Starting phenix.real_space_refine on Sat Jan 25 00:49:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cui_45934/01_2025/9cui_45934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cui_45934/01_2025/9cui_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_45934/01_2025/9cui_45934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cui_45934/01_2025/9cui_45934.map" model { file = "/net/cci-nas-00/data/ceres_data/9cui_45934/01_2025/9cui_45934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cui_45934/01_2025/9cui_45934.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 356 Unusual residues: {' CA': 2, 'CLR': 1, 'PCW': 12, 'Y01': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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-2': 3, 'PCW:plan-3': 9, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 358 Unusual residues: {' CA': 1, 'CLR': 1, 'PCW': 9, 'Y01': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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-2': 1, 'PCW:plan-3': 6, 'PCW:plan-4': 6} 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-2': 1, 'PCW:plan-3': 7, 'PCW:plan-4': 7} 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-2': 2, 'PCW:plan-3': 9, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.29, per 1000 atoms: 0.59 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: 5.72 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.07 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: 5.95 Time building geometry restraints manager: 6.44 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 1.980 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 46.380 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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= 0.660 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.002 TRP C 45 HIS 0.014 0.002 HIS B 522 PHE 0.033 0.002 PHE D 508 TYR 0.022 0.002 TYR C 547 ARG 0.008 0.001 ARG D 350 *********************** 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 : 2.468 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: 0.7960 (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: 0.8300 (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: 0.3940 time to fit residues: 352.5682 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 : 2.501 ------------------------------------------------------------------------------- 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 222 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 131 ASN B 174 ASN B 185 HIS B 206 GLN B 252 ASN B 267 GLN B 365 ASN B 418 GLN B 426 HIS B 572 ASN B 587 HIS C 74 GLN C 158 ASN C 214 GLN 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 572 ASN D 587 HIS E 49 GLN E 53 ASN E 107 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130922 restraints weight = 33727.884| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.71 r_work: 0.3455 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2697 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= 0.193 Angle : 0.725 11.146 31210 Z= 0.371 Chirality : 0.042 0.200 3443 Planarity : 0.006 0.065 3850 Dihedral : 16.191 177.900 4506 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.69 % Favored : 89.01 % Rotamer: Outliers : 2.48 % Allowed : 11.96 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.13), residues: 2638 helix: -2.70 (0.10), residues: 1529 sheet: -3.97 (0.39), residues: 89 loop : -3.40 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 29 HIS 0.010 0.001 HIS B 587 PHE 0.027 0.002 PHE A 531 TYR 0.017 0.001 TYR A 524 ARG 0.008 0.001 ARG A 363 *********************** 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 462 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8465 (m-80) cc_final: 0.8249 (m-10) REVERT: A 195 LEU cc_start: 0.8314 (mm) cc_final: 0.8085 (mt) REVERT: A 308 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 549 VAL cc_start: 0.9182 (t) cc_final: 0.8812 (p) REVERT: A 565 ILE cc_start: 0.9110 (pp) cc_final: 0.8857 (mp) REVERT: B 266 THR cc_start: 0.8728 (t) cc_final: 0.8514 (m) REVERT: B 410 MET cc_start: 0.6062 (mpp) cc_final: 0.5263 (ppp) REVERT: B 613 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.7139 (t60) REVERT: C 63 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8545 (tppt) REVERT: C 78 MET cc_start: 0.7395 (mmt) cc_final: 0.6863 (mmt) REVERT: C 80 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: C 265 HIS cc_start: 0.7508 (t70) cc_final: 0.7107 (t-170) REVERT: C 294 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 368 LEU cc_start: 0.8443 (pt) cc_final: 0.8054 (mp) REVERT: C 410 MET cc_start: 0.3956 (mtt) cc_final: 0.3735 (mtp) REVERT: C 432 TYR cc_start: 0.8925 (t80) cc_final: 0.8028 (t80) REVERT: C 473 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 485 MET cc_start: 0.8167 (mmt) cc_final: 0.7948 (mmt) REVERT: D 96 MET cc_start: 0.9184 (mmt) cc_final: 0.8967 (mmm) REVERT: D 210 THR cc_start: 0.8933 (m) cc_final: 0.8707 (p) REVERT: D 319 LEU cc_start: 0.8786 (mm) cc_final: 0.8536 (mt) REVERT: D 554 MET cc_start: 0.8393 (tpt) cc_final: 0.8187 (tpp) REVERT: D 594 ARG cc_start: 0.8372 (mpp80) cc_final: 0.7990 (mpp80) REVERT: D 611 CYS cc_start: 0.7861 (t) cc_final: 0.7618 (m) REVERT: E 49 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8111 (tp40) REVERT: E 86 ARG cc_start: 0.7942 (ttm170) cc_final: 0.7633 (ttm-80) REVERT: E 144 MET cc_start: 0.7568 (mmm) cc_final: 0.6847 (tpp) outliers start: 57 outliers final: 28 residues processed: 442 average time/residue: 0.3488 time to fit residues: 238.8314 Evaluate side-chains 362 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 330 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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 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 489 ASP Chi-restraints excluded: chain B residue 373 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 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL 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 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 522 HIS B 546 ASN B 637 GLN C 74 GLN C 118 GLN C 158 ASN C 694 ASN D 522 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 53 ASN E 107 HIS E 111 ASN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129017 restraints weight = 33635.528| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.92 r_work: 0.3424 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23173 Z= 0.202 Angle : 0.668 9.858 31210 Z= 0.338 Chirality : 0.042 0.194 3443 Planarity : 0.005 0.060 3850 Dihedral : 14.939 163.289 4506 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.92 % Favored : 88.86 % Rotamer: Outliers : 2.78 % Allowed : 13.39 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.83 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.15), residues: 2638 helix: -1.59 (0.12), residues: 1532 sheet: -4.11 (0.40), residues: 84 loop : -3.22 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 29 HIS 0.004 0.001 HIS B 522 PHE 0.021 0.001 PHE B 478 TYR 0.013 0.001 TYR D 324 ARG 0.005 0.000 ARG C 140 *********************** 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 413 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 349 time to evaluate : 3.406 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8385 (mm) cc_final: 0.8144 (mt) REVERT: A 502 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8880 (mt) REVERT: A 549 VAL cc_start: 0.9170 (t) cc_final: 0.8765 (p) REVERT: A 554 MET cc_start: 0.8448 (tpt) cc_final: 0.8223 (tpp) REVERT: A 565 ILE cc_start: 0.9170 (pp) cc_final: 0.8802 (mp) REVERT: B 128 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6673 (tm-30) REVERT: B 211 PHE cc_start: 0.8534 (m-80) cc_final: 0.8332 (m-10) REVERT: B 270 TYR cc_start: 0.8468 (t80) cc_final: 0.8004 (t80) REVERT: B 301 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8018 (mtpt) REVERT: B 410 MET cc_start: 0.6032 (mpp) cc_final: 0.5339 (ppp) REVERT: B 577 MET cc_start: 0.8442 (ttm) cc_final: 0.8241 (ttp) REVERT: B 613 TRP cc_start: 0.8587 (OUTLIER) cc_final: 0.7257 (t60) REVERT: B 637 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6798 (pp30) REVERT: C 63 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8560 (tppt) REVERT: C 78 MET cc_start: 0.7401 (mmt) cc_final: 0.6885 (mmt) REVERT: C 265 HIS cc_start: 0.7585 (t70) cc_final: 0.6537 (t-170) REVERT: C 368 LEU cc_start: 0.8564 (pt) cc_final: 0.8095 (mp) REVERT: C 394 ILE cc_start: 0.8923 (mt) cc_final: 0.8663 (mm) REVERT: C 410 MET cc_start: 0.3956 (mtt) cc_final: 0.3678 (mtp) REVERT: C 473 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 26 ARG cc_start: 0.5584 (mtm180) cc_final: 0.5254 (mtm180) REVERT: D 188 ASP cc_start: 0.6816 (t0) cc_final: 0.6223 (p0) REVERT: D 210 THR cc_start: 0.8956 (m) cc_final: 0.8705 (p) REVERT: D 319 LEU cc_start: 0.8758 (mm) cc_final: 0.8503 (mt) REVERT: D 594 ARG cc_start: 0.8423 (mpp80) cc_final: 0.8102 (mpp80) REVERT: D 611 CYS cc_start: 0.7728 (t) cc_final: 0.7487 (m) REVERT: E 49 GLN cc_start: 0.8378 (tp40) cc_final: 0.8141 (tp40) REVERT: E 72 MET cc_start: 0.7745 (mmm) cc_final: 0.7079 (mmt) REVERT: E 144 MET cc_start: 0.7541 (mmm) cc_final: 0.6788 (tpp) outliers start: 64 outliers final: 34 residues processed: 393 average time/residue: 0.3595 time to fit residues: 219.2408 Evaluate side-chains 359 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 235 VAL 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 455 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 502 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 390 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 578 MET 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 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL 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 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 3 optimal weight: 5.9990 chunk 144 optimal weight: 0.0000 chunk 176 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 202 optimal weight: 0.0040 chunk 215 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 74 GLN C 158 ASN C 642 GLN C 694 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS E 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130654 restraints weight = 34032.550| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.60 r_work: 0.3426 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3441 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= 0.173 Angle : 0.637 9.599 31210 Z= 0.320 Chirality : 0.041 0.221 3443 Planarity : 0.005 0.060 3850 Dihedral : 14.241 154.184 4506 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.96 % Favored : 88.82 % Rotamer: Outliers : 2.78 % Allowed : 13.87 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.16), residues: 2638 helix: -0.93 (0.13), residues: 1531 sheet: -3.78 (0.43), residues: 80 loop : -3.10 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.004 0.001 HIS D 225 PHE 0.020 0.001 PHE B 478 TYR 0.015 0.001 TYR D 555 ARG 0.006 0.000 ARG A 359 *********************** 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 410 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8377 (mm) cc_final: 0.8124 (mt) REVERT: A 368 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8216 (mm) REVERT: A 565 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8925 (pt) REVERT: B 99 MET cc_start: 0.7307 (mmm) cc_final: 0.6998 (mmp) REVERT: B 128 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6719 (tm-30) REVERT: B 301 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8045 (mtpt) REVERT: B 410 MET cc_start: 0.6029 (mpp) cc_final: 0.5368 (ppp) REVERT: B 577 MET cc_start: 0.8392 (ttm) cc_final: 0.8090 (ttp) REVERT: C 63 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8564 (tppt) REVERT: C 265 HIS cc_start: 0.7445 (t70) cc_final: 0.6426 (t-170) REVERT: C 270 TYR cc_start: 0.8501 (t80) cc_final: 0.8061 (t80) REVERT: C 294 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 368 LEU cc_start: 0.8563 (pt) cc_final: 0.8079 (mp) REVERT: C 394 ILE cc_start: 0.8936 (mt) cc_final: 0.8703 (mm) REVERT: C 410 MET cc_start: 0.3817 (mtt) cc_final: 0.3591 (mtp) REVERT: C 473 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 485 MET cc_start: 0.8081 (mmt) cc_final: 0.7871 (mmt) REVERT: C 578 MET cc_start: 0.8231 (mtt) cc_final: 0.7907 (mtt) REVERT: D 188 ASP cc_start: 0.6734 (t0) cc_final: 0.6128 (p0) REVERT: D 210 THR cc_start: 0.8942 (m) cc_final: 0.8691 (p) REVERT: D 257 GLN cc_start: 0.8499 (mt0) cc_final: 0.8270 (mm-40) REVERT: D 319 LEU cc_start: 0.8755 (mm) cc_final: 0.8473 (mt) REVERT: D 435 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8123 (mtp) REVERT: D 481 MET cc_start: 0.8542 (mmt) cc_final: 0.8254 (mmm) REVERT: D 594 ARG cc_start: 0.8397 (mpp80) cc_final: 0.8070 (mpp80) REVERT: D 611 CYS cc_start: 0.7785 (t) cc_final: 0.7458 (m) REVERT: E 49 GLN cc_start: 0.8326 (tp40) cc_final: 0.8004 (tp40) REVERT: E 72 MET cc_start: 0.7806 (mmm) cc_final: 0.7107 (mmt) REVERT: E 109 MET cc_start: 0.6646 (mmt) cc_final: 0.6435 (mmp) REVERT: E 126 ARG cc_start: 0.7560 (mtp180) cc_final: 0.7193 (ttp-170) outliers start: 64 outliers final: 39 residues processed: 391 average time/residue: 0.3313 time to fit residues: 204.0186 Evaluate side-chains 366 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 323 time to evaluate : 2.426 ------------------------------------------------------------------------------- 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 235 VAL 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 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 540 ILE Chi-restraints excluded: chain B residue 554 MET 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 235 VAL 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 574 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 143 VAL 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 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 230 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 164 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 262 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.0980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN C 158 ASN C 694 ASN ** D 546 ASN ** 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 = 0.4085 r_free = 0.4085 target = 0.170104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131286 restraints weight = 33841.076| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.56 r_work: 0.3461 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23173 Z= 0.145 Angle : 0.612 14.051 31210 Z= 0.305 Chirality : 0.039 0.191 3443 Planarity : 0.004 0.062 3850 Dihedral : 13.475 154.246 4506 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 2.83 % Allowed : 14.61 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2638 helix: -0.34 (0.13), residues: 1529 sheet: -3.58 (0.46), residues: 79 loop : -3.07 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 29 HIS 0.004 0.001 HIS D 426 PHE 0.019 0.001 PHE D 256 TYR 0.019 0.001 TYR A 555 ARG 0.006 0.000 ARG D 302 *********************** 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 432 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 367 time to evaluate : 2.570 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8912 (tt) cc_final: 0.8621 (mt) REVERT: A 195 LEU cc_start: 0.8402 (mm) cc_final: 0.8165 (mt) REVERT: A 347 CYS cc_start: 0.8004 (m) cc_final: 0.7800 (m) REVERT: A 565 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8882 (pt) REVERT: B 99 MET cc_start: 0.7438 (mmm) cc_final: 0.7126 (mmm) REVERT: B 128 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6838 (tm-30) REVERT: B 217 ASN cc_start: 0.8012 (m-40) cc_final: 0.7361 (p0) REVERT: B 301 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8024 (mtpt) REVERT: B 490 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 577 MET cc_start: 0.8230 (ttm) cc_final: 0.7994 (ttp) REVERT: B 637 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6657 (pp30) REVERT: C 78 MET cc_start: 0.7062 (mmt) cc_final: 0.6755 (mmt) REVERT: C 294 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 368 LEU cc_start: 0.8497 (pt) cc_final: 0.8029 (mp) REVERT: C 394 ILE cc_start: 0.8879 (mt) cc_final: 0.8661 (mm) REVERT: C 473 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 628 ARG cc_start: 0.8204 (ptp-110) cc_final: 0.7586 (ptt90) REVERT: D 188 ASP cc_start: 0.6672 (t0) cc_final: 0.6140 (p0) REVERT: D 210 THR cc_start: 0.8895 (m) cc_final: 0.8656 (p) REVERT: D 294 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: D 315 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: D 319 LEU cc_start: 0.8694 (mm) cc_final: 0.8431 (mt) REVERT: D 594 ARG cc_start: 0.8385 (mpp80) cc_final: 0.8084 (mpp80) REVERT: E 49 GLN cc_start: 0.8365 (tp40) cc_final: 0.8052 (tp40) REVERT: E 72 MET cc_start: 0.7733 (mmm) cc_final: 0.7007 (mmt) REVERT: E 109 MET cc_start: 0.6504 (mmt) cc_final: 0.6233 (mmp) REVERT: E 135 GLN cc_start: 0.7848 (tt0) cc_final: 0.7457 (tt0) outliers start: 65 outliers final: 31 residues processed: 413 average time/residue: 0.3429 time to fit residues: 224.0266 Evaluate side-chains 356 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 2.647 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 499 VAL 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 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 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 143 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain E residue 28 THR 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 7 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 370 GLN A 464 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 582 HIS C 694 ASN D 62 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123502 restraints weight = 32888.999| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.53 r_work: 0.3284 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23173 Z= 0.239 Angle : 0.650 12.254 31210 Z= 0.325 Chirality : 0.042 0.231 3443 Planarity : 0.005 0.065 3850 Dihedral : 13.393 154.133 4504 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.45 % Favored : 88.48 % Rotamer: Outliers : 2.65 % Allowed : 15.70 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2638 helix: -0.17 (0.13), residues: 1523 sheet: -3.48 (0.47), residues: 78 loop : -2.98 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 29 HIS 0.004 0.001 HIS D 426 PHE 0.021 0.001 PHE B 434 TYR 0.014 0.001 TYR C 377 ARG 0.007 0.000 ARG D 302 *********************** 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 399 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 2.517 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8929 (tt) cc_final: 0.8644 (mt) REVERT: A 195 LEU cc_start: 0.8569 (mm) cc_final: 0.8274 (mt) REVERT: B 217 ASN cc_start: 0.8097 (m-40) cc_final: 0.7427 (p0) REVERT: B 255 MET cc_start: 0.8106 (mmm) cc_final: 0.7832 (mmt) REVERT: B 301 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8105 (mtpt) REVERT: B 490 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8222 (tp) REVERT: C 63 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8565 (tppt) REVERT: C 78 MET cc_start: 0.7299 (mmt) cc_final: 0.6958 (mmt) REVERT: C 265 HIS cc_start: 0.7519 (t70) cc_final: 0.6694 (t-170) REVERT: C 270 TYR cc_start: 0.8580 (t80) cc_final: 0.8113 (t80) REVERT: C 368 LEU cc_start: 0.8610 (pt) cc_final: 0.8129 (mp) REVERT: C 473 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 574 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8240 (tp) REVERT: C 578 MET cc_start: 0.8179 (mtt) cc_final: 0.7879 (mtt) REVERT: C 628 ARG cc_start: 0.8195 (ptp-110) cc_final: 0.7634 (ptt90) REVERT: D 54 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7457 (ttpt) REVERT: D 188 ASP cc_start: 0.6658 (t0) cc_final: 0.6187 (p0) REVERT: D 210 THR cc_start: 0.8994 (m) cc_final: 0.8739 (p) REVERT: D 250 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 294 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: D 319 LEU cc_start: 0.8702 (mm) cc_final: 0.8418 (mt) REVERT: D 594 ARG cc_start: 0.8417 (mpp80) cc_final: 0.8092 (mpp80) REVERT: E 49 GLN cc_start: 0.8389 (tp40) cc_final: 0.8092 (tp40) REVERT: E 72 MET cc_start: 0.7828 (mmm) cc_final: 0.7085 (mmt) REVERT: E 109 MET cc_start: 0.6861 (mmt) cc_final: 0.6576 (mmp) outliers start: 61 outliers final: 41 residues processed: 382 average time/residue: 0.3510 time to fit residues: 209.8730 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 : 2.578 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 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 592 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 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 574 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 143 VAL 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 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 28 THR 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 195 optimal weight: 10.0000 chunk 235 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 186 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 374 GLN B 637 GLN C 694 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125897 restraints weight = 33055.928| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.50 r_work: 0.3322 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23173 Z= 0.172 Angle : 0.626 12.693 31210 Z= 0.310 Chirality : 0.040 0.237 3443 Planarity : 0.004 0.068 3850 Dihedral : 13.048 153.153 4504 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.69 % Favored : 89.23 % Rotamer: Outliers : 2.30 % Allowed : 16.70 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2638 helix: 0.09 (0.14), residues: 1527 sheet: -3.35 (0.48), residues: 78 loop : -2.91 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 PHE 0.020 0.001 PHE D 456 TYR 0.014 0.001 TYR D 524 ARG 0.006 0.000 ARG D 302 *********************** 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 389 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8916 (tt) cc_final: 0.8669 (mt) REVERT: A 195 LEU cc_start: 0.8374 (mm) cc_final: 0.8111 (mt) REVERT: A 280 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8102 (tt) REVERT: A 410 MET cc_start: 0.6772 (tmm) cc_final: 0.6443 (tmm) REVERT: A 565 ILE cc_start: 0.9117 (pp) cc_final: 0.8717 (mp) REVERT: B 96 MET cc_start: 0.8256 (mmm) cc_final: 0.8032 (mmm) REVERT: B 173 VAL cc_start: 0.8446 (t) cc_final: 0.8215 (p) REVERT: B 217 ASN cc_start: 0.8107 (m-40) cc_final: 0.7485 (p0) REVERT: B 255 MET cc_start: 0.7999 (mmm) cc_final: 0.7705 (mmt) REVERT: B 301 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8118 (mtpt) REVERT: B 410 MET cc_start: 0.6153 (mpp) cc_final: 0.5436 (ppp) REVERT: B 637 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7068 (pp30) REVERT: C 63 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8552 (tppt) REVERT: C 78 MET cc_start: 0.7283 (mmt) cc_final: 0.6947 (mmt) REVERT: C 234 LEU cc_start: 0.7894 (mt) cc_final: 0.7637 (mt) REVERT: C 265 HIS cc_start: 0.7511 (t70) cc_final: 0.6728 (t-170) REVERT: C 270 TYR cc_start: 0.8520 (t80) cc_final: 0.8051 (t80) REVERT: C 368 LEU cc_start: 0.8595 (pt) cc_final: 0.8148 (mp) REVERT: C 473 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 628 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7655 (ptt90) REVERT: D 54 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7406 (ttpt) REVERT: D 188 ASP cc_start: 0.6618 (t0) cc_final: 0.6093 (p0) REVERT: D 210 THR cc_start: 0.8934 (m) cc_final: 0.8697 (p) REVERT: D 250 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7786 (mm-30) REVERT: D 319 LEU cc_start: 0.8622 (mm) cc_final: 0.8358 (mt) REVERT: D 481 MET cc_start: 0.8525 (mmm) cc_final: 0.8261 (mmm) REVERT: D 553 PHE cc_start: 0.8653 (t80) cc_final: 0.8379 (t80) REVERT: D 594 ARG cc_start: 0.8402 (mpp80) cc_final: 0.8132 (mpp80) REVERT: E 49 GLN cc_start: 0.8437 (tp40) cc_final: 0.8164 (tp40) REVERT: E 72 MET cc_start: 0.7721 (mmm) cc_final: 0.6999 (mmt) REVERT: E 135 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: E 144 MET cc_start: 0.7269 (mmm) cc_final: 0.6837 (tpp) outliers start: 53 outliers final: 37 residues processed: 374 average time/residue: 0.3409 time to fit residues: 200.2896 Evaluate side-chains 358 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 383 ASP 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 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 574 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 315 GLU 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 135 GLN 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 79 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 232 optimal weight: 0.2980 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 637 GLN ** D 546 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 = 0.3946 r_free = 0.3946 target = 0.162082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126055 restraints weight = 32982.913| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.42 r_work: 0.3313 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23173 Z= 0.171 Angle : 0.628 11.398 31210 Z= 0.310 Chirality : 0.041 0.233 3443 Planarity : 0.004 0.072 3850 Dihedral : 12.817 152.855 4504 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.03 % Favored : 88.93 % Rotamer: Outliers : 2.43 % Allowed : 16.74 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2638 helix: 0.26 (0.14), residues: 1528 sheet: -3.32 (0.48), residues: 78 loop : -2.84 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 PHE 0.026 0.001 PHE B 434 TYR 0.022 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 *********************** 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 376 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 2.434 Fit side-chains REVERT: A 51 LEU cc_start: 0.8894 (tt) cc_final: 0.8634 (mt) REVERT: A 110 MET cc_start: 0.5679 (mtt) cc_final: 0.5418 (mmt) REVERT: A 195 LEU cc_start: 0.8492 (mm) cc_final: 0.8225 (mt) REVERT: A 565 ILE cc_start: 0.9098 (pp) cc_final: 0.8669 (mp) REVERT: B 96 MET cc_start: 0.8301 (mmm) cc_final: 0.8052 (mmm) REVERT: B 217 ASN cc_start: 0.8024 (m-40) cc_final: 0.7429 (p0) REVERT: B 255 MET cc_start: 0.8170 (mmm) cc_final: 0.7964 (mmt) REVERT: B 301 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8141 (mtpt) REVERT: B 637 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6991 (pp30) REVERT: C 63 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8508 (tppt) REVERT: C 234 LEU cc_start: 0.7873 (mt) cc_final: 0.7608 (mt) REVERT: C 265 HIS cc_start: 0.7587 (t70) cc_final: 0.6869 (t-170) REVERT: C 270 TYR cc_start: 0.8521 (t80) cc_final: 0.8066 (t80) REVERT: C 345 MET cc_start: 0.8773 (mmm) cc_final: 0.8449 (mmm) REVERT: C 368 LEU cc_start: 0.8610 (pt) cc_final: 0.8170 (mp) REVERT: C 473 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 578 MET cc_start: 0.7985 (mtt) cc_final: 0.7693 (mtt) REVERT: C 628 ARG cc_start: 0.8141 (ptp-110) cc_final: 0.7685 (ptt90) REVERT: D 54 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7407 (ttpt) REVERT: D 188 ASP cc_start: 0.6603 (t0) cc_final: 0.6096 (p0) REVERT: D 210 THR cc_start: 0.8914 (m) cc_final: 0.8695 (p) REVERT: D 250 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 319 LEU cc_start: 0.8585 (mm) cc_final: 0.8325 (mt) REVERT: D 481 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8233 (mmm) REVERT: D 553 PHE cc_start: 0.8660 (t80) cc_final: 0.8398 (t80) REVERT: D 594 ARG cc_start: 0.8396 (mpp80) cc_final: 0.8139 (mpp80) REVERT: E 41 GLN cc_start: 0.8616 (pt0) cc_final: 0.8331 (pt0) REVERT: E 49 GLN cc_start: 0.8439 (tp40) cc_final: 0.8075 (tp40) REVERT: E 72 MET cc_start: 0.7638 (mmm) cc_final: 0.6915 (mmt) REVERT: E 135 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: E 144 MET cc_start: 0.7218 (mmm) cc_final: 0.6517 (tpp) outliers start: 56 outliers final: 35 residues processed: 359 average time/residue: 0.3269 time to fit residues: 185.4532 Evaluate side-chains 350 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 383 ASP 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 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 574 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 90 ASP 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 481 MET 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 28 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 135 GLN Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN ** D 546 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 = 0.3923 r_free = 0.3923 target = 0.159955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124900 restraints weight = 33121.325| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.17 r_work: 0.3314 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23173 Z= 0.215 Angle : 0.658 13.580 31210 Z= 0.323 Chirality : 0.042 0.224 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.798 152.623 4504 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.99 % Favored : 88.97 % Rotamer: Outliers : 1.96 % Allowed : 17.09 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2638 helix: 0.24 (0.14), residues: 1534 sheet: -3.28 (0.50), residues: 76 loop : -2.80 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 PHE 0.020 0.001 PHE E 65 TYR 0.021 0.001 TYR A 555 ARG 0.007 0.000 ARG D 302 *********************** 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 367 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 2.335 Fit side-chains REVERT: A 51 LEU cc_start: 0.8929 (tt) cc_final: 0.8649 (mt) REVERT: A 195 LEU cc_start: 0.8568 (mm) cc_final: 0.8302 (mt) REVERT: A 410 MET cc_start: 0.6566 (tmm) cc_final: 0.6279 (tmm) REVERT: A 565 ILE cc_start: 0.9159 (pp) cc_final: 0.8731 (mp) REVERT: B 96 MET cc_start: 0.8454 (mmm) cc_final: 0.8141 (mmm) REVERT: B 100 GLU cc_start: 0.7708 (mp0) cc_final: 0.7402 (pm20) REVERT: B 217 ASN cc_start: 0.8072 (m-40) cc_final: 0.7425 (p0) REVERT: B 301 LYS cc_start: 0.8719 (mmtp) cc_final: 0.8096 (mtpt) REVERT: C 63 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8459 (tppt) REVERT: C 115 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: C 265 HIS cc_start: 0.7817 (t70) cc_final: 0.6929 (t-170) REVERT: C 270 TYR cc_start: 0.8595 (t80) cc_final: 0.8144 (t80) REVERT: C 301 LYS cc_start: 0.8209 (tttt) cc_final: 0.7754 (tptt) REVERT: C 345 MET cc_start: 0.8936 (mmm) cc_final: 0.8640 (mmm) REVERT: C 368 LEU cc_start: 0.8682 (pt) cc_final: 0.8180 (mp) REVERT: C 473 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8726 (tm-30) REVERT: C 578 MET cc_start: 0.8225 (mtt) cc_final: 0.7959 (mtt) REVERT: C 628 ARG cc_start: 0.8337 (ptp-110) cc_final: 0.7737 (ptt90) REVERT: C 641 ARG cc_start: 0.6568 (mmt-90) cc_final: 0.5998 (mmt-90) REVERT: D 54 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7430 (ttpt) REVERT: D 63 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8248 (ptpt) REVERT: D 188 ASP cc_start: 0.6870 (t0) cc_final: 0.6279 (p0) REVERT: D 210 THR cc_start: 0.8968 (m) cc_final: 0.8739 (p) REVERT: D 250 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 319 LEU cc_start: 0.8783 (mm) cc_final: 0.8505 (mt) REVERT: D 553 PHE cc_start: 0.8793 (t80) cc_final: 0.8483 (t80) REVERT: D 555 TYR cc_start: 0.8476 (t80) cc_final: 0.8269 (t80) REVERT: D 594 ARG cc_start: 0.8642 (mpp80) cc_final: 0.8391 (mpp80) REVERT: E 49 GLN cc_start: 0.8371 (tp40) cc_final: 0.7960 (tp40) REVERT: E 72 MET cc_start: 0.7742 (mmm) cc_final: 0.7061 (mmt) REVERT: E 109 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6358 (mmp) REVERT: E 135 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: E 144 MET cc_start: 0.6830 (mmm) cc_final: 0.6577 (tpp) outliers start: 45 outliers final: 37 residues processed: 353 average time/residue: 0.3302 time to fit residues: 183.7574 Evaluate side-chains 358 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 2.768 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 383 ASP 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 592 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 115 TYR 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 574 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 90 ASP 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 386 LEU 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 28 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 135 GLN 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 41 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN C 694 ASN ** D 546 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 = 0.3924 r_free = 0.3924 target = 0.160032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125019 restraints weight = 33001.356| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.23 r_work: 0.3303 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23173 Z= 0.205 Angle : 0.657 13.716 31210 Z= 0.322 Chirality : 0.042 0.296 3443 Planarity : 0.004 0.073 3850 Dihedral : 12.710 152.067 4504 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.07 % Favored : 88.89 % Rotamer: Outliers : 1.91 % Allowed : 17.78 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2638 helix: 0.32 (0.14), residues: 1535 sheet: -3.29 (0.48), residues: 78 loop : -2.77 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 PHE 0.030 0.001 PHE B 434 TYR 0.026 0.001 TYR B 555 ARG 0.008 0.000 ARG D 302 ********************** 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 368 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 324 time to evaluate : 3.171 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8514 (mt) cc_final: 0.8112 (mt) REVERT: A 51 LEU cc_start: 0.8898 (tt) cc_final: 0.8612 (mt) REVERT: A 195 LEU cc_start: 0.8403 (mm) cc_final: 0.8136 (mt) REVERT: A 410 MET cc_start: 0.6732 (tmm) cc_final: 0.6465 (tmm) REVERT: A 528 MET cc_start: 0.8048 (tpp) cc_final: 0.7727 (ttp) REVERT: A 565 ILE cc_start: 0.9128 (pp) cc_final: 0.8692 (mp) REVERT: B 96 MET cc_start: 0.8327 (mmm) cc_final: 0.8051 (mmm) REVERT: B 217 ASN cc_start: 0.7991 (m-40) cc_final: 0.7421 (p0) REVERT: B 301 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8145 (mtpt) REVERT: B 637 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7142 (pp30) REVERT: C 63 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8485 (tppt) REVERT: C 115 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: C 265 HIS cc_start: 0.7468 (t70) cc_final: 0.6650 (t-170) REVERT: C 270 TYR cc_start: 0.8567 (t80) cc_final: 0.8109 (t80) REVERT: C 301 LYS cc_start: 0.8290 (tttt) cc_final: 0.8033 (tptt) REVERT: C 345 MET cc_start: 0.8844 (mmm) cc_final: 0.8556 (mmm) REVERT: C 368 LEU cc_start: 0.8622 (pt) cc_final: 0.8145 (mp) REVERT: C 578 MET cc_start: 0.8082 (mtt) cc_final: 0.7804 (mtt) REVERT: C 628 ARG cc_start: 0.8163 (ptp-110) cc_final: 0.7683 (ptt90) REVERT: D 54 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7352 (ttpt) REVERT: D 63 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8297 (ptpt) REVERT: D 188 ASP cc_start: 0.6688 (t0) cc_final: 0.6154 (p0) REVERT: D 210 THR cc_start: 0.8914 (m) cc_final: 0.8679 (p) REVERT: D 250 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7829 (mm-30) REVERT: D 319 LEU cc_start: 0.8666 (mm) cc_final: 0.8361 (mt) REVERT: D 553 PHE cc_start: 0.8741 (t80) cc_final: 0.8441 (t80) REVERT: D 594 ARG cc_start: 0.8379 (mpp80) cc_final: 0.8126 (mpp80) REVERT: E 30 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7919 (tttm) REVERT: E 49 GLN cc_start: 0.8372 (tp40) cc_final: 0.7977 (tp40) REVERT: E 72 MET cc_start: 0.7495 (mmm) cc_final: 0.6796 (mmt) REVERT: E 135 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7885 (tt0) outliers start: 44 outliers final: 38 residues processed: 355 average time/residue: 0.3596 time to fit residues: 203.0122 Evaluate side-chains 360 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 383 ASP 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 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 115 TYR 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 574 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 90 ASP 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 386 LEU Chi-restraints excluded: chain D residue 481 MET 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 28 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 135 GLN 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 222 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN C 694 ASN D 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125673 restraints weight = 33022.196| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.34 r_work: 0.3324 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23173 Z= 0.167 Angle : 0.652 14.205 31210 Z= 0.317 Chirality : 0.041 0.280 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.481 151.415 4504 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.65 % Favored : 89.31 % Rotamer: Outliers : 1.96 % Allowed : 18.09 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2638 helix: 0.47 (0.14), residues: 1530 sheet: -3.22 (0.50), residues: 74 loop : -2.77 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 PHE 0.022 0.001 PHE D 434 TYR 0.021 0.001 TYR D 555 ARG 0.013 0.000 ARG B 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10316.68 seconds wall clock time: 185 minutes 44.96 seconds (11144.96 seconds total)