Starting phenix.real_space_refine on Thu Jun 19 15:43:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cui_45934/06_2025/9cui_45934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cui_45934/06_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_45934/06_2025/9cui_45934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cui_45934/06_2025/9cui_45934.map" model { file = "/net/cci-nas-00/data/ceres_data/9cui_45934/06_2025/9cui_45934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cui_45934/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.31, per 1000 atoms: 0.63 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: 5.86 Conformation dependent library (CDL) restraints added in 2.9 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: 2.24 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: 6.96 Time building geometry restraints manager: 6.91 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 51.330 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- 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= 0.561 Angle : 1.429 16.659 31210 Z= 0.744 Chirality : 0.056 0.459 3443 Planarity : 0.012 0.287 3850 Dihedral : 15.901 175.916 9660 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.30 % Favored : 88.17 % Rotamer: Outliers : 0.39 % Allowed : 5.87 % Favored : 93.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.24 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.33788 ( 796) hydrogen bonds : angle 10.41366 ( 2307) covalent geometry : bond 0.01128 (23173) covalent geometry : angle 1.42850 (31210) *********************** 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 : 2.455 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: 0.3775 time to fit residues: 339.2729 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 : 2.383 ------------------------------------------------------------------------------- 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= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 796) hydrogen bonds : angle 4.99865 ( 2307) covalent geometry : bond 0.00300 (23173) covalent geometry : angle 0.72532 (31210) *********************** 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 : 2.363 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: 0.8313 (mm) cc_final: 0.8084 (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: 0.8811 (p) REVERT: A 565 ILE cc_start: 0.9111 (pp) cc_final: 0.8857 (mp) REVERT: B 266 THR cc_start: 0.8728 (t) cc_final: 0.8513 (m) REVERT: B 410 MET cc_start: 0.6061 (mpp) cc_final: 0.5263 (ppp) REVERT: B 613 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7138 (t60) REVERT: C 63 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8545 (tppt) REVERT: C 78 MET cc_start: 0.7393 (mmt) cc_final: 0.6861 (mmt) REVERT: C 80 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7149 (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: 0.7807 (mt-10) REVERT: C 368 LEU cc_start: 0.8442 (pt) cc_final: 0.8053 (mp) REVERT: C 410 MET cc_start: 0.3955 (mtt) cc_final: 0.3734 (mtp) REVERT: C 432 TYR cc_start: 0.8924 (t80) cc_final: 0.8027 (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: 0.9185 (mmt) cc_final: 0.8968 (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: 0.8392 (tpt) cc_final: 0.8188 (tpp) REVERT: D 594 ARG cc_start: 0.8372 (mpp80) cc_final: 0.7991 (mpp80) REVERT: D 611 CYS cc_start: 0.7862 (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: 0.7943 (ttm170) cc_final: 0.7634 (ttm-80) REVERT: E 144 MET cc_start: 0.7567 (mmm) cc_final: 0.6847 (tpp) outliers start: 57 outliers final: 28 residues processed: 442 average time/residue: 0.3473 time to fit residues: 239.2071 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 : 2.272 ------------------------------------------------------------------------------- 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: 1.9990 chunk 158 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 177 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** D 582 HIS E 49 GLN E 53 ASN E 107 HIS E 111 ASN E 135 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130195 restraints weight = 33602.680| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.79 r_work: 0.3420 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3168 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= 0.129 Angle : 0.660 10.178 31210 Z= 0.334 Chirality : 0.041 0.189 3443 Planarity : 0.005 0.058 3850 Dihedral : 14.884 163.217 4506 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.99 % Favored : 88.82 % Rotamer: Outliers : 2.70 % Allowed : 13.39 % Favored : 83.91 % 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: -3.46 (0.15), residues: 2638 helix: -1.53 (0.12), residues: 1529 sheet: -4.09 (0.40), residues: 84 loop : -3.25 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 29 HIS 0.004 0.001 HIS D 426 PHE 0.022 0.001 PHE A 531 TYR 0.016 0.001 TYR D 324 ARG 0.005 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 796) hydrogen bonds : angle 4.42645 ( 2307) covalent geometry : bond 0.00282 (23173) covalent geometry : angle 0.66020 (31210) *********************** 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 422 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 360 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8933 (tt) cc_final: 0.8610 (mt) REVERT: A 195 LEU cc_start: 0.8363 (mm) cc_final: 0.8127 (mt) REVERT: A 502 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8837 (mt) REVERT: A 549 VAL cc_start: 0.9157 (t) cc_final: 0.8746 (p) REVERT: A 565 ILE cc_start: 0.9161 (pp) cc_final: 0.8781 (mp) REVERT: B 128 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6694 (tm-30) REVERT: B 270 TYR cc_start: 0.8399 (t80) cc_final: 0.8006 (t80) REVERT: B 301 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8005 (mtpt) REVERT: B 410 MET cc_start: 0.6018 (mpp) cc_final: 0.5327 (ppp) REVERT: B 613 TRP cc_start: 0.8563 (OUTLIER) cc_final: 0.7190 (t60) REVERT: B 637 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6788 (pp30) REVERT: C 78 MET cc_start: 0.7308 (mmt) cc_final: 0.6772 (mmt) REVERT: C 368 LEU cc_start: 0.8544 (pt) cc_final: 0.8071 (mp) REVERT: C 394 ILE cc_start: 0.8921 (mt) cc_final: 0.8654 (mm) REVERT: C 410 MET cc_start: 0.3952 (mtt) cc_final: 0.3669 (mtp) REVERT: C 473 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 26 ARG cc_start: 0.5591 (mtm180) cc_final: 0.5285 (mtm180) REVERT: D 188 ASP cc_start: 0.6705 (t0) cc_final: 0.6132 (p0) REVERT: D 210 THR cc_start: 0.8945 (m) cc_final: 0.8697 (p) REVERT: D 319 LEU cc_start: 0.8758 (mm) cc_final: 0.8516 (mt) REVERT: D 594 ARG cc_start: 0.8406 (mpp80) cc_final: 0.8076 (mpp80) REVERT: D 611 CYS cc_start: 0.7714 (t) cc_final: 0.7473 (m) REVERT: E 49 GLN cc_start: 0.8375 (tp40) cc_final: 0.8133 (tp40) REVERT: E 72 MET cc_start: 0.7734 (mmm) cc_final: 0.7066 (mmt) REVERT: E 144 MET cc_start: 0.7540 (mmm) cc_final: 0.6826 (tpp) outliers start: 62 outliers final: 26 residues processed: 403 average time/residue: 0.3358 time to fit residues: 211.4927 Evaluate side-chains 348 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 540 ILE 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 367 LEU Chi-restraints excluded: chain C residue 397 ILE 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: 10.0000 chunk 144 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN C 642 GLN C 694 ASN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.165470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127463 restraints weight = 34162.570| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.76 r_work: 0.3380 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23173 Z= 0.159 Angle : 0.667 13.221 31210 Z= 0.334 Chirality : 0.042 0.236 3443 Planarity : 0.005 0.060 3850 Dihedral : 14.347 153.755 4506 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.41 % Favored : 88.44 % Rotamer: Outliers : 3.00 % Allowed : 13.83 % Favored : 83.17 % 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: -2.81 (0.16), residues: 2638 helix: -0.97 (0.13), residues: 1538 sheet: -3.90 (0.43), residues: 83 loop : -3.06 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 29 HIS 0.004 0.001 HIS D 522 PHE 0.020 0.001 PHE B 478 TYR 0.014 0.001 TYR A 555 ARG 0.005 0.000 ARG D 606 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 796) hydrogen bonds : angle 4.32117 ( 2307) covalent geometry : bond 0.00374 (23173) covalent geometry : angle 0.66682 (31210) *********************** 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 401 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 332 time to evaluate : 2.472 Fit side-chains revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8519 (mm) cc_final: 0.8261 (mt) REVERT: A 565 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8935 (pt) REVERT: B 96 MET cc_start: 0.8455 (mmm) cc_final: 0.8229 (mmm) REVERT: B 128 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6825 (tm-30) REVERT: B 216 TYR cc_start: 0.7698 (t80) cc_final: 0.7480 (t80) REVERT: B 301 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8047 (mtpt) REVERT: B 410 MET cc_start: 0.6182 (mpp) cc_final: 0.5438 (ppp) REVERT: B 613 TRP cc_start: 0.8671 (OUTLIER) cc_final: 0.7342 (t60) REVERT: C 63 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8548 (tppt) REVERT: C 265 HIS cc_start: 0.7456 (t70) cc_final: 0.6499 (t-170) REVERT: C 270 TYR cc_start: 0.8543 (t80) cc_final: 0.8089 (t80) REVERT: C 294 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 368 LEU cc_start: 0.8612 (pt) cc_final: 0.8106 (mp) REVERT: C 394 ILE cc_start: 0.8873 (mt) cc_final: 0.8659 (mm) REVERT: C 410 MET cc_start: 0.3805 (mtt) cc_final: 0.3569 (mtp) REVERT: C 473 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 578 MET cc_start: 0.8334 (mtt) cc_final: 0.8085 (mtt) REVERT: D 188 ASP cc_start: 0.6971 (t0) cc_final: 0.6317 (p0) REVERT: D 210 THR cc_start: 0.8963 (m) cc_final: 0.8712 (p) REVERT: D 319 LEU cc_start: 0.8788 (mm) cc_final: 0.8498 (mt) REVERT: D 594 ARG cc_start: 0.8464 (mpp80) cc_final: 0.8144 (mpp80) REVERT: D 611 CYS cc_start: 0.7690 (t) cc_final: 0.7378 (m) REVERT: E 49 GLN cc_start: 0.8328 (tp40) cc_final: 0.7996 (tp40) REVERT: E 72 MET cc_start: 0.7842 (mmm) cc_final: 0.7156 (mmt) REVERT: E 126 ARG cc_start: 0.7708 (mtp180) cc_final: 0.7245 (ttp-170) outliers start: 69 outliers final: 46 residues processed: 382 average time/residue: 0.3396 time to fit residues: 205.8246 Evaluate side-chains 356 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 2.845 ------------------------------------------------------------------------------- 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 502 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 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 175 SER 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 587 HIS 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 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 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 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: 0.0870 chunk 68 optimal weight: 0.0970 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 141 optimal weight: 0.0370 chunk 8 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- 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** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4075 r_free = 0.4075 target = 0.169140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130272 restraints weight = 33865.492| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.06 r_work: 0.3447 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23173 Z= 0.105 Angle : 0.605 10.730 31210 Z= 0.304 Chirality : 0.039 0.191 3443 Planarity : 0.004 0.063 3850 Dihedral : 13.539 154.187 4506 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.50 % Favored : 89.39 % Rotamer: Outliers : 2.43 % Allowed : 14.65 % Favored : 82.91 % 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: -2.24 (0.16), residues: 2638 helix: -0.36 (0.13), residues: 1529 sheet: -3.61 (0.45), residues: 79 loop : -3.07 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.004 0.001 HIS A 185 PHE 0.017 0.001 PHE D 256 TYR 0.016 0.001 TYR A 555 ARG 0.005 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 796) hydrogen bonds : angle 4.01790 ( 2307) covalent geometry : bond 0.00225 (23173) covalent geometry : angle 0.60519 (31210) *********************** 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 417 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 361 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8298 (mm) cc_final: 0.8045 (mt) REVERT: A 367 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7022 (mp) REVERT: A 368 LEU cc_start: 0.8305 (mp) cc_final: 0.8088 (mm) REVERT: A 565 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (pt) REVERT: B 128 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 217 ASN cc_start: 0.8092 (m-40) cc_final: 0.7370 (p0) REVERT: B 301 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8050 (mtpt) REVERT: B 490 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 577 MET cc_start: 0.8421 (ttm) cc_final: 0.8190 (ttp) REVERT: B 637 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6686 (pp30) REVERT: C 63 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8556 (tppt) REVERT: C 78 MET cc_start: 0.7158 (mmt) cc_final: 0.6845 (mmt) REVERT: C 294 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 368 LEU cc_start: 0.8565 (pt) cc_final: 0.8069 (mp) REVERT: C 394 ILE cc_start: 0.8908 (mt) cc_final: 0.8695 (mm) REVERT: C 410 MET cc_start: 0.3611 (mtt) cc_final: 0.3403 (mtp) REVERT: C 473 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 628 ARG cc_start: 0.8270 (ptp-110) cc_final: 0.7628 (ptt90) REVERT: D 188 ASP cc_start: 0.6720 (t0) cc_final: 0.6120 (p0) REVERT: D 210 THR cc_start: 0.8905 (m) cc_final: 0.8665 (p) REVERT: D 294 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: D 319 LEU cc_start: 0.8716 (mm) cc_final: 0.8454 (mt) REVERT: D 553 PHE cc_start: 0.8570 (t80) cc_final: 0.8335 (t80) REVERT: D 594 ARG cc_start: 0.8440 (mpp80) cc_final: 0.8142 (mpp80) REVERT: D 606 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7529 (ttm-80) REVERT: D 611 CYS cc_start: 0.7724 (t) cc_final: 0.7304 (m) REVERT: E 30 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8322 (ttmm) REVERT: E 49 GLN cc_start: 0.8433 (tp40) cc_final: 0.8152 (tp40) REVERT: E 72 MET cc_start: 0.7823 (mmm) cc_final: 0.7079 (mmt) REVERT: E 99 TYR cc_start: 0.7681 (m-80) cc_final: 0.7463 (m-80) REVERT: E 126 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7220 (ttp-170) outliers start: 56 outliers final: 30 residues processed: 401 average time/residue: 0.3382 time to fit residues: 212.9755 Evaluate side-chains 358 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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 367 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 565 ILE 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 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 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 143 VAL Chi-restraints excluded: chain D residue 179 VAL 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 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: 3.9990 chunk 19 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 0.0070 chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 374 GLN B 637 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 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 = 0.162054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125784 restraints weight = 32878.592| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.46 r_work: 0.3326 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23173 Z= 0.112 Angle : 0.624 15.224 31210 Z= 0.310 Chirality : 0.040 0.188 3443 Planarity : 0.004 0.064 3850 Dihedral : 13.241 153.667 4506 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.99 % Favored : 88.93 % Rotamer: Outliers : 2.96 % Allowed : 15.57 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.16), residues: 2638 helix: -0.06 (0.13), residues: 1526 sheet: -3.50 (0.46), residues: 80 loop : -3.00 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 PHE 0.022 0.001 PHE B 434 TYR 0.022 0.001 TYR B 216 ARG 0.006 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 796) hydrogen bonds : angle 4.00294 ( 2307) covalent geometry : bond 0.00249 (23173) covalent geometry : angle 0.62445 (31210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 333 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8907 (tt) cc_final: 0.8616 (mt) REVERT: A 195 LEU cc_start: 0.8477 (mm) cc_final: 0.8182 (mt) REVERT: B 217 ASN cc_start: 0.8054 (m-40) cc_final: 0.7474 (p0) REVERT: B 301 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8114 (mtpt) REVERT: B 490 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 577 MET cc_start: 0.8379 (ttm) cc_final: 0.8165 (ttp) REVERT: B 637 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6898 (pp30) REVERT: C 63 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8596 (tppt) REVERT: C 78 MET cc_start: 0.7230 (mmt) cc_final: 0.6923 (mmt) REVERT: C 265 HIS cc_start: 0.7434 (t70) cc_final: 0.6596 (t-170) REVERT: C 270 TYR cc_start: 0.8501 (t80) cc_final: 0.8040 (t80) REVERT: C 294 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 368 LEU cc_start: 0.8578 (pt) cc_final: 0.8149 (mp) REVERT: C 410 MET cc_start: 0.3427 (mtt) cc_final: 0.3212 (mtp) REVERT: C 432 TYR cc_start: 0.8941 (t80) cc_final: 0.8342 (t80) REVERT: C 473 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 578 MET cc_start: 0.8106 (mtt) cc_final: 0.7903 (mtt) REVERT: C 628 ARG cc_start: 0.8147 (ptp-110) cc_final: 0.7661 (ptt90) REVERT: D 54 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7478 (ttpt) REVERT: D 188 ASP cc_start: 0.6573 (t0) cc_final: 0.6130 (p0) REVERT: D 210 THR cc_start: 0.8943 (m) cc_final: 0.8708 (p) REVERT: D 250 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7626 (mm-30) REVERT: D 294 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: D 319 LEU cc_start: 0.8640 (mm) cc_final: 0.8368 (mt) REVERT: D 382 ASP cc_start: 0.8013 (m-30) cc_final: 0.7503 (m-30) REVERT: D 435 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8128 (mtp) REVERT: D 553 PHE cc_start: 0.8561 (t80) cc_final: 0.8314 (t80) REVERT: D 594 ARG cc_start: 0.8391 (mpp80) cc_final: 0.8118 (mpp80) REVERT: E 49 GLN cc_start: 0.8459 (tp40) cc_final: 0.8185 (tp40) REVERT: E 72 MET cc_start: 0.7757 (mmm) cc_final: 0.6996 (mmt) REVERT: E 109 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6383 (mmp) REVERT: E 126 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7229 (ttp-170) outliers start: 68 outliers final: 41 residues processed: 377 average time/residue: 0.3259 time to fit residues: 193.6218 Evaluate side-chains 365 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 440 MET 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 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 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 C residue 698 LEU 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 315 GLU Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 109 MET 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: 3.9990 chunk 215 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 464 ASN B 374 GLN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125796 restraints weight = 33146.284| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.21 r_work: 0.3299 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23173 Z= 0.137 Angle : 0.637 14.591 31210 Z= 0.315 Chirality : 0.041 0.234 3443 Planarity : 0.004 0.067 3850 Dihedral : 13.099 153.493 4504 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.14 % Favored : 88.78 % Rotamer: Outliers : 2.57 % Allowed : 16.17 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.38 (0.47), residues: 78 loop : -2.90 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 PHE 0.011 0.001 PHE B 478 TYR 0.021 0.001 TYR A 555 ARG 0.005 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 796) hydrogen bonds : angle 4.04720 ( 2307) covalent geometry : bond 0.00320 (23173) covalent geometry : angle 0.63672 (31210) *********************** 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 390 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8910 (tt) cc_final: 0.8636 (mt) REVERT: A 195 LEU cc_start: 0.8520 (mm) cc_final: 0.8255 (mt) REVERT: A 410 MET cc_start: 0.6701 (tmm) cc_final: 0.6351 (tmm) REVERT: A 528 MET cc_start: 0.8146 (tpp) cc_final: 0.7836 (tpp) REVERT: A 565 ILE cc_start: 0.9119 (pp) cc_final: 0.8713 (mp) REVERT: B 217 ASN cc_start: 0.8079 (m-40) cc_final: 0.7435 (p0) REVERT: B 301 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8117 (mtpt) REVERT: B 410 MET cc_start: 0.6207 (mpp) cc_final: 0.5450 (ppp) REVERT: C 63 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8535 (tppt) REVERT: C 78 MET cc_start: 0.7299 (mmt) cc_final: 0.6959 (mmt) REVERT: C 265 HIS cc_start: 0.7494 (t70) cc_final: 0.6755 (t-170) REVERT: C 270 TYR cc_start: 0.8563 (t80) cc_final: 0.8098 (t80) REVERT: C 301 LYS cc_start: 0.8311 (tttt) cc_final: 0.7983 (tptt) REVERT: C 345 MET cc_start: 0.8726 (mmm) cc_final: 0.8334 (mmm) REVERT: C 368 LEU cc_start: 0.8622 (pt) cc_final: 0.8149 (mp) REVERT: C 454 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8141 (ttm) REVERT: C 473 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 628 ARG cc_start: 0.8139 (ptp-110) cc_final: 0.7660 (ptt90) REVERT: D 54 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7428 (ttpt) REVERT: D 188 ASP cc_start: 0.6639 (t0) cc_final: 0.6097 (p0) REVERT: D 210 THR cc_start: 0.8949 (m) cc_final: 0.8708 (p) REVERT: D 294 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7748 (mp0) REVERT: D 319 LEU cc_start: 0.8634 (mm) cc_final: 0.8372 (mt) REVERT: D 435 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: D 481 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8188 (mmm) REVERT: D 553 PHE cc_start: 0.8638 (t80) cc_final: 0.8375 (t80) REVERT: D 594 ARG cc_start: 0.8430 (mpp80) cc_final: 0.8159 (mpp80) REVERT: E 49 GLN cc_start: 0.8434 (tp40) cc_final: 0.8156 (tp40) REVERT: E 72 MET cc_start: 0.7822 (mmm) cc_final: 0.7090 (mmt) REVERT: E 126 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7260 (ttp-170) REVERT: E 135 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7860 (tt0) outliers start: 59 outliers final: 44 residues processed: 370 average time/residue: 0.3319 time to fit residues: 192.8265 Evaluate side-chains 365 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 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 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 454 MET 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 143 VAL 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 435 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 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: 0.4980 chunk 139 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 365 ASN B 206 GLN B 374 GLN B 637 GLN ** 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 = 0.3938 r_free = 0.3938 target = 0.161326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126947 restraints weight = 32953.248| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.13 r_work: 0.3329 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4177 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= 0.112 Angle : 0.626 14.055 31210 Z= 0.308 Chirality : 0.040 0.230 3443 Planarity : 0.004 0.071 3850 Dihedral : 12.854 152.834 4504 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 2.57 % Allowed : 16.39 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.28 (0.49), residues: 78 loop : -2.85 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 PHE 0.025 0.001 PHE B 434 TYR 0.023 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 796) hydrogen bonds : angle 3.97452 ( 2307) covalent geometry : bond 0.00255 (23173) covalent geometry : angle 0.62610 (31210) *********************** 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 377 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 2.467 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8923 (tt) cc_final: 0.8634 (mt) REVERT: A 195 LEU cc_start: 0.8555 (mm) cc_final: 0.8284 (mt) REVERT: A 216 TYR cc_start: 0.8532 (t80) cc_final: 0.8057 (t80) REVERT: A 528 MET cc_start: 0.8410 (tpp) cc_final: 0.8069 (tpp) REVERT: A 565 ILE cc_start: 0.9144 (pp) cc_final: 0.8729 (mp) REVERT: B 217 ASN cc_start: 0.8184 (m-40) cc_final: 0.7535 (p0) REVERT: B 301 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8077 (mtpt) REVERT: B 637 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7181 (pp30) REVERT: C 63 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8472 (tppt) REVERT: C 78 MET cc_start: 0.7484 (mmt) cc_final: 0.7126 (mmt) REVERT: C 234 LEU cc_start: 0.8077 (mt) cc_final: 0.7825 (mt) REVERT: C 265 HIS cc_start: 0.7785 (t70) cc_final: 0.7011 (t-170) REVERT: C 270 TYR cc_start: 0.8570 (t80) cc_final: 0.8117 (t80) REVERT: C 301 LYS cc_start: 0.8263 (tttt) cc_final: 0.7918 (tptt) REVERT: C 345 MET cc_start: 0.8858 (mmm) cc_final: 0.8522 (mmm) REVERT: C 368 LEU cc_start: 0.8680 (pt) cc_final: 0.8189 (mp) REVERT: C 473 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 578 MET cc_start: 0.8267 (mtt) cc_final: 0.8018 (mtt) REVERT: C 628 ARG cc_start: 0.8297 (ptp-110) cc_final: 0.7722 (ptt90) REVERT: D 54 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7435 (ttpt) REVERT: D 188 ASP cc_start: 0.6885 (t0) cc_final: 0.6281 (p0) REVERT: D 210 THR cc_start: 0.8957 (m) cc_final: 0.8737 (p) REVERT: D 319 LEU cc_start: 0.8700 (mm) cc_final: 0.8442 (mt) REVERT: D 481 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8467 (mmm) REVERT: D 553 PHE cc_start: 0.8706 (t80) cc_final: 0.8430 (t80) REVERT: D 594 ARG cc_start: 0.8640 (mpp80) cc_final: 0.8386 (mpp80) REVERT: E 41 GLN cc_start: 0.8620 (pt0) cc_final: 0.8375 (pt0) REVERT: E 49 GLN cc_start: 0.8371 (tp40) cc_final: 0.7958 (tp40) REVERT: E 72 MET cc_start: 0.7771 (mmm) cc_final: 0.7076 (mmt) REVERT: E 126 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7232 (ttp-170) outliers start: 59 outliers final: 36 residues processed: 359 average time/residue: 0.3290 time to fit residues: 186.1829 Evaluate side-chains 348 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 182 LEU 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 C residue 698 LEU 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 481 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 546 ASN B 637 GLN C 582 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.160566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125816 restraints weight = 33270.308| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.14 r_work: 0.3329 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4279 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= 0.126 Angle : 0.650 14.083 31210 Z= 0.317 Chirality : 0.041 0.222 3443 Planarity : 0.004 0.075 3850 Dihedral : 12.738 152.563 4504 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.33 % Favored : 88.63 % Rotamer: Outliers : 2.13 % Allowed : 16.74 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.46 (0.17), residues: 2638 helix: 0.30 (0.14), residues: 1528 sheet: -3.23 (0.49), residues: 78 loop : -2.80 (0.19), residues: 1032 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 0.022 0.001 PHE D 456 TYR 0.024 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 796) hydrogen bonds : angle 4.00869 ( 2307) covalent geometry : bond 0.00293 (23173) covalent geometry : angle 0.64951 (31210) *********************** 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 371 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 2.661 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8577 (mt) cc_final: 0.8141 (mt) REVERT: A 51 LEU cc_start: 0.8910 (tt) cc_final: 0.8647 (mt) REVERT: A 195 LEU cc_start: 0.8515 (mm) cc_final: 0.8253 (mt) REVERT: A 216 TYR cc_start: 0.8624 (t80) cc_final: 0.8226 (t80) REVERT: A 410 MET cc_start: 0.6705 (tmm) cc_final: 0.6443 (tmm) REVERT: A 528 MET cc_start: 0.8423 (tpp) cc_final: 0.8070 (tpp) REVERT: A 565 ILE cc_start: 0.9160 (pp) cc_final: 0.8751 (mp) REVERT: B 217 ASN cc_start: 0.8117 (m-40) cc_final: 0.7495 (p0) REVERT: B 255 MET cc_start: 0.8267 (mmp) cc_final: 0.7870 (mmm) REVERT: B 301 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8103 (mtpt) REVERT: B 637 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: C 63 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8451 (tppt) REVERT: C 115 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: C 234 LEU cc_start: 0.7979 (mt) cc_final: 0.7713 (mt) REVERT: C 265 HIS cc_start: 0.7728 (t70) cc_final: 0.6860 (t-170) REVERT: C 270 TYR cc_start: 0.8591 (t80) cc_final: 0.8130 (t80) REVERT: C 301 LYS cc_start: 0.8284 (tttt) cc_final: 0.7986 (tptt) REVERT: C 345 MET cc_start: 0.8909 (mmm) cc_final: 0.8603 (mmm) REVERT: C 368 LEU cc_start: 0.8696 (pt) cc_final: 0.8205 (mp) REVERT: C 578 MET cc_start: 0.8280 (mtt) cc_final: 0.8007 (mtt) REVERT: C 628 ARG cc_start: 0.8266 (ptp-110) cc_final: 0.7721 (ptt90) REVERT: C 641 ARG cc_start: 0.6537 (mmt-90) cc_final: 0.5936 (mmt-90) REVERT: D 54 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7409 (ttpt) REVERT: D 188 ASP cc_start: 0.6827 (t0) cc_final: 0.6286 (p0) REVERT: D 210 THR cc_start: 0.8942 (m) cc_final: 0.8719 (p) REVERT: D 319 LEU cc_start: 0.8747 (mm) cc_final: 0.8461 (mt) REVERT: D 481 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8509 (mmm) REVERT: D 553 PHE cc_start: 0.8742 (t80) cc_final: 0.8452 (t80) REVERT: D 594 ARG cc_start: 0.8633 (mpp80) cc_final: 0.8389 (mpp80) REVERT: E 41 GLN cc_start: 0.8638 (pt0) cc_final: 0.8389 (pt0) REVERT: E 49 GLN cc_start: 0.8344 (tp40) cc_final: 0.7920 (tp40) REVERT: E 72 MET cc_start: 0.7746 (mmm) cc_final: 0.7051 (mmt) REVERT: E 126 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7186 (ttp-170) REVERT: E 137 ASN cc_start: 0.8221 (p0) cc_final: 0.8014 (p0) outliers start: 49 outliers final: 40 residues processed: 357 average time/residue: 0.3524 time to fit residues: 198.6990 Evaluate side-chains 358 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 383 ASP 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 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 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 79 THR 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: 0.0670 chunk 245 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN D 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128110 restraints weight = 33106.052| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.17 r_work: 0.3343 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23173 Z= 0.108 Angle : 0.643 14.272 31210 Z= 0.314 Chirality : 0.040 0.220 3443 Planarity : 0.004 0.073 3850 Dihedral : 12.472 151.868 4504 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.58 % Favored : 89.39 % Rotamer: Outliers : 1.96 % Allowed : 17.26 % Favored : 80.78 % 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: 1528 sheet: -3.18 (0.50), residues: 76 loop : -2.75 (0.19), residues: 1034 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 0.026 0.001 PHE D 456 TYR 0.023 0.001 TYR A 555 ARG 0.010 0.000 ARG B 636 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 796) hydrogen bonds : angle 3.93213 ( 2307) covalent geometry : bond 0.00241 (23173) covalent geometry : angle 0.64314 (31210) ********************** 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 361 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8891 (tt) cc_final: 0.8553 (mt) REVERT: A 195 LEU cc_start: 0.8449 (mm) cc_final: 0.8204 (mt) REVERT: A 216 TYR cc_start: 0.8568 (t80) cc_final: 0.8230 (t80) REVERT: A 410 MET cc_start: 0.6647 (tmm) cc_final: 0.6390 (tmm) REVERT: A 528 MET cc_start: 0.8205 (tpp) cc_final: 0.7868 (tpp) REVERT: A 565 ILE cc_start: 0.9099 (pp) cc_final: 0.8653 (mm) REVERT: B 217 ASN cc_start: 0.7946 (m-40) cc_final: 0.7416 (p0) REVERT: B 255 MET cc_start: 0.8080 (mmp) cc_final: 0.7679 (mmm) REVERT: B 301 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8144 (mtpt) REVERT: B 637 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7073 (pp30) REVERT: C 63 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8497 (tppt) REVERT: C 234 LEU cc_start: 0.8107 (mt) cc_final: 0.7889 (mt) REVERT: C 265 HIS cc_start: 0.7507 (t70) cc_final: 0.6625 (t-170) REVERT: C 270 TYR cc_start: 0.8528 (t80) cc_final: 0.8075 (t80) REVERT: C 301 LYS cc_start: 0.8270 (tttt) cc_final: 0.8030 (tptt) REVERT: C 345 MET cc_start: 0.8739 (mmm) cc_final: 0.8433 (mmm) REVERT: C 368 LEU cc_start: 0.8621 (pt) cc_final: 0.8156 (mp) REVERT: C 578 MET cc_start: 0.8095 (mtt) cc_final: 0.7858 (mtt) REVERT: C 628 ARG cc_start: 0.8079 (ptp-110) cc_final: 0.7642 (ptt90) REVERT: D 54 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7365 (ttpt) REVERT: D 188 ASP cc_start: 0.6639 (t0) cc_final: 0.6199 (p0) REVERT: D 210 THR cc_start: 0.8878 (m) cc_final: 0.8659 (p) REVERT: D 319 LEU cc_start: 0.8605 (mm) cc_final: 0.8308 (mt) REVERT: D 553 PHE cc_start: 0.8624 (t80) cc_final: 0.8358 (t80) REVERT: D 594 ARG cc_start: 0.8371 (mpp80) cc_final: 0.8014 (mpp80) REVERT: E 30 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7908 (tttm) REVERT: E 41 GLN cc_start: 0.8626 (pt0) cc_final: 0.8319 (pt0) REVERT: E 49 GLN cc_start: 0.8374 (tp40) cc_final: 0.7984 (tp40) REVERT: E 72 MET cc_start: 0.7471 (mmm) cc_final: 0.6753 (mmt) outliers start: 45 outliers final: 31 residues processed: 348 average time/residue: 0.3541 time to fit residues: 195.3956 Evaluate side-chains 340 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 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 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 D residue 54 LYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU 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: 2.9990 chunk 241 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.161768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125807 restraints weight = 33125.765| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.26 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4444 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= 0.119 Angle : 0.650 14.168 31210 Z= 0.317 Chirality : 0.041 0.256 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.378 151.682 4504 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 1.61 % Allowed : 17.43 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (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: -1.23 (0.17), residues: 2638 helix: 0.51 (0.14), residues: 1530 sheet: -3.13 (0.51), residues: 74 loop : -2.74 (0.19), residues: 1034 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 0.039 0.001 PHE D 456 TYR 0.023 0.001 TYR D 555 ARG 0.008 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 796) hydrogen bonds : angle 3.96686 ( 2307) covalent geometry : bond 0.00276 (23173) covalent geometry : angle 0.65015 (31210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10791.80 seconds wall clock time: 185 minutes 51.07 seconds (11151.07 seconds total)