtm180) REVERT: D 210 THR cc_start: 0.8943 (m) cc_final: 0.8701 (p) REVERT: D 319 LEU cc_start: 0.8752 (mm) cc_final: 0.8504 (mt) REVERT: D 324 TYR cc_start: 0.7679 (m-80) cc_final: 0.7412 (m-80) REVERT: D 594 ARG cc_start: 0.8425 (mpp80) cc_final: 0.7987 (mpp80) REVERT: D 611 CYS cc_start: 0.7858 (t) cc_final: 0.7633 (m) REVERT: E 49 GLN cc_start: 0.8375 (tp40) cc_final: 0.8133 (tp40) REVERT: E 72 MET cc_start: 0.7785 (mmm) cc_final: 0.7122 (mmt) REVERT: E 144 MET cc_start: 0.7546 (mmm) cc_final: 0.6818 (tpp) outliers start: 71 outliers final: 35 residues processed: 421 average time/residue: 0.1519 time to fit residues: 101.0669 Evaluate side-chains 361 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 322 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 199 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 147 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 HIS B 374 GLN B 546 ASN C 158 ASN C 642 GLN C 694 ASN D 582 HIS E 143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131343 restraints weight = 33894.966| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.72 r_work: 0.3428 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23173 Z= 0.115 Angle : 0.644 14.073 31210 Z= 0.322 Chirality : 0.040 0.203 3443 Planarity : 0.005 0.060 3850 Dihedral : 14.206 153.744 4506 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.22 % Favored : 88.55 % Rotamer: Outliers : 2.87 % Allowed : 14.13 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.16), residues: 2638 helix: -0.87 (0.13), residues: 1529 sheet: -3.71 (0.45), residues: 77 loop : -3.06 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 606 TYR 0.014 0.001 TYR D 324 PHE 0.020 0.001 PHE D 456 TRP 0.010 0.001 TRP A 29 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (23173) covalent geometry : angle 0.64359 / 0.32 (31210) hydrogen bonds : bond 0.03497 / 2.32 ( 796) hydrogen bonds : angle 4.21944 / 2.90 ( 2307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 350 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8447 (mm) cc_final: 0.8200 (mt) REVERT: A 347 CYS cc_start: 0.8056 (m) cc_final: 0.7822 (m) REVERT: A 368 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 565 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8901 (pt) REVERT: B 128 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6676 (tm-30) REVERT: B 301 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8102 (mtpt) REVERT: B 410 MET cc_start: 0.6131 (mpp) cc_final: 0.5431 (ppp) REVERT: B 621 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6477 (mtm-85) REVERT: C 63 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8554 (tppt) REVERT: C 260 MET cc_start: 0.8673 (tpt) cc_final: 0.8375 (tpt) REVERT: C 265 HIS cc_start: 0.7367 (t70) cc_final: 0.6391 (t-170) REVERT: C 270 TYR cc_start: 0.8480 (t80) cc_final: 0.8041 (t80) REVERT: C 294 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 368 LEU cc_start: 0.8528 (pt) cc_final: 0.8060 (mp) REVERT: C 410 MET cc_start: 0.3967 (mtt) cc_final: 0.3715 (mtp) REVERT: C 473 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 485 MET cc_start: 0.8073 (mmt) cc_final: 0.7864 (mmt) REVERT: C 578 MET cc_start: 0.8221 (mtt) cc_final: 0.7953 (mtt) REVERT: D 26 ARG cc_start: 0.5606 (mtm180) cc_final: 0.5404 (mtm180) REVERT: D 188 ASP cc_start: 0.6815 (t0) cc_final: 0.6173 (p0) REVERT: D 210 THR cc_start: 0.8852 (m) cc_final: 0.8650 (p) REVERT: D 257 GLN cc_start: 0.8502 (mt0) cc_final: 0.8235 (mm-40) REVERT: D 319 LEU cc_start: 0.8742 (mm) cc_final: 0.8471 (mt) REVERT: D 324 TYR cc_start: 0.7501 (m-80) cc_final: 0.7255 (m-10) REVERT: D 435 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8123 (mtp) REVERT: D 481 MET cc_start: 0.8497 (mmt) cc_final: 0.8199 (mmm) REVERT: D 594 ARG cc_start: 0.8391 (mpp80) cc_final: 0.8073 (mpp80) REVERT: D 611 CYS cc_start: 0.7682 (t) cc_final: 0.7354 (m) REVERT: E 49 GLN cc_start: 0.8326 (tp40) cc_final: 0.8007 (tp40) REVERT: E 72 MET cc_start: 0.7826 (mmm) cc_final: 0.7144 (mmt) outliers start: 66 outliers final: 43 residues processed: 397 average time/residue: 0.1481 time to fit residues: 93.2077 Evaluate side-chains 365 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 186 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 240 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129085 restraints weight = 33637.843| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.70 r_work: 0.3428 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23173 Z= 0.124 Angle : 0.630 12.863 31210 Z= 0.315 Chirality : 0.041 0.191 3443 Planarity : 0.004 0.062 3850 Dihedral : 13.672 154.595 4506 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.77 % Favored : 89.08 % Rotamer: Outliers : 3.35 % Allowed : 14.26 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2638 helix: -0.42 (0.13), residues: 1534 sheet: -3.60 (0.46), residues: 80 loop : -3.09 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 302 TYR 0.017 0.001 TYR D 270 PHE 0.016 0.001 PHE B 478 TRP 0.014 0.001 TRP A 29 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (23173) covalent geometry : angle 0.63045 / 0.32 (31210) hydrogen bonds : bond 0.03375 / 2.25 ( 796) hydrogen bonds : angle 4.11021 / 2.83 ( 2307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 344 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8916 (tt) cc_final: 0.8618 (mt) REVERT: A 195 LEU cc_start: 0.8406 (mm) cc_final: 0.8164 (mt) REVERT: A 565 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8905 (pt) REVERT: B 128 GLN cc_start: 0.7416 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 490 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 574 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 637 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6717 (pp30) REVERT: C 63 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8544 (tppt) REVERT: C 78 MET cc_start: 0.7221 (mmt) cc_final: 0.6892 (mmt) REVERT: C 260 MET cc_start: 0.8739 (tpt) cc_final: 0.8478 (tpt) REVERT: C 265 HIS cc_start: 0.7498 (t70) cc_final: 0.6575 (t-170) REVERT: C 270 TYR cc_start: 0.8504 (t80) cc_final: 0.8065 (t80) REVERT: C 294 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 368 LEU cc_start: 0.8606 (pt) cc_final: 0.8101 (mp) REVERT: C 473 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 628 ARG cc_start: 0.8263 (ptp-110) cc_final: 0.7638 (ptt90) REVERT: D 26 ARG cc_start: 0.5638 (mtm180) cc_final: 0.5437 (mtm180) REVERT: D 188 ASP cc_start: 0.6840 (t0) cc_final: 0.6165 (p0) REVERT: D 210 THR cc_start: 0.8927 (m) cc_final: 0.8670 (p) REVERT: D 294 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 319 LEU cc_start: 0.8727 (mm) cc_final: 0.8450 (mt) REVERT: D 324 TYR cc_start: 0.7524 (m-80) cc_final: 0.7268 (m-10) REVERT: D 594 ARG cc_start: 0.8432 (mpp80) cc_final: 0.8003 (mpp80) REVERT: D 611 CYS cc_start: 0.7849 (t) cc_final: 0.7409 (m) REVERT: E 49 GLN cc_start: 0.8406 (tp40) cc_final: 0.8129 (tp40) REVERT: E 72 MET cc_start: 0.7804 (mmm) cc_final: 0.7138 (mmt) outliers start: 77 outliers final: 46 residues processed: 397 average time/residue: 0.1525 time to fit residues: 95.3925 Evaluate side-chains 370 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 318 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 99 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126013 restraints weight = 33077.934| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.23 r_work: 0.3312 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23173 Z= 0.125 Angle : 0.635 14.114 31210 Z= 0.316 Chirality : 0.041 0.192 3443 Planarity : 0.004 0.066 3850 Dihedral : 13.409 153.539 4506 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.18 % Favored : 88.74 % Rotamer: Outliers : 3.00 % Allowed : 15.52 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2638 helix: -0.19 (0.13), residues: 1538 sheet: -3.52 (0.46), residues: 80 loop : -3.03 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 302 TYR 0.018 0.001 TYR D 555 PHE 0.015 0.001 PHE B 478 TRP 0.014 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (23173) covalent geometry : angle 0.63539 / 0.32 (31210) hydrogen bonds : bond 0.03244 / 2.15 ( 796) hydrogen bonds : angle 4.07064 / 2.81 ( 2307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 332 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8945 (tt) cc_final: 0.8642 (mt) REVERT: A 195 LEU cc_start: 0.8608 (mm) cc_final: 0.8301 (mt) REVERT: A 367 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 565 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8867 (pt) REVERT: B 217 ASN cc_start: 0.8146 (m-40) cc_final: 0.7413 (p0) REVERT: B 301 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8104 (mtpt) REVERT: B 574 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 637 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7041 (pp30) REVERT: C 63 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8554 (tppt) REVERT: C 78 MET cc_start: 0.7503 (mmt) cc_final: 0.7178 (mmt) REVERT: C 260 MET cc_start: 0.8780 (tpt) cc_final: 0.8553 (tpt) REVERT: C 265 HIS cc_start: 0.7813 (t70) cc_final: 0.6993 (t-170) REVERT: C 270 TYR cc_start: 0.8570 (t80) cc_final: 0.8120 (t80) REVERT: C 301 LYS cc_start: 0.8332 (tttt) cc_final: 0.7924 (tptt) REVERT: C 368 LEU cc_start: 0.8662 (pt) cc_final: 0.8161 (mp) REVERT: C 432 TYR cc_start: 0.9019 (t80) cc_final: 0.8413 (t80) REVERT: C 473 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8503 (tm-30) REVERT: C 628 ARG cc_start: 0.8354 (ptp-110) cc_final: 0.7740 (ptt90) REVERT: D 26 ARG cc_start: 0.5632 (mtm180) cc_final: 0.5421 (mtm180) REVERT: D 54 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7518 (ttpt) REVERT: D 188 ASP cc_start: 0.6911 (t0) cc_final: 0.6194 (p0) REVERT: D 210 THR cc_start: 0.8986 (m) cc_final: 0.8748 (p) REVERT: D 319 LEU cc_start: 0.8786 (mm) cc_final: 0.8519 (mt) REVERT: D 324 TYR cc_start: 0.7718 (m-80) cc_final: 0.7434 (m-10) REVERT: D 546 ASN cc_start: 0.8443 (t0) cc_final: 0.8239 (t0) REVERT: D 553 PHE cc_start: 0.8743 (t80) cc_final: 0.8436 (t80) REVERT: D 594 ARG cc_start: 0.8647 (mpp80) cc_final: 0.8286 (mpp80) REVERT: D 611 CYS cc_start: 0.7828 (t) cc_final: 0.7429 (m) REVERT: E 49 GLN cc_start: 0.8433 (tp40) cc_final: 0.8152 (tp40) REVERT: E 72 MET cc_start: 0.7927 (mmm) cc_final: 0.7225 (mmt) REVERT: E 124 MET cc_start: 0.7482 (mtp) cc_final: 0.7161 (mtp) REVERT: E 126 ARG cc_start: 0.7573 (mtp180) cc_final: 0.7218 (ttp-170) outliers start: 69 outliers final: 47 residues processed: 379 average time/residue: 0.1493 time to fit residues: 90.0796 Evaluate side-chains 375 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 322 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 78 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 374 GLN B 546 ASN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 258 HIS C 582 HIS ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121031 restraints weight = 33140.243| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.08 r_work: 0.3235 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23173 Z= 0.228 Angle : 0.722 15.534 31210 Z= 0.357 Chirality : 0.045 0.230 3443 Planarity : 0.005 0.068 3850 Dihedral : 13.749 153.766 4506 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.02 % Favored : 87.83 % Rotamer: Outliers : 3.04 % Allowed : 16.35 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2638 helix: -0.32 (0.13), residues: 1538 sheet: -3.69 (0.44), residues: 85 loop : -3.01 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 302 TYR 0.018 0.002 TYR D 555 PHE 0.017 0.002 PHE B 478 TRP 0.015 0.001 TRP A 29 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (23173) covalent geometry : angle 0.72246 / 0.36 (31210) hydrogen bonds : bond 0.03941 / 2.59 ( 796) hydrogen bonds : angle 4.38374 / 3.03 ( 2307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 327 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8622 (mt) cc_final: 0.8224 (mt) REVERT: A 51 LEU cc_start: 0.8945 (tt) cc_final: 0.8661 (mt) REVERT: A 90 ASP cc_start: 0.8207 (t0) cc_final: 0.7990 (t0) REVERT: A 195 LEU cc_start: 0.8566 (mm) cc_final: 0.8306 (mt) REVERT: A 410 MET cc_start: 0.6760 (tmm) cc_final: 0.6352 (tmm) REVERT: B 301 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8128 (mtpt) REVERT: B 410 MET cc_start: 0.6316 (mpp) cc_final: 0.5540 (ppp) REVERT: B 490 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 555 TYR cc_start: 0.8614 (t80) cc_final: 0.8388 (t80) REVERT: B 574 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 637 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7304 (pp30) REVERT: C 63 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8499 (tppt) REVERT: C 78 MET cc_start: 0.7689 (mmt) cc_final: 0.7329 (mmt) REVERT: C 260 MET cc_start: 0.8769 (tpt) cc_final: 0.8464 (tpt) REVERT: C 265 HIS cc_start: 0.7976 (t70) cc_final: 0.7074 (t-170) REVERT: C 368 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 454 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8459 (ttm) REVERT: C 473 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 628 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7810 (ptt90) REVERT: D 26 ARG cc_start: 0.5414 (mtm180) cc_final: 0.5121 (mtm180) REVERT: D 54 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7538 (ttpt) REVERT: D 210 THR cc_start: 0.9006 (m) cc_final: 0.8764 (p) REVERT: D 319 LEU cc_start: 0.8822 (mm) cc_final: 0.8532 (mt) REVERT: D 324 TYR cc_start: 0.7953 (m-80) cc_final: 0.7612 (m-80) REVERT: D 481 MET cc_start: 0.8859 (mmm) cc_final: 0.8658 (mmt) REVERT: D 553 PHE cc_start: 0.8926 (t80) cc_final: 0.8524 (t80) REVERT: D 555 TYR cc_start: 0.8555 (t80) cc_final: 0.8275 (t80) REVERT: D 594 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8430 (mpp80) REVERT: D 611 CYS cc_start: 0.7953 (t) cc_final: 0.7529 (m) REVERT: E 49 GLN cc_start: 0.8407 (tp40) cc_final: 0.8117 (tp40) REVERT: E 72 MET cc_start: 0.7959 (mmm) cc_final: 0.7303 (mmt) REVERT: E 126 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7345 (ttp-170) outliers start: 70 outliers final: 53 residues processed: 375 average time/residue: 0.1454 time to fit residues: 87.1004 Evaluate side-chains 370 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 310 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 48 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125440 restraints weight = 32738.445| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.23 r_work: 0.3300 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23173 Z= 0.116 Angle : 0.646 15.383 31210 Z= 0.318 Chirality : 0.040 0.233 3443 Planarity : 0.004 0.071 3850 Dihedral : 13.178 152.052 4506 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.80 % Favored : 89.16 % Rotamer: Outliers : 2.52 % Allowed : 17.22 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 2638 helix: 0.04 (0.14), residues: 1541 sheet: -3.36 (0.47), residues: 80 loop : -2.91 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 302 TYR 0.017 0.001 TYR D 555 PHE 0.012 0.001 PHE B 478 TRP 0.016 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (23173) covalent geometry : angle 0.64582 / 0.32 (31210) hydrogen bonds : bond 0.03211 / 2.12 ( 796) hydrogen bonds : angle 4.07096 / 2.81 ( 2307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 338 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8516 (mt) cc_final: 0.8091 (mt) REVERT: A 51 LEU cc_start: 0.8918 (tt) cc_final: 0.8630 (mt) REVERT: A 195 LEU cc_start: 0.8326 (mm) cc_final: 0.8063 (mt) REVERT: B 96 MET cc_start: 0.8424 (mmm) cc_final: 0.8123 (mmm) REVERT: B 217 ASN cc_start: 0.8077 (m-40) cc_final: 0.7436 (p0) REVERT: B 301 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8138 (mtpt) REVERT: B 574 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 637 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7012 (pp30) REVERT: C 63 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8504 (tppt) REVERT: C 78 MET cc_start: 0.7396 (mmt) cc_final: 0.7077 (mmt) REVERT: C 260 MET cc_start: 0.8718 (tpt) cc_final: 0.8495 (tpt) REVERT: C 265 HIS cc_start: 0.7468 (t70) cc_final: 0.6654 (t-170) REVERT: C 270 TYR cc_start: 0.8545 (t80) cc_final: 0.8097 (t80) REVERT: C 301 LYS cc_start: 0.8343 (tttt) cc_final: 0.8078 (tptt) REVERT: C 368 LEU cc_start: 0.8608 (pt) cc_final: 0.8149 (mp) REVERT: C 473 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 628 ARG cc_start: 0.8211 (ptp-110) cc_final: 0.7712 (ptt90) REVERT: D 26 ARG cc_start: 0.5336 (mtm180) cc_final: 0.5062 (mtm180) REVERT: D 54 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7412 (ttpt) REVERT: D 210 THR cc_start: 0.8908 (m) cc_final: 0.8684 (p) REVERT: D 319 LEU cc_start: 0.8624 (mm) cc_final: 0.8349 (mt) REVERT: D 324 TYR cc_start: 0.7555 (m-80) cc_final: 0.7195 (m-10) REVERT: D 456 PHE cc_start: 0.8727 (m-80) cc_final: 0.8512 (m-80) REVERT: D 553 PHE cc_start: 0.8722 (t80) cc_final: 0.8464 (t80) REVERT: D 594 ARG cc_start: 0.8376 (mpp80) cc_final: 0.8024 (mpp80) REVERT: D 611 CYS cc_start: 0.7812 (t) cc_final: 0.7394 (m) REVERT: E 49 GLN cc_start: 0.8435 (tp40) cc_final: 0.8090 (tp40) REVERT: E 72 MET cc_start: 0.7651 (mmm) cc_final: 0.6968 (mmt) REVERT: E 126 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7315 (ttp-170) outliers start: 58 outliers final: 42 residues processed: 378 average time/residue: 0.1432 time to fit residues: 86.6744 Evaluate side-chains 363 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 145 optimal weight: 0.1980 chunk 160 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124027 restraints weight = 33092.422| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.23 r_work: 0.3293 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23173 Z= 0.128 Angle : 0.651 15.080 31210 Z= 0.320 Chirality : 0.041 0.215 3443 Planarity : 0.004 0.072 3850 Dihedral : 13.013 152.000 4506 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.14 % Favored : 88.82 % Rotamer: Outliers : 2.57 % Allowed : 17.26 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2638 helix: 0.14 (0.14), residues: 1540 sheet: -3.32 (0.47), residues: 80 loop : -2.86 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 302 TYR 0.021 0.001 TYR A 555 PHE 0.026 0.001 PHE A 434 TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (23173) covalent geometry : angle 0.65068 / 0.32 (31210) hydrogen bonds : bond 0.03250 / 2.15 ( 796) hydrogen bonds : angle 4.09076 / 2.82 ( 2307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8558 (mt) cc_final: 0.8144 (mt) REVERT: A 51 LEU cc_start: 0.8879 (tt) cc_final: 0.8585 (mt) REVERT: A 195 LEU cc_start: 0.8442 (mm) cc_final: 0.8181 (mt) REVERT: A 410 MET cc_start: 0.6510 (tmm) cc_final: 0.6276 (tmm) REVERT: B 96 MET cc_start: 0.8423 (mmm) cc_final: 0.8148 (mmm) REVERT: B 217 ASN cc_start: 0.8132 (m-40) cc_final: 0.7468 (p0) REVERT: B 301 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8126 (mtpt) REVERT: B 490 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8222 (tp) REVERT: B 574 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 637 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6973 (pp30) REVERT: C 63 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8496 (tppt) REVERT: C 78 MET cc_start: 0.7467 (mmt) cc_final: 0.7155 (mmt) REVERT: C 260 MET cc_start: 0.8700 (tpt) cc_final: 0.8467 (tpt) REVERT: C 265 HIS cc_start: 0.7417 (t70) cc_final: 0.6651 (t-170) REVERT: C 270 TYR cc_start: 0.8568 (t80) cc_final: 0.8114 (t80) REVERT: C 301 LYS cc_start: 0.8376 (tttt) cc_final: 0.8114 (tptt) REVERT: C 368 LEU cc_start: 0.8638 (pt) cc_final: 0.8160 (mp) REVERT: C 473 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8565 (tm-30) REVERT: C 628 ARG cc_start: 0.8195 (ptp-110) cc_final: 0.7708 (ptt90) REVERT: D 26 ARG cc_start: 0.5392 (mtm180) cc_final: 0.5117 (mtm180) REVERT: D 54 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7393 (ttpt) REVERT: D 210 THR cc_start: 0.8931 (m) cc_final: 0.8699 (p) REVERT: D 319 LEU cc_start: 0.8621 (mm) cc_final: 0.8328 (mt) REVERT: D 553 PHE cc_start: 0.8728 (t80) cc_final: 0.8430 (t80) REVERT: D 594 ARG cc_start: 0.8363 (mpp80) cc_final: 0.7995 (mpp80) REVERT: E 49 GLN cc_start: 0.8413 (tp40) cc_final: 0.8064 (tp40) REVERT: E 72 MET cc_start: 0.7648 (mmm) cc_final: 0.6961 (mmt) REVERT: E 126 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7317 (ttp-170) outliers start: 59 outliers final: 43 residues processed: 368 average time/residue: 0.1427 time to fit residues: 83.3534 Evaluate side-chains 363 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 88 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 105 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN C 158 ASN C 640 ASN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125367 restraints weight = 33135.253| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.27 r_work: 0.3314 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23173 Z= 0.111 Angle : 0.646 15.009 31210 Z= 0.318 Chirality : 0.040 0.192 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.750 151.249 4506 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.61 % Favored : 89.35 % Rotamer: Outliers : 2.22 % Allowed : 17.83 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2638 helix: 0.29 (0.14), residues: 1544 sheet: -3.14 (0.49), residues: 78 loop : -2.82 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 302 TYR 0.022 0.001 TYR A 555 PHE 0.017 0.001 PHE A 456 TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (23173) covalent geometry : angle 0.64573 / 0.32 (31210) hydrogen bonds : bond 0.03041 / 2.02 ( 796) hydrogen bonds : angle 3.98457 / 2.76 ( 2307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8875 (tt) cc_final: 0.8586 (mt) REVERT: A 195 LEU cc_start: 0.8405 (mm) cc_final: 0.8125 (mt) REVERT: A 410 MET cc_start: 0.6499 (tmm) cc_final: 0.6259 (tmm) REVERT: A 565 ILE cc_start: 0.9087 (pp) cc_final: 0.8673 (mm) REVERT: B 96 MET cc_start: 0.8449 (mmm) cc_final: 0.8221 (mmm) REVERT: B 217 ASN cc_start: 0.8050 (m-40) cc_final: 0.7420 (p0) REVERT: B 255 MET cc_start: 0.8339 (mmm) cc_final: 0.8117 (mmm) REVERT: B 301 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8148 (mtpt) REVERT: B 574 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 610 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7365 (tpp80) REVERT: B 637 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6966 (pp30) REVERT: C 63 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8488 (tppt) REVERT: C 78 MET cc_start: 0.7390 (mmt) cc_final: 0.7072 (mmt) REVERT: C 255 MET cc_start: 0.8780 (mmt) cc_final: 0.8292 (mmp) REVERT: C 260 MET cc_start: 0.8742 (tpt) cc_final: 0.8525 (tpt) REVERT: C 265 HIS cc_start: 0.7432 (t70) cc_final: 0.6678 (t-170) REVERT: C 270 TYR cc_start: 0.8478 (t80) cc_final: 0.8063 (t80) REVERT: C 301 LYS cc_start: 0.8338 (tttt) cc_final: 0.8016 (tptt) REVERT: C 368 LEU cc_start: 0.8609 (pt) cc_final: 0.8140 (mp) REVERT: C 473 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 628 ARG cc_start: 0.8189 (ptp-110) cc_final: 0.7749 (ptt90) REVERT: D 26 ARG cc_start: 0.5426 (mtm180) cc_final: 0.5176 (mtm180) REVERT: D 54 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7343 (ttpt) REVERT: D 210 THR cc_start: 0.8906 (m) cc_final: 0.8689 (p) REVERT: D 319 LEU cc_start: 0.8586 (mm) cc_final: 0.8306 (mp) REVERT: D 553 PHE cc_start: 0.8692 (t80) cc_final: 0.8436 (t80) REVERT: D 594 ARG cc_start: 0.8409 (mpp80) cc_final: 0.8069 (mpp80) REVERT: E 49 GLN cc_start: 0.8382 (tp40) cc_final: 0.7998 (tp40) REVERT: E 72 MET cc_start: 0.7689 (mmm) cc_final: 0.7001 (mmt) REVERT: E 75 LYS cc_start: 0.7005 (tppt) cc_final: 0.6664 (mmtm) REVERT: E 126 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7290 (ttp-170) outliers start: 51 outliers final: 39 residues processed: 363 average time/residue: 0.1410 time to fit residues: 81.5476 Evaluate side-chains 359 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 316 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 640 ASN Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 237 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 246 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125760 restraints weight = 33071.831| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.17 r_work: 0.3320 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 23173 Z= 0.188 Angle : 0.781 59.190 31210 Z= 0.419 Chirality : 0.047 1.454 3443 Planarity : 0.005 0.100 3850 Dihedral : 12.752 151.248 4506 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.58 % Favored : 89.39 % Rotamer: Outliers : 2.17 % Allowed : 18.22 % Favored : 79.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.17), residues: 2638 helix: 0.31 (0.14), residues: 1544 sheet: -3.14 (0.49), residues: 78 loop : -2.81 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 641 TYR 0.018 0.001 TYR A 555 PHE 0.014 0.001 PHE A 456 TRP 0.015 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (23173) covalent geometry : angle 0.78146 / 0.42 (31210) hydrogen bonds : bond 0.03042 / 2.02 ( 796) hydrogen bonds : angle 3.98843 / 2.76 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5061.47 seconds wall clock time: 87 minutes 41.61 seconds (5261.61 seconds total)