Starting phenix.real_space_refine on Fri Sep 19 03:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cui_45934/09_2025/9cui_45934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cui_45934/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cui_45934/09_2025/9cui_45934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cui_45934/09_2025/9cui_45934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cui_45934/09_2025/9cui_45934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cui_45934/09_2025/9cui_45934.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 12 5.49 5 S 161 5.16 5 C 14943 2.51 5 N 3657 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4916 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 26, 'TRANS': 585} Chain: "B" Number of atoms: 4991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4991 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "C" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5286 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 26, 'TRANS': 626} Chain breaks: 1 Chain: "D" Number of atoms: 4972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4972 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 26, 'TRANS': 590} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 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-3': 9, 'PCW:plan-4': 9, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 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-3': 6, 'PCW:plan-4': 6, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 338 Unusual residues: {'CLR': 1, 'PCW': 10, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PCW:plan-1': 7, 'PCW:plan-3': 7, 'PCW:plan-4': 7, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 327 Unusual residues: {'CLR': 1, 'PCW': 12, 'Y01': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PCW:plan-1': 9, 'PCW:plan-3': 9, 'PCW:plan-4': 9, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.15, per 1000 atoms: 0.23 Number of scatterers: 22713 At special positions: 0 Unit cell: (137.643, 139.777, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 161 16.00 P 12 15.00 O 3933 8.00 N 3657 7.00 C 14943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 982.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5004 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 7 sheets defined 61.4% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 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: 2.81 Time building geometry restraints manager: 1.63 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.430 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.40 (0.11), residues: 2638 helix: -4.43 (0.06), residues: 1476 sheet: -4.36 (0.38), residues: 79 loop : -3.75 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 350 TYR 0.022 0.002 TYR C 547 PHE 0.033 0.002 PHE D 508 TRP 0.034 0.002 TRP C 45 HIS 0.014 0.002 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.01128 (23173) covalent geometry : angle 1.42850 (31210) hydrogen bonds : bond 0.33788 ( 796) hydrogen bonds : angle 10.41366 ( 2307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 594 time to evaluate : 0.833 Fit side-chains revert: symmetry clash 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: 0.8156 (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: 0.6792 (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: 0.8507 (mm) REVERT: C 410 MET cc_start: 0.4268 (mtt) cc_final: 0.3948 (mtp) REVERT: C 694 ASN cc_start: 0.7434 (m-40) cc_final: 0.7171 (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: 0.8611 (p) REVERT: D 233 ASP cc_start: 0.7582 (p0) cc_final: 0.7280 (p0) REVERT: D 295 LEU cc_start: 0.8177 (mm) cc_final: 0.7909 (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: 0.7270 (mmm) REVERT: D 594 ARG cc_start: 0.7875 (mpp80) cc_final: 0.7655 (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: 0.1671 time to fit residues: 151.1967 Evaluate side-chains 348 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 345 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain C residue 367 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 128 GLN B 131 ASN B 174 ASN B 252 ASN B 267 GLN B 365 ASN B 426 HIS B 522 HIS B 572 ASN B 587 HIS C 74 GLN C 118 GLN C 158 ASN C 214 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 267 GLN C 358 ASN C 370 GLN C 572 ASN C 637 GLN D 31 GLN D 84 HIS D 129 ASN D 257 GLN D 290 GLN D 365 ASN D 464 ASN D 522 HIS D 572 ASN D 587 HIS E 49 GLN E 53 ASN E 107 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126582 restraints weight = 33902.989| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.79 r_work: 0.3408 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23173 Z= 0.185 Angle : 0.756 11.004 31210 Z= 0.389 Chirality : 0.043 0.202 3443 Planarity : 0.006 0.068 3850 Dihedral : 16.465 179.608 4506 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.99 % Favored : 88.63 % Rotamer: Outliers : 2.70 % Allowed : 11.70 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.13), residues: 2638 helix: -2.72 (0.10), residues: 1524 sheet: -4.00 (0.39), residues: 90 loop : -3.38 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 180 TYR 0.015 0.002 TYR A 524 PHE 0.026 0.002 PHE A 531 TRP 0.020 0.001 TRP A 29 HIS 0.010 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00419 (23173) covalent geometry : angle 0.75556 (31210) hydrogen bonds : bond 0.05452 ( 796) hydrogen bonds : angle 5.15604 ( 2307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 383 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8374 (mm) cc_final: 0.8126 (mt) REVERT: A 308 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 410 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.6011 (tmm) REVERT: A 549 VAL cc_start: 0.9218 (t) cc_final: 0.8848 (p) REVERT: A 565 ILE cc_start: 0.9180 (pp) cc_final: 0.8863 (mp) REVERT: B 410 MET cc_start: 0.6044 (mpp) cc_final: 0.5191 (ppp) REVERT: B 613 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.7235 (t60) REVERT: C 63 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8554 (tppt) REVERT: C 78 MET cc_start: 0.7512 (mmt) cc_final: 0.6954 (mmt) REVERT: C 80 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: C 265 HIS cc_start: 0.7652 (t70) cc_final: 0.7196 (t-170) REVERT: C 294 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 368 LEU cc_start: 0.8469 (pt) cc_final: 0.8067 (mt) REVERT: C 410 MET cc_start: 0.3958 (mtt) cc_final: 0.3572 (mtp) REVERT: C 432 TYR cc_start: 0.8949 (t80) cc_final: 0.8127 (t80) REVERT: C 473 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 96 MET cc_start: 0.9138 (mmt) cc_final: 0.8874 (mmm) REVERT: D 210 THR cc_start: 0.8966 (m) cc_final: 0.8729 (p) REVERT: D 302 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7723 (ttm110) REVERT: D 319 LEU cc_start: 0.8791 (mm) cc_final: 0.8521 (mt) REVERT: D 456 PHE cc_start: 0.8922 (m-80) cc_final: 0.8664 (m-80) REVERT: D 554 MET cc_start: 0.8561 (tpt) cc_final: 0.8271 (tpp) REVERT: D 594 ARG cc_start: 0.8434 (mpp80) cc_final: 0.8101 (mpp80) REVERT: E 49 GLN cc_start: 0.8451 (tp-100) cc_final: 0.8155 (tp40) REVERT: E 86 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7674 (ttm-80) REVERT: E 144 MET cc_start: 0.7642 (mmm) cc_final: 0.6897 (tpp) outliers start: 62 outliers final: 33 residues processed: 424 average time/residue: 0.1496 time to fit residues: 99.0935 Evaluate side-chains 356 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 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 28 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 572 ASN B 185 HIS B 258 HIS B 637 GLN C 158 ASN C 694 ASN E 49 GLN E 53 ASN E 107 HIS E 111 ASN E 135 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.165786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127914 restraints weight = 33978.525| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.77 r_work: 0.3388 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23173 Z= 0.143 Angle : 0.680 10.387 31210 Z= 0.345 Chirality : 0.042 0.186 3443 Planarity : 0.005 0.060 3850 Dihedral : 15.077 165.591 4506 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.07 % Favored : 88.70 % Rotamer: Outliers : 3.26 % Allowed : 13.00 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.83 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.15), residues: 2638 helix: -1.55 (0.12), residues: 1544 sheet: -4.10 (0.40), residues: 85 loop : -3.20 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 363 TYR 0.014 0.001 TYR D 377 PHE 0.021 0.001 PHE A 531 TRP 0.020 0.001 TRP A 29 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00328 (23173) covalent geometry : angle 0.67952 (31210) hydrogen bonds : bond 0.04208 ( 796) hydrogen bonds : angle 4.49175 ( 2307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 358 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8330 (mm) cc_final: 0.8103 (mt) REVERT: A 549 VAL cc_start: 0.9188 (t) cc_final: 0.8778 (p) REVERT: A 565 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8813 (mp) REVERT: B 128 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6830 (tm-30) REVERT: B 211 PHE cc_start: 0.8578 (m-80) cc_final: 0.8336 (m-10) REVERT: B 410 MET cc_start: 0.6059 (mpp) cc_final: 0.5340 (ppp) REVERT: B 613 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7269 (t60) REVERT: B 621 ARG cc_start: 0.7420 (ttm110) cc_final: 0.6679 (mtm-85) REVERT: B 637 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6764 (pp30) REVERT: B 640 ASN cc_start: 0.7887 (t0) cc_final: 0.7604 (t0) REVERT: C 78 MET cc_start: 0.7426 (mmt) cc_final: 0.6859 (mmt) REVERT: C 175 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 265 HIS cc_start: 0.7617 (t70) cc_final: 0.6571 (t-170) REVERT: C 368 LEU cc_start: 0.8587 (pt) cc_final: 0.8102 (mp) REVERT: C 410 MET cc_start: 0.3990 (mtt) cc_final: 0.3704 (mtp) REVERT: C 473 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 26 ARG cc_start: 0.5661 (mtm180) cc_final: 0.5425 (mtm180) REVERT: D 210 THR cc_start: 0.8958 (m) cc_final: 0.8712 (p) REVERT: D 319 LEU cc_start: 0.8744 (mm) cc_final: 0.8492 (mt) REVERT: D 324 TYR cc_start: 0.7778 (m-80) cc_final: 0.7505 (m-80) REVERT: D 389 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: D 390 LEU cc_start: 0.8997 (mt) cc_final: 0.8796 (mt) REVERT: D 458 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8423 (mm) REVERT: D 594 ARG cc_start: 0.8470 (mpp80) cc_final: 0.8052 (mpp80) REVERT: D 611 CYS cc_start: 0.7877 (t) cc_final: 0.7618 (m) REVERT: E 49 GLN cc_start: 0.8377 (tp40) cc_final: 0.8142 (tp40) REVERT: E 72 MET cc_start: 0.7775 (mmm) cc_final: 0.7139 (mmt) REVERT: E 126 ARG cc_start: 0.7711 (mtp-110) cc_final: 0.7210 (ttp-170) REVERT: E 144 MET cc_start: 0.7555 (mmm) cc_final: 0.6836 (tpp) outliers start: 75 outliers final: 40 residues processed: 409 average time/residue: 0.1460 time to fit residues: 94.5243 Evaluate side-chains 359 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 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 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 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 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 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 199 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS B 546 ASN C 158 ASN C 642 GLN C 694 ASN D 582 HIS E 143 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131942 restraints weight = 33894.338| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.70 r_work: 0.3435 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3490 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= 0.111 Angle : 0.633 9.636 31210 Z= 0.319 Chirality : 0.040 0.195 3443 Planarity : 0.004 0.060 3850 Dihedral : 14.177 152.740 4506 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.11 % Favored : 88.70 % Rotamer: Outliers : 2.74 % Allowed : 13.78 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.16), residues: 2638 helix: -0.87 (0.13), residues: 1541 sheet: -3.70 (0.45), residues: 78 loop : -3.06 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.016 0.001 TYR D 555 PHE 0.020 0.001 PHE D 456 TRP 0.011 0.001 TRP A 29 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00242 (23173) covalent geometry : angle 0.63322 (31210) hydrogen bonds : bond 0.03430 ( 796) hydrogen bonds : angle 4.19292 ( 2307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 363 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8471 (mm) cc_final: 0.8233 (mt) REVERT: A 347 CYS cc_start: 0.8063 (m) cc_final: 0.7823 (m) REVERT: A 368 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 128 GLN cc_start: 0.7330 (tm-30) cc_final: 0.6694 (tm-30) REVERT: B 211 PHE cc_start: 0.8535 (m-80) cc_final: 0.8326 (m-10) REVERT: B 266 THR cc_start: 0.8645 (t) cc_final: 0.8434 (m) REVERT: B 301 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8091 (mtpt) REVERT: B 410 MET cc_start: 0.6173 (mpp) cc_final: 0.5464 (ppp) REVERT: B 613 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.7246 (t60) REVERT: B 621 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6484 (mtm-85) REVERT: C 63 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8554 (tppt) REVERT: C 260 MET cc_start: 0.8643 (tpt) cc_final: 0.8410 (tpt) REVERT: C 265 HIS cc_start: 0.7332 (t70) cc_final: 0.6320 (t-170) REVERT: C 294 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 368 LEU cc_start: 0.8521 (pt) cc_final: 0.8059 (mp) REVERT: C 410 MET cc_start: 0.3845 (mtt) cc_final: 0.3597 (mtp) REVERT: C 473 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 485 MET cc_start: 0.8035 (mmt) cc_final: 0.7834 (mmt) REVERT: C 578 MET cc_start: 0.8270 (mtt) cc_final: 0.7867 (mtt) REVERT: D 188 ASP cc_start: 0.6780 (t0) cc_final: 0.6167 (p0) REVERT: D 210 THR cc_start: 0.8873 (m) cc_final: 0.8640 (p) REVERT: D 257 GLN cc_start: 0.8521 (mt0) cc_final: 0.8307 (mm-40) REVERT: D 319 LEU cc_start: 0.8741 (mm) cc_final: 0.8469 (mt) REVERT: D 324 TYR cc_start: 0.7483 (m-80) cc_final: 0.7254 (m-10) REVERT: D 390 LEU cc_start: 0.8998 (mt) cc_final: 0.8788 (mt) REVERT: D 594 ARG cc_start: 0.8426 (mpp80) cc_final: 0.8019 (mpp80) REVERT: D 611 CYS cc_start: 0.7811 (t) cc_final: 0.7475 (m) REVERT: E 49 GLN cc_start: 0.8328 (tp40) cc_final: 0.8005 (tp40) REVERT: E 72 MET cc_start: 0.7791 (mmm) cc_final: 0.7118 (mmt) REVERT: E 126 ARG cc_start: 0.7576 (mtp-110) cc_final: 0.7227 (ttp-170) outliers start: 63 outliers final: 34 residues processed: 407 average time/residue: 0.1436 time to fit residues: 92.4335 Evaluate side-chains 358 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 373 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 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 137 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 186 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 240 optimal weight: 0.0970 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 546 ASN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125817 restraints weight = 33779.788| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.69 r_work: 0.3373 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23173 Z= 0.197 Angle : 0.698 14.276 31210 Z= 0.347 Chirality : 0.044 0.187 3443 Planarity : 0.005 0.063 3850 Dihedral : 14.111 155.407 4506 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.83 % Favored : 87.98 % Rotamer: Outliers : 3.48 % Allowed : 14.22 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.16), residues: 2638 helix: -0.63 (0.13), residues: 1543 sheet: -3.83 (0.43), residues: 85 loop : -3.03 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 224 TYR 0.020 0.002 TYR B 526 PHE 0.018 0.002 PHE B 478 TRP 0.012 0.001 TRP A 29 HIS 0.006 0.001 HIS D 522 Details of bonding type rmsd covalent geometry : bond 0.00469 (23173) covalent geometry : angle 0.69836 (31210) hydrogen bonds : bond 0.03910 ( 796) hydrogen bonds : angle 4.39029 ( 2307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 333 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8496 (mm) cc_final: 0.8219 (mt) REVERT: B 128 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 211 PHE cc_start: 0.8593 (m-80) cc_final: 0.8314 (m-10) REVERT: B 410 MET cc_start: 0.6232 (mpp) cc_final: 0.5441 (ppp) REVERT: B 490 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 577 MET cc_start: 0.8593 (ttm) cc_final: 0.8375 (ttp) REVERT: B 637 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6823 (pp30) REVERT: C 63 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8542 (tppt) REVERT: C 78 MET cc_start: 0.7283 (mmt) cc_final: 0.6953 (mmt) REVERT: C 96 MET cc_start: 0.8574 (mmm) cc_final: 0.8334 (mmt) REVERT: C 260 MET cc_start: 0.8729 (tpt) cc_final: 0.8498 (tpt) REVERT: C 265 HIS cc_start: 0.7665 (t70) cc_final: 0.6873 (t-170) REVERT: C 368 LEU cc_start: 0.8638 (pt) cc_final: 0.8115 (mp) REVERT: C 473 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 628 ARG cc_start: 0.8258 (ptp-110) cc_final: 0.7683 (ptt90) REVERT: D 54 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7440 (ttpt) REVERT: D 210 THR cc_start: 0.8970 (m) cc_final: 0.8715 (p) REVERT: D 315 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: D 319 LEU cc_start: 0.8781 (mm) cc_final: 0.8475 (mt) REVERT: D 324 TYR cc_start: 0.7705 (m-80) cc_final: 0.7418 (m-10) REVERT: D 546 ASN cc_start: 0.8395 (t0) cc_final: 0.8172 (t0) REVERT: D 555 TYR cc_start: 0.8451 (t80) cc_final: 0.8204 (t80) REVERT: D 594 ARG cc_start: 0.8507 (mpp80) cc_final: 0.8094 (mpp80) REVERT: D 611 CYS cc_start: 0.8030 (t) cc_final: 0.7662 (m) REVERT: E 49 GLN cc_start: 0.8392 (tp40) cc_final: 0.8094 (tp40) REVERT: E 72 MET cc_start: 0.7866 (mmm) cc_final: 0.7151 (mmt) REVERT: E 99 TYR cc_start: 0.7818 (m-80) cc_final: 0.7564 (m-80) REVERT: E 126 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7369 (ttp-170) outliers start: 80 outliers final: 57 residues processed: 394 average time/residue: 0.1439 time to fit residues: 89.3590 Evaluate side-chains 372 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 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 B residue 167 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 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 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 611 CYS Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 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 183 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 99 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 17 optimal weight: 0.0060 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 261 GLN A 572 ASN B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123977 restraints weight = 33073.000| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.23 r_work: 0.3283 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3860 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= 0.136 Angle : 0.651 15.089 31210 Z= 0.323 Chirality : 0.041 0.187 3443 Planarity : 0.004 0.065 3850 Dihedral : 13.698 153.177 4506 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.22 % Favored : 88.67 % Rotamer: Outliers : 3.09 % Allowed : 15.57 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.16), residues: 2638 helix: -0.34 (0.13), residues: 1546 sheet: -3.74 (0.44), residues: 85 loop : -3.03 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 621 TYR 0.019 0.001 TYR A 555 PHE 0.015 0.001 PHE B 478 TRP 0.013 0.001 TRP A 29 HIS 0.006 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00316 (23173) covalent geometry : angle 0.65067 (31210) hydrogen bonds : bond 0.03445 ( 796) hydrogen bonds : angle 4.22102 ( 2307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8427 (mm) cc_final: 0.8156 (mt) REVERT: A 528 MET cc_start: 0.8216 (tpp) cc_final: 0.7999 (tpp) REVERT: A 565 ILE cc_start: 0.9173 (pp) cc_final: 0.8808 (mp) REVERT: B 211 PHE cc_start: 0.8616 (m-80) cc_final: 0.8363 (m-10) REVERT: B 301 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8111 (mtpt) REVERT: B 410 MET cc_start: 0.6088 (mpp) cc_final: 0.5358 (ppp) REVERT: B 490 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8394 (tp) REVERT: B 577 MET cc_start: 0.8818 (ttm) cc_final: 0.8594 (ttp) REVERT: B 637 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6877 (pp30) REVERT: C 63 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8531 (tppt) REVERT: C 78 MET cc_start: 0.7577 (mmt) cc_final: 0.7244 (mmt) REVERT: C 260 MET cc_start: 0.8803 (tpt) cc_final: 0.8586 (tpt) REVERT: C 265 HIS cc_start: 0.7788 (t70) cc_final: 0.7286 (t-170) REVERT: C 270 TYR cc_start: 0.8586 (t80) cc_final: 0.8133 (t80) REVERT: C 345 MET cc_start: 0.8922 (mmm) cc_final: 0.8601 (mmm) REVERT: C 368 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8177 (mp) REVERT: C 410 MET cc_start: 0.2797 (mtm) cc_final: 0.2552 (mtp) REVERT: C 473 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 485 MET cc_start: 0.8241 (mmt) cc_final: 0.7968 (mmt) REVERT: C 628 ARG cc_start: 0.8388 (ptp-110) cc_final: 0.7745 (ptt90) REVERT: D 54 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7501 (ttpt) REVERT: D 181 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8810 (tt) REVERT: D 210 THR cc_start: 0.8974 (m) cc_final: 0.8744 (p) REVERT: D 319 LEU cc_start: 0.8838 (mm) cc_final: 0.8578 (mt) REVERT: D 324 TYR cc_start: 0.7810 (m-80) cc_final: 0.7521 (m-10) REVERT: D 553 PHE cc_start: 0.8792 (t80) cc_final: 0.8540 (t80) REVERT: D 594 ARG cc_start: 0.8693 (mpp80) cc_final: 0.8344 (mpp80) REVERT: D 611 CYS cc_start: 0.8106 (t) cc_final: 0.7666 (m) REVERT: E 49 GLN cc_start: 0.8434 (tp40) cc_final: 0.8135 (tp40) REVERT: E 72 MET cc_start: 0.7954 (mmm) cc_final: 0.7253 (mmt) REVERT: E 99 TYR cc_start: 0.7832 (m-80) cc_final: 0.7597 (m-80) REVERT: E 126 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7344 (ttp-170) outliers start: 71 outliers final: 50 residues processed: 373 average time/residue: 0.1420 time to fit residues: 84.8686 Evaluate side-chains 371 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 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 B residue 200 LEU Chi-restraints excluded: chain B residue 203 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 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 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 338 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 78 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120801 restraints weight = 33112.936| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.22 r_work: 0.3251 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23173 Z= 0.193 Angle : 0.693 13.837 31210 Z= 0.342 Chirality : 0.043 0.233 3443 Planarity : 0.005 0.066 3850 Dihedral : 13.709 153.833 4506 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.79 % Favored : 88.06 % Rotamer: Outliers : 3.26 % Allowed : 15.96 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.16), residues: 2638 helix: -0.29 (0.13), residues: 1543 sheet: -3.71 (0.44), residues: 85 loop : -3.02 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 636 TYR 0.019 0.002 TYR A 555 PHE 0.013 0.001 PHE B 478 TRP 0.015 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00460 (23173) covalent geometry : angle 0.69332 (31210) hydrogen bonds : bond 0.03706 ( 796) hydrogen bonds : angle 4.31550 ( 2307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 313 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8666 (mt) cc_final: 0.8283 (mt) REVERT: A 51 LEU cc_start: 0.8943 (tt) cc_final: 0.8645 (mt) REVERT: A 195 LEU cc_start: 0.8533 (mm) cc_final: 0.8291 (mt) REVERT: A 410 MET cc_start: 0.6465 (tmm) cc_final: 0.5901 (tmm) REVERT: A 528 MET cc_start: 0.8255 (tpp) cc_final: 0.8011 (tpp) REVERT: A 565 ILE cc_start: 0.9195 (pp) cc_final: 0.8795 (mp) REVERT: B 255 MET cc_start: 0.8289 (mmm) cc_final: 0.8009 (mmt) REVERT: B 301 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8119 (mtpt) REVERT: B 319 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 410 MET cc_start: 0.6101 (mpp) cc_final: 0.5811 (mpp) REVERT: B 637 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7030 (pp30) REVERT: C 63 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8498 (tppt) REVERT: C 78 MET cc_start: 0.7663 (mmt) cc_final: 0.7313 (mmt) REVERT: C 260 MET cc_start: 0.8765 (tpt) cc_final: 0.8536 (tpt) REVERT: C 265 HIS cc_start: 0.7920 (t70) cc_final: 0.7053 (t-170) REVERT: C 345 MET cc_start: 0.9074 (mmm) cc_final: 0.8867 (mmm) REVERT: C 368 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 410 MET cc_start: 0.2815 (mtm) cc_final: 0.2585 (mtp) REVERT: C 473 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8790 (tm-30) REVERT: C 628 ARG cc_start: 0.8404 (ptp-110) cc_final: 0.7764 (ptt90) REVERT: D 54 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (ttpt) REVERT: D 140 ARG cc_start: 0.7965 (mmp80) cc_final: 0.7753 (mmp80) REVERT: D 181 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8867 (tt) REVERT: D 210 THR cc_start: 0.8968 (m) cc_final: 0.8735 (p) REVERT: D 319 LEU cc_start: 0.8871 (mm) cc_final: 0.8535 (mt) REVERT: D 553 PHE cc_start: 0.8902 (t80) cc_final: 0.8522 (t80) REVERT: D 594 ARG cc_start: 0.8677 (mpp80) cc_final: 0.8308 (mpp80) REVERT: D 611 CYS cc_start: 0.8121 (t) cc_final: 0.7694 (m) REVERT: E 49 GLN cc_start: 0.8437 (tp40) cc_final: 0.8141 (tp40) REVERT: E 72 MET cc_start: 0.7939 (mmm) cc_final: 0.7276 (mmt) REVERT: E 99 TYR cc_start: 0.7902 (m-80) cc_final: 0.7671 (m-80) outliers start: 75 outliers final: 58 residues processed: 366 average time/residue: 0.1451 time to fit residues: 84.5422 Evaluate side-chains 372 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN 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 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 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 577 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 319 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 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 175 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 587 HIS Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 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 48 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125162 restraints weight = 32677.317| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.24 r_work: 0.3301 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23173 Z= 0.114 Angle : 0.640 16.468 31210 Z= 0.316 Chirality : 0.041 0.230 3443 Planarity : 0.004 0.069 3850 Dihedral : 13.245 152.014 4506 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.80 % Favored : 89.16 % Rotamer: Outliers : 3.00 % Allowed : 16.57 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.17), residues: 2638 helix: 0.03 (0.14), residues: 1547 sheet: -3.37 (0.47), residues: 80 loop : -2.93 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 86 TYR 0.025 0.001 TYR B 555 PHE 0.019 0.001 PHE A 434 TRP 0.016 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00257 (23173) covalent geometry : angle 0.63979 (31210) hydrogen bonds : bond 0.03204 ( 796) hydrogen bonds : angle 4.09063 ( 2307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8643 (mt) cc_final: 0.8247 (mt) REVERT: A 51 LEU cc_start: 0.8920 (tt) cc_final: 0.8627 (mt) REVERT: A 195 LEU cc_start: 0.8393 (mm) cc_final: 0.8120 (mt) REVERT: A 410 MET cc_start: 0.6780 (tmm) cc_final: 0.6375 (tmm) REVERT: A 528 MET cc_start: 0.8266 (tpp) cc_final: 0.8050 (tpp) REVERT: B 217 ASN cc_start: 0.8066 (m-40) cc_final: 0.7430 (p0) REVERT: B 255 MET cc_start: 0.8426 (mmm) cc_final: 0.8160 (mmt) REVERT: B 301 LYS cc_start: 0.8770 (mmtp) cc_final: 0.8125 (mtpt) REVERT: B 490 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8304 (tp) REVERT: B 637 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6916 (pp30) REVERT: C 63 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8470 (tppt) REVERT: C 78 MET cc_start: 0.7721 (mmt) cc_final: 0.7410 (mmt) REVERT: C 260 MET cc_start: 0.8802 (tpt) cc_final: 0.8528 (tpt) REVERT: C 265 HIS cc_start: 0.7790 (t70) cc_final: 0.6925 (t-170) REVERT: C 270 TYR cc_start: 0.8567 (t80) cc_final: 0.8136 (t80) REVERT: C 368 LEU cc_start: 0.8672 (pt) cc_final: 0.8164 (mp) REVERT: C 410 MET cc_start: 0.2832 (mtm) cc_final: 0.2608 (mtp) REVERT: C 473 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8609 (tm-30) REVERT: C 628 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.7729 (ptt90) REVERT: D 54 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7510 (ttpt) REVERT: D 140 ARG cc_start: 0.7928 (mmp80) cc_final: 0.7718 (mmp80) REVERT: D 210 THR cc_start: 0.8931 (m) cc_final: 0.8719 (p) REVERT: D 319 LEU cc_start: 0.8839 (mm) cc_final: 0.8529 (mt) REVERT: D 553 PHE cc_start: 0.8762 (t80) cc_final: 0.8485 (t80) REVERT: D 594 ARG cc_start: 0.8634 (mpp80) cc_final: 0.8282 (mpp80) REVERT: D 611 CYS cc_start: 0.8086 (t) cc_final: 0.7608 (m) REVERT: E 49 GLN cc_start: 0.8451 (tp40) cc_final: 0.8091 (tp40) REVERT: E 72 MET cc_start: 0.7981 (mmm) cc_final: 0.7308 (mmt) REVERT: E 99 TYR cc_start: 0.7814 (m-80) cc_final: 0.7577 (m-80) REVERT: E 124 MET cc_start: 0.7693 (mtp) cc_final: 0.7481 (mtp) outliers start: 69 outliers final: 47 residues processed: 384 average time/residue: 0.1464 time to fit residues: 89.7376 Evaluate side-chains 361 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 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 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 338 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 546 ASN Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 145 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 240 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 637 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123783 restraints weight = 33188.675| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3280 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4201 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= 0.137 Angle : 0.664 16.399 31210 Z= 0.326 Chirality : 0.042 0.212 3443 Planarity : 0.004 0.072 3850 Dihedral : 13.129 151.985 4506 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.26 % Favored : 88.70 % Rotamer: Outliers : 2.70 % Allowed : 16.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.17), residues: 2638 helix: 0.10 (0.14), residues: 1546 sheet: -3.29 (0.48), residues: 78 loop : -2.89 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 606 TYR 0.022 0.001 TYR A 555 PHE 0.028 0.001 PHE B 434 TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00323 (23173) covalent geometry : angle 0.66434 (31210) hydrogen bonds : bond 0.03266 ( 796) hydrogen bonds : angle 4.11601 ( 2307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.8651 (mt) cc_final: 0.8250 (mt) REVERT: A 51 LEU cc_start: 0.8899 (tt) cc_final: 0.8594 (mt) REVERT: A 195 LEU cc_start: 0.8472 (mm) cc_final: 0.8202 (mt) REVERT: A 410 MET cc_start: 0.6800 (tmm) cc_final: 0.6444 (tmm) REVERT: A 528 MET cc_start: 0.8034 (tpp) cc_final: 0.7781 (tpp) REVERT: B 217 ASN cc_start: 0.8046 (m-40) cc_final: 0.7405 (p0) REVERT: B 255 MET cc_start: 0.8241 (mmm) cc_final: 0.7935 (mmt) REVERT: B 301 LYS cc_start: 0.8735 (mmtp) cc_final: 0.8184 (mtpt) REVERT: B 490 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8212 (tp) REVERT: B 637 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6854 (pp30) REVERT: C 63 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8493 (tppt) REVERT: C 78 MET cc_start: 0.7498 (mmt) cc_final: 0.7172 (mmt) REVERT: C 260 MET cc_start: 0.8711 (tpt) cc_final: 0.8437 (tpt) REVERT: C 265 HIS cc_start: 0.7481 (t70) cc_final: 0.6729 (t-170) REVERT: C 270 TYR cc_start: 0.8571 (t80) cc_final: 0.8122 (t80) REVERT: C 301 LYS cc_start: 0.8358 (tttt) cc_final: 0.8108 (tptt) REVERT: C 368 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8160 (mp) REVERT: C 473 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 628 ARG cc_start: 0.8175 (ptp-110) cc_final: 0.7657 (ptt90) REVERT: D 54 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7362 (ttpt) REVERT: D 140 ARG cc_start: 0.7868 (mmp80) cc_final: 0.7654 (mmp80) REVERT: D 210 THR cc_start: 0.8880 (m) cc_final: 0.8667 (p) REVERT: D 319 LEU cc_start: 0.8707 (mm) cc_final: 0.8313 (mt) REVERT: D 435 MET cc_start: 0.8287 (mtp) cc_final: 0.8055 (mtp) REVERT: D 553 PHE cc_start: 0.8748 (t80) cc_final: 0.8460 (t80) REVERT: D 594 ARG cc_start: 0.8418 (mpp80) cc_final: 0.8079 (mpp80) REVERT: D 611 CYS cc_start: 0.7980 (t) cc_final: 0.7497 (m) REVERT: E 49 GLN cc_start: 0.8458 (tp40) cc_final: 0.8106 (tp40) REVERT: E 72 MET cc_start: 0.7822 (mmm) cc_final: 0.7140 (mmt) REVERT: E 99 TYR cc_start: 0.7734 (m-80) cc_final: 0.7488 (m-80) outliers start: 62 outliers final: 47 residues processed: 360 average time/residue: 0.1524 time to fit residues: 86.2789 Evaluate side-chains 361 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain 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 98 LEU 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 235 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 ASN Chi-restraints excluded: chain C residue 651 PHE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 18 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 88 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN C 158 ASN C 546 ASN ** C 640 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 = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125909 restraints weight = 33089.640| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.26 r_work: 0.3308 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23173 Z= 0.114 Angle : 0.657 16.551 31210 Z= 0.321 Chirality : 0.040 0.191 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.851 151.232 4506 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.77 % Favored : 89.20 % Rotamer: Outliers : 2.39 % Allowed : 17.35 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.17), residues: 2638 helix: 0.26 (0.14), residues: 1544 sheet: -3.21 (0.48), residues: 78 loop : -2.83 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 606 TYR 0.023 0.001 TYR D 555 PHE 0.018 0.001 PHE E 65 TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00259 (23173) covalent geometry : angle 0.65677 (31210) hydrogen bonds : bond 0.03065 ( 796) hydrogen bonds : angle 4.03394 ( 2307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 318 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8853 (tt) cc_final: 0.8565 (mt) REVERT: A 110 MET cc_start: 0.6189 (mmm) cc_final: 0.5914 (mtp) REVERT: A 195 LEU cc_start: 0.8419 (mm) cc_final: 0.8133 (mt) REVERT: A 280 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 410 MET cc_start: 0.6683 (tmm) cc_final: 0.6402 (tmm) REVERT: A 528 MET cc_start: 0.8050 (tpp) cc_final: 0.7789 (tpp) REVERT: A 565 ILE cc_start: 0.9122 (pp) cc_final: 0.8709 (mm) REVERT: B 217 ASN cc_start: 0.7957 (m-40) cc_final: 0.7378 (p0) REVERT: B 255 MET cc_start: 0.8184 (mmm) cc_final: 0.7943 (mmp) REVERT: B 301 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8165 (mtpt) REVERT: B 410 MET cc_start: 0.6226 (mpp) cc_final: 0.5505 (ppp) REVERT: B 490 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 637 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6824 (pp30) REVERT: C 63 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8480 (tppt) REVERT: C 115 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: C 255 MET cc_start: 0.8757 (mmt) cc_final: 0.8395 (mmp) REVERT: C 260 MET cc_start: 0.8702 (tpt) cc_final: 0.8444 (tpt) REVERT: C 265 HIS cc_start: 0.7459 (t70) cc_final: 0.6697 (t-170) REVERT: C 270 TYR cc_start: 0.8483 (t80) cc_final: 0.8060 (t80) REVERT: C 301 LYS cc_start: 0.8311 (tttt) cc_final: 0.8071 (tptt) REVERT: C 368 LEU cc_start: 0.8621 (pt) cc_final: 0.8146 (mp) REVERT: C 473 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 628 ARG cc_start: 0.8156 (ptp-110) cc_final: 0.7676 (ptt90) REVERT: D 54 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7381 (ttpt) REVERT: D 140 ARG cc_start: 0.7821 (mmp80) cc_final: 0.7615 (mmp80) REVERT: D 210 THR cc_start: 0.8872 (m) cc_final: 0.8662 (p) REVERT: D 319 LEU cc_start: 0.8664 (mm) cc_final: 0.8367 (mt) REVERT: D 435 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: D 553 PHE cc_start: 0.8702 (t80) cc_final: 0.8415 (t80) REVERT: D 594 ARG cc_start: 0.8424 (mpp80) cc_final: 0.8094 (mpp80) REVERT: E 30 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7847 (tttm) REVERT: E 49 GLN cc_start: 0.8364 (tp40) cc_final: 0.7969 (tp40) REVERT: E 72 MET cc_start: 0.7726 (mmm) cc_final: 0.7039 (mmt) REVERT: E 75 LYS cc_start: 0.7014 (tppt) cc_final: 0.6670 (mmtm) outliers start: 55 outliers final: 41 residues processed: 358 average time/residue: 0.1451 time to fit residues: 82.0700 Evaluate side-chains 362 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 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 98 LEU 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 338 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 546 ASN 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 435 MET Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 135 GLN Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 237 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 226 optimal weight: 0.2980 chunk 188 optimal weight: 0.6980 chunk 246 optimal weight: 0.2980 chunk 253 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 637 GLN C 546 ASN ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126627 restraints weight = 33032.199| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.19 r_work: 0.3331 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23173 Z= 0.108 Angle : 0.645 16.623 31210 Z= 0.316 Chirality : 0.040 0.187 3443 Planarity : 0.004 0.074 3850 Dihedral : 12.596 150.722 4506 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.73 % Favored : 89.23 % Rotamer: Outliers : 2.13 % Allowed : 17.83 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.17), residues: 2638 helix: 0.39 (0.14), residues: 1545 sheet: -3.14 (0.49), residues: 78 loop : -2.76 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 606 TYR 0.022 0.001 TYR D 555 PHE 0.014 0.001 PHE B 478 TRP 0.017 0.001 TRP A 29 HIS 0.007 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00241 (23173) covalent geometry : angle 0.64547 (31210) hydrogen bonds : bond 0.02918 ( 796) hydrogen bonds : angle 3.96662 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.77 seconds wall clock time: 85 minutes 50.07 seconds (5150.07 seconds total)