Starting phenix.real_space_refine on Fri Feb 6 17:20:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802.map" model { file = "/net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nue_49802/02_2026/9nue_49802_neut.cif" } resolution = 3.36 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= 0.007 sd= 0.076 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 P 33 5.49 5 Mg 7 5.21 5 S 123 5.16 5 C 16443 2.51 5 N 4537 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26280 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "C" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "D" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "E" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "F" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3907 Classifications: {'peptide': 502} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "G" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2452 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.55, per 1000 atoms: 0.25 Number of scatterers: 26280 At special positions: 0 Unit cell: (156.325, 134.83, 163.164, 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) S 123 16.00 P 33 15.00 Mg 7 11.99 O 5137 8.00 N 4537 7.00 C 16443 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 14 sheets defined 60.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.908A pdb=" N LYS A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.767A pdb=" N ILE A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.584A pdb=" N ILE A 266 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 4.018A pdb=" N ILE A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.877A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.203A pdb=" N PHE A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.583A pdb=" N MET A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.712A pdb=" N LEU A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 420 through 438 removed outlier: 5.484A pdb=" N LYS A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.940A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.507A pdb=" N LYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.607A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.551A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 551 removed outlier: 3.849A pdb=" N ASN A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 3.833A pdb=" N LEU A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 598 through 613 Processing helix chain 'A' and resid 625 through 630 removed outlier: 3.784A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.562A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.640A pdb=" N LEU A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.946A pdb=" N LYS A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 745 through 758 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.535A pdb=" N ARG B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.079A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.699A pdb=" N ILE B 266 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.919A pdb=" N MET B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.802A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 369 through 381 removed outlier: 3.582A pdb=" N LYS B 378 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.080A pdb=" N ARG B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 437 removed outlier: 5.287A pdb=" N LYS B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N MET B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.751A pdb=" N LEU B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 475 removed outlier: 3.673A pdb=" N ILE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 498 through 506 removed outlier: 4.270A pdb=" N PHE B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.036A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 removed outlier: 3.895A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 595 removed outlier: 3.785A pdb=" N SER B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.706A pdb=" N TYR B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 630 removed outlier: 3.736A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.816A pdb=" N LEU B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 676 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.761A pdb=" N CYS B 681 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'B' and resid 693 through 705 removed outlier: 3.748A pdb=" N LEU B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 723 removed outlier: 4.515A pdb=" N ARG B 721 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.705A pdb=" N GLU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.549A pdb=" N ARG C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 removed outlier: 3.594A pdb=" N ILE C 260 " --> pdb=" O ALA C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 257 through 260' Processing helix chain 'C' and resid 262 through 270 removed outlier: 3.665A pdb=" N ILE C 266 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.664A pdb=" N ILE C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.777A pdb=" N LYS C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.058A pdb=" N ILE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.776A pdb=" N MET C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 420 through 438 removed outlier: 5.338A pdb=" N LYS C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N MET C 435 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 454 removed outlier: 3.610A pdb=" N LEU C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.788A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.820A pdb=" N LYS C 494 " --> pdb=" O ASP C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.634A pdb=" N LEU C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 549 removed outlier: 4.244A pdb=" N ASN C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 580 removed outlier: 3.508A pdb=" N LYS C 580 " --> pdb=" O GLU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 595 removed outlier: 4.028A pdb=" N LEU C 594 " --> pdb=" O SER C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 613 Processing helix chain 'C' and resid 625 through 630 removed outlier: 3.733A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.913A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 Processing helix chain 'C' and resid 693 through 704 removed outlier: 3.700A pdb=" N LEU C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 723 removed outlier: 4.113A pdb=" N LYS C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 715 " --> pdb=" O GLY C 711 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 716 " --> pdb=" O ARG C 712 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG C 721 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 removed outlier: 3.737A pdb=" N GLU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 removed outlier: 3.525A pdb=" N VAL C 751 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.992A pdb=" N ILE D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 262 through 270 removed outlier: 3.786A pdb=" N ILE D 266 " --> pdb=" O PRO D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.639A pdb=" N ILE D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.530A pdb=" N LYS D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 327 removed outlier: 3.596A pdb=" N ILE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG D 324 " --> pdb=" O GLU D 320 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 351 through 356 removed outlier: 4.337A pdb=" N PHE D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.668A pdb=" N LYS D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 420 through 437 removed outlier: 5.463A pdb=" N LYS D 434 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N MET D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 454 removed outlier: 3.669A pdb=" N LEU D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 476 removed outlier: 3.709A pdb=" N LYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 516 through 522 Processing helix chain 'D' and resid 532 through 551 removed outlier: 4.138A pdb=" N ASN D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 551 " --> pdb=" O ARG D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.521A pdb=" N LYS D 580 " --> pdb=" O GLU D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 625 through 630 removed outlier: 3.729A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.726A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 Processing helix chain 'D' and resid 693 through 705 removed outlier: 3.630A pdb=" N LEU D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 723 removed outlier: 4.021A pdb=" N LYS D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 715 " --> pdb=" O GLY D 711 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 716 " --> pdb=" O ARG D 712 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 721 " --> pdb=" O ASN D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 742 removed outlier: 3.568A pdb=" N THR D 733 " --> pdb=" O GLY D 729 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 758 Processing helix chain 'E' and resid 246 through 256 removed outlier: 4.446A pdb=" N LYS E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.818A pdb=" N ILE E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'E' and resid 262 through 270 Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.508A pdb=" N ILE E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 315 through 327 removed outlier: 4.002A pdb=" N ILE E 323 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG E 324 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.785A pdb=" N ARG E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 351 through 356 removed outlier: 4.045A pdb=" N PHE E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 381 Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.992A pdb=" N LEU E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.804A pdb=" N ARG E 406 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 437 removed outlier: 5.576A pdb=" N LYS E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET E 435 " --> pdb=" O GLN E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 removed outlier: 3.792A pdb=" N LEU E 450 " --> pdb=" O ASN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 476 removed outlier: 3.649A pdb=" N PHE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 476 " --> pdb=" O PHE E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 removed outlier: 3.759A pdb=" N LYS E 494 " --> pdb=" O ASP E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 506 Processing helix chain 'E' and resid 516 through 522 removed outlier: 3.591A pdb=" N LEU E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 551 removed outlier: 3.971A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 582 removed outlier: 3.670A pdb=" N SER E 581 " --> pdb=" O ILE E 577 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 613 Processing helix chain 'E' and resid 625 through 630 removed outlier: 3.598A pdb=" N VAL E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.570A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 676 Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.688A pdb=" N LEU E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.999A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 742 removed outlier: 3.868A pdb=" N GLU E 738 " --> pdb=" O LEU E 734 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 758 removed outlier: 3.904A pdb=" N LEU E 750 " --> pdb=" O PRO E 746 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL E 751 " --> pdb=" O VAL E 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.922A pdb=" N ILE F 260 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 256 through 261' Processing helix chain 'F' and resid 262 through 270 Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.635A pdb=" N MET F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 314 removed outlier: 3.691A pdb=" N LYS F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 327 removed outlier: 4.107A pdb=" N ILE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG F 324 " --> pdb=" O GLU F 320 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 Processing helix chain 'F' and resid 339 through 341 No H-bonds generated for 'chain 'F' and resid 339 through 341' Processing helix chain 'F' and resid 351 through 356 removed outlier: 3.751A pdb=" N PHE F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.762A pdb=" N MET F 379 " --> pdb=" O LEU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.520A pdb=" N LEU F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 405 Processing helix chain 'F' and resid 420 through 437 removed outlier: 5.416A pdb=" N LYS F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 removed outlier: 3.621A pdb=" N LEU F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 452 " --> pdb=" O ALA F 448 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU F 453 " --> pdb=" O GLU F 449 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 454 " --> pdb=" O LEU F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 476 removed outlier: 3.859A pdb=" N LYS F 476 " --> pdb=" O PHE F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 removed outlier: 3.804A pdb=" N LYS F 494 " --> pdb=" O ASP F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 507 removed outlier: 4.040A pdb=" N ASN F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.610A pdb=" N CYS F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 551 removed outlier: 3.736A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG F 550 " --> pdb=" O VAL F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 580 removed outlier: 3.644A pdb=" N LYS F 580 " --> pdb=" O GLU F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.947A pdb=" N LEU F 594 " --> pdb=" O SER F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.682A pdb=" N ASP F 612 " --> pdb=" O ASN F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 627 through 631 Processing helix chain 'F' and resid 641 through 651 removed outlier: 3.544A pdb=" N GLN F 645 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET F 646 " --> pdb=" O ASN F 642 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 647 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 677 Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.649A pdb=" N PHE F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 705 removed outlier: 3.612A pdb=" N LEU F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 723 removed outlier: 4.061A pdb=" N LYS F 714 " --> pdb=" O ALA F 710 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE F 716 " --> pdb=" O ARG F 712 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 742 removed outlier: 4.179A pdb=" N GLU F 738 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR F 739 " --> pdb=" O THR F 735 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 758 Processing helix chain 'G' and resid 425 through 437 removed outlier: 4.749A pdb=" N LYS G 434 " --> pdb=" O ILE G 430 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 454 removed outlier: 3.861A pdb=" N LEU G 450 " --> pdb=" O ASN G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 477 removed outlier: 4.050A pdb=" N THR G 477 " --> pdb=" O ALA G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 506 Processing helix chain 'G' and resid 516 through 522 Processing helix chain 'G' and resid 532 through 551 removed outlier: 3.845A pdb=" N ASN G 536 " --> pdb=" O SER G 532 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 580 Processing helix chain 'G' and resid 590 through 595 removed outlier: 3.969A pdb=" N LEU G 594 " --> pdb=" O SER G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 613 Processing helix chain 'G' and resid 625 through 630 removed outlier: 3.617A pdb=" N VAL G 630 " --> pdb=" O LEU G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 640 through 651 removed outlier: 3.875A pdb=" N LEU G 644 " --> pdb=" O SER G 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 669 through 676 Processing helix chain 'G' and resid 693 through 704 removed outlier: 3.668A pdb=" N LEU G 697 " --> pdb=" O ASN G 693 " (cutoff:3.500A) Processing helix chain 'G' and resid 708 through 723 removed outlier: 4.017A pdb=" N ARG G 721 " --> pdb=" O ASN G 717 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS G 723 " --> pdb=" O LEU G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 729 through 742 removed outlier: 3.787A pdb=" N GLU G 738 " --> pdb=" O LEU G 734 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N HIS G 742 " --> pdb=" O GLU G 738 " (cutoff:3.500A) Processing helix chain 'G' and resid 745 through 758 removed outlier: 3.679A pdb=" N GLU G 752 " --> pdb=" O ASN G 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.432A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 412 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.786A pdb=" N PHE A 585 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 666 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 558 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR A 665 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 560 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR A 667 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 562 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.417A pdb=" N LYS B 304 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP B 349 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 306 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 393 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 277 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR B 394 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 279 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 587 through 589 removed outlier: 6.465A pdb=" N VAL B 558 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THR B 665 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 560 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR B 667 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 562 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ASN B 684 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER B 559 " --> pdb=" O ASN B 684 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE B 686 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 561 " --> pdb=" O ILE B 686 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 304 through 307 removed outlier: 6.309A pdb=" N LYS C 304 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP C 349 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 306 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 393 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 557 through 559 removed outlier: 6.602A pdb=" N VAL C 558 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR C 665 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 557 through 559 removed outlier: 6.602A pdb=" N VAL C 558 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR C 665 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 304 through 307 removed outlier: 6.269A pdb=" N LYS D 304 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP D 349 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 306 " --> pdb=" O ASP D 349 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 277 " --> pdb=" O GLY D 392 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR D 394 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 279 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 412 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 587 through 589 removed outlier: 6.513A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR D 667 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE D 562 " --> pdb=" O THR D 667 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 684 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 304 through 307 removed outlier: 3.503A pdb=" N LYS E 304 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 586 through 589 removed outlier: 3.730A pdb=" N VAL E 558 " --> pdb=" O LEU E 661 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 665 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ASN E 684 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER E 559 " --> pdb=" O ASN E 684 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE E 686 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU E 561 " --> pdb=" O ILE E 686 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 304 through 307 removed outlier: 6.628A pdb=" N LYS F 304 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP F 349 " --> pdb=" O LYS F 304 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 306 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 585 through 589 removed outlier: 3.855A pdb=" N PHE F 585 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN F 619 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N MET F 664 " --> pdb=" O ASN F 619 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU F 621 " --> pdb=" O MET F 664 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR F 666 " --> pdb=" O LEU F 621 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE F 623 " --> pdb=" O THR F 666 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 558 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR F 665 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU F 560 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 587 through 589 removed outlier: 6.641A pdb=" N ASN G 619 " --> pdb=" O LEU G 662 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N MET G 664 " --> pdb=" O ASN G 619 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU G 621 " --> pdb=" O MET G 664 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR G 666 " --> pdb=" O LEU G 621 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE G 623 " --> pdb=" O THR G 666 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL G 558 " --> pdb=" O ILE G 663 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR G 665 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU G 560 " --> pdb=" O THR G 665 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR G 667 " --> pdb=" O LEU G 560 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE G 562 " --> pdb=" O THR G 667 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE G 686 " --> pdb=" O SER G 559 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU G 561 " --> pdb=" O ILE G 686 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8771 1.34 - 1.46: 3036 1.46 - 1.58: 14557 1.58 - 1.69: 53 1.69 - 1.81: 225 Bond restraints: 26642 Sorted by residual: bond pdb=" C4 ADP C 902 " pdb=" C5 ADP C 902 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C1' ATP D 903 " pdb=" O4' ATP D 903 " ideal model delta sigma weight residual 1.416 1.399 0.017 1.30e-02 5.92e+03 1.63e+00 bond pdb=" C4 ADP D 902 " pdb=" C5 ADP D 902 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C4 ADP B 902 " pdb=" C5 ADP B 902 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 26637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 34981 1.33 - 2.66: 808 2.66 - 3.99: 148 3.99 - 5.32: 34 5.32 - 6.65: 51 Bond angle restraints: 36022 Sorted by residual: angle pdb=" N ILE F 678 " pdb=" CA ILE F 678 " pdb=" C ILE F 678 " ideal model delta sigma weight residual 113.20 108.91 4.29 9.60e-01 1.09e+00 2.00e+01 angle pdb=" N ILE A 492 " pdb=" CA ILE A 492 " pdb=" C ILE A 492 " ideal model delta sigma weight residual 106.21 109.79 -3.58 1.07e+00 8.73e-01 1.12e+01 angle pdb=" N ALA B 493 " pdb=" CA ALA B 493 " pdb=" C ALA B 493 " ideal model delta sigma weight residual 113.88 110.43 3.45 1.23e+00 6.61e-01 7.89e+00 angle pdb=" C1' ATP B 903 " pdb=" O4' ATP B 903 " pdb=" C4' ATP B 903 " ideal model delta sigma weight residual 109.40 105.14 4.26 1.61e+00 3.87e-01 7.02e+00 angle pdb=" C1' ATP F 903 " pdb=" O4' ATP F 903 " pdb=" C4' ATP F 903 " ideal model delta sigma weight residual 109.40 105.25 4.15 1.61e+00 3.87e-01 6.66e+00 ... (remaining 36017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 15687 16.77 - 33.54: 758 33.54 - 50.31: 132 50.31 - 67.08: 38 67.08 - 83.84: 12 Dihedral angle restraints: 16627 sinusoidal: 7013 harmonic: 9614 Sorted by residual: dihedral pdb=" CA PRO D 511 " pdb=" C PRO D 511 " pdb=" N ALA D 512 " pdb=" CA ALA D 512 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PRO C 511 " pdb=" C PRO C 511 " pdb=" N ALA C 512 " pdb=" CA ALA C 512 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA PRO B 511 " pdb=" C PRO B 511 " pdb=" N ALA B 512 " pdb=" CA ALA B 512 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 16624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3664 0.060 - 0.119: 462 0.119 - 0.179: 45 0.179 - 0.239: 4 0.239 - 0.299: 17 Chirality restraints: 4192 Sorted by residual: chirality pdb=" C3' ATP B 903 " pdb=" C2' ATP B 903 " pdb=" C4' ATP B 903 " pdb=" O3' ATP B 903 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP A 903 " pdb=" C2' ATP A 903 " pdb=" C4' ATP A 903 " pdb=" O3' ATP A 903 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ATP F 903 " pdb=" C2' ATP F 903 " pdb=" C4' ATP F 903 " pdb=" O3' ATP F 903 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4189 not shown) Planarity restraints: 4614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 308 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO D 309 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 309 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 309 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 248 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C PHE D 248 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE D 248 " 0.010 2.00e-02 2.50e+03 pdb=" N THR D 249 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 308 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 309 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.019 5.00e-02 4.00e+02 ... (remaining 4611 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 17 2.47 - 3.08: 18706 3.08 - 3.69: 35099 3.69 - 4.29: 50313 4.29 - 4.90: 85294 Nonbonded interactions: 189429 Sorted by model distance: nonbonded pdb=" OG1 THR A 571 " pdb="MG MG A 901 " model vdw 1.868 2.170 nonbonded pdb="MG MG F 901 " pdb=" O2B ATP F 903 " model vdw 1.947 2.170 nonbonded pdb=" OG1 THR E 571 " pdb="MG MG E 901 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR D 571 " pdb="MG MG D 901 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR F 571 " pdb="MG MG F 901 " model vdw 2.223 2.170 ... (remaining 189424 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.002 0.026 26642 Z= 0.114 Angle : 0.566 6.647 36022 Z= 0.314 Chirality : 0.043 0.299 4192 Planarity : 0.003 0.054 4614 Dihedral : 10.728 83.844 10373 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.24 % Allowed : 2.06 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3287 helix: 1.57 (0.14), residues: 1477 sheet: 0.69 (0.24), residues: 398 loop : -0.65 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 396 TYR 0.011 0.001 TYR E 280 PHE 0.009 0.001 PHE C 457 TRP 0.004 0.000 TRP E 632 HIS 0.002 0.001 HIS E 563 Details of bonding type rmsd covalent geometry : bond 0.00214 (26642) covalent geometry : angle 0.56567 (36022) hydrogen bonds : bond 0.20745 ( 1202) hydrogen bonds : angle 5.88341 ( 3498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 288 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 440 MET cc_start: 0.5785 (mpp) cc_final: 0.5559 (mpp) REVERT: A 675 GLN cc_start: 0.7718 (tm130) cc_final: 0.7209 (tt0) REVERT: D 705 ASN cc_start: 0.8400 (t0) cc_final: 0.8161 (t0) REVERT: E 518 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6566 (mm-30) REVERT: F 506 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6670 (mm) REVERT: F 676 MET cc_start: 0.5647 (mmp) cc_final: 0.5423 (mmt) REVERT: G 472 PHE cc_start: 0.6156 (m-80) cc_final: 0.5730 (m-80) REVERT: G 528 MET cc_start: 0.4606 (tpt) cc_final: 0.4273 (tpt) REVERT: G 615 LYS cc_start: 0.5506 (mtpt) cc_final: 0.4779 (tttt) outliers start: 7 outliers final: 0 residues processed: 293 average time/residue: 0.1863 time to fit residues: 84.6828 Evaluate side-chains 186 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 548 GLN A 641 ASN B 344 HIS B 657 GLN C 344 HIS C 690 ASN C 717 ASN C 756 GLN D 373 ASN D 386 ASN E 273 HIS E 374 GLN E 693 ASN F 417 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.156264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107928 restraints weight = 44701.931| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.23 r_work: 0.3224 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26642 Z= 0.147 Angle : 0.591 7.943 36022 Z= 0.302 Chirality : 0.042 0.155 4192 Planarity : 0.004 0.052 4614 Dihedral : 7.948 87.994 3846 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.10 % Allowed : 6.37 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3287 helix: 1.51 (0.13), residues: 1608 sheet: 0.95 (0.23), residues: 416 loop : -0.73 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 544 TYR 0.023 0.002 TYR F 545 PHE 0.015 0.002 PHE C 457 TRP 0.008 0.001 TRP E 632 HIS 0.004 0.001 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00338 (26642) covalent geometry : angle 0.59125 (36022) hydrogen bonds : bond 0.05288 ( 1202) hydrogen bonds : angle 4.54930 ( 3498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 PHE cc_start: 0.3164 (OUTLIER) cc_final: 0.1826 (t80) REVERT: B 441 MET cc_start: 0.8620 (ttm) cc_final: 0.8239 (ttm) REVERT: B 474 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6493 (tt) REVERT: D 386 ASN cc_start: 0.7261 (m-40) cc_final: 0.6853 (t0) REVERT: D 705 ASN cc_start: 0.8493 (t0) cc_final: 0.8271 (t0) REVERT: E 307 ASN cc_start: 0.7377 (t0) cc_final: 0.7099 (t0) REVERT: E 375 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (mp) REVERT: F 440 MET cc_start: 0.3449 (mmt) cc_final: 0.2371 (mtm) REVERT: F 506 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6713 (mm) REVERT: G 472 PHE cc_start: 0.6113 (m-80) cc_final: 0.5437 (m-80) REVERT: G 528 MET cc_start: 0.4177 (tpt) cc_final: 0.3956 (tpt) REVERT: G 615 LYS cc_start: 0.4394 (mtpt) cc_final: 0.4130 (tttt) outliers start: 32 outliers final: 11 residues processed: 214 average time/residue: 0.1711 time to fit residues: 59.5476 Evaluate side-chains 186 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 374 GLN Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 506 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 29 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 239 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 209 optimal weight: 0.4980 chunk 230 optimal weight: 1.9990 chunk 267 optimal weight: 0.0670 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN E 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.158697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115252 restraints weight = 46094.754| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.89 r_work: 0.3291 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26642 Z= 0.102 Angle : 0.509 6.378 36022 Z= 0.258 Chirality : 0.040 0.177 4192 Planarity : 0.004 0.050 4614 Dihedral : 7.664 85.605 3846 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.27 % Allowed : 7.30 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3287 helix: 1.75 (0.13), residues: 1620 sheet: 1.06 (0.23), residues: 428 loop : -0.77 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 611 TYR 0.013 0.001 TYR E 280 PHE 0.013 0.001 PHE F 256 TRP 0.005 0.001 TRP E 632 HIS 0.005 0.000 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00209 (26642) covalent geometry : angle 0.50933 (36022) hydrogen bonds : bond 0.03784 ( 1202) hydrogen bonds : angle 4.20872 ( 3498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 472 PHE cc_start: 0.3413 (OUTLIER) cc_final: 0.1888 (t80) REVERT: B 441 MET cc_start: 0.8728 (ttm) cc_final: 0.8498 (ttm) REVERT: B 461 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: B 474 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6762 (tt) REVERT: C 545 TYR cc_start: 0.8360 (m-80) cc_final: 0.7840 (m-80) REVERT: D 386 ASN cc_start: 0.7242 (m-40) cc_final: 0.6902 (t0) REVERT: E 393 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: F 440 MET cc_start: 0.3406 (mmt) cc_final: 0.2424 (mtm) REVERT: F 495 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4832 (pt) REVERT: F 707 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7100 (pp) REVERT: G 472 PHE cc_start: 0.6189 (m-80) cc_final: 0.5580 (m-10) REVERT: G 528 MET cc_start: 0.4131 (tpt) cc_final: 0.3858 (tpt) REVERT: G 615 LYS cc_start: 0.4617 (mtpt) cc_final: 0.4228 (tttt) outliers start: 37 outliers final: 12 residues processed: 210 average time/residue: 0.1641 time to fit residues: 56.4292 Evaluate side-chains 183 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 236 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 258 optimal weight: 30.0000 chunk 25 optimal weight: 0.0070 chunk 160 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 314 optimal weight: 30.0000 chunk 232 optimal weight: 0.7980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 384 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN E 386 ASN F 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113835 restraints weight = 45931.279| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.93 r_work: 0.3269 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26642 Z= 0.110 Angle : 0.510 6.879 36022 Z= 0.256 Chirality : 0.040 0.161 4192 Planarity : 0.004 0.049 4614 Dihedral : 7.547 88.537 3846 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.55 % Allowed : 8.29 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3287 helix: 1.91 (0.13), residues: 1611 sheet: 1.16 (0.23), residues: 428 loop : -0.77 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 547 TYR 0.013 0.001 TYR E 280 PHE 0.011 0.001 PHE C 457 TRP 0.005 0.001 TRP E 632 HIS 0.005 0.001 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00245 (26642) covalent geometry : angle 0.50952 (36022) hydrogen bonds : bond 0.03808 ( 1202) hydrogen bonds : angle 4.07039 ( 3498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 461 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 474 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6801 (tt) REVERT: C 545 TYR cc_start: 0.8441 (m-80) cc_final: 0.7977 (m-80) REVERT: D 386 ASN cc_start: 0.7303 (m-40) cc_final: 0.6980 (t0) REVERT: E 316 VAL cc_start: 0.2457 (OUTLIER) cc_final: 0.2215 (m) REVERT: E 393 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: F 440 MET cc_start: 0.3741 (mmt) cc_final: 0.2879 (mtm) REVERT: F 495 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.4866 (pt) REVERT: F 707 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7127 (pp) REVERT: G 472 PHE cc_start: 0.6108 (m-80) cc_final: 0.5425 (m-10) REVERT: G 528 MET cc_start: 0.4116 (tpt) cc_final: 0.3888 (tpt) REVERT: G 615 LYS cc_start: 0.4560 (mtpt) cc_final: 0.4208 (ttpt) outliers start: 45 outliers final: 16 residues processed: 212 average time/residue: 0.1650 time to fit residues: 58.0072 Evaluate side-chains 185 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain G residue 610 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 57 optimal weight: 0.4980 chunk 178 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 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 384 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106708 restraints weight = 45470.010| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.64 r_work: 0.3202 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26642 Z= 0.096 Angle : 0.492 11.803 36022 Z= 0.245 Chirality : 0.040 0.144 4192 Planarity : 0.003 0.049 4614 Dihedral : 7.373 88.739 3846 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.51 % Allowed : 8.64 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 3287 helix: 2.08 (0.14), residues: 1598 sheet: 1.22 (0.23), residues: 428 loop : -0.72 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 712 TYR 0.013 0.001 TYR E 280 PHE 0.008 0.001 PHE A 248 TRP 0.004 0.001 TRP E 632 HIS 0.004 0.000 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00211 (26642) covalent geometry : angle 0.49152 (36022) hydrogen bonds : bond 0.03217 ( 1202) hydrogen bonds : angle 3.94106 ( 3498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: B 461 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 474 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6774 (tt) REVERT: C 545 TYR cc_start: 0.8451 (m-80) cc_final: 0.7882 (m-80) REVERT: D 386 ASN cc_start: 0.7352 (m-40) cc_final: 0.7037 (t0) REVERT: E 393 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: F 440 MET cc_start: 0.3789 (mmt) cc_final: 0.3149 (mtm) REVERT: F 495 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.4816 (pt) REVERT: G 615 LYS cc_start: 0.4301 (mtpt) cc_final: 0.4037 (ttpt) outliers start: 44 outliers final: 19 residues processed: 209 average time/residue: 0.1442 time to fit residues: 51.4121 Evaluate side-chains 185 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain G residue 610 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 115 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 237 optimal weight: 0.0020 chunk 310 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN D 374 GLN E 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106352 restraints weight = 45558.019| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.54 r_work: 0.3213 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26642 Z= 0.094 Angle : 0.486 6.764 36022 Z= 0.241 Chirality : 0.039 0.145 4192 Planarity : 0.003 0.051 4614 Dihedral : 7.181 89.517 3846 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.20 % Allowed : 9.57 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3287 helix: 2.09 (0.13), residues: 1635 sheet: 1.50 (0.23), residues: 416 loop : -0.62 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 436 TYR 0.012 0.001 TYR E 280 PHE 0.021 0.001 PHE C 256 TRP 0.005 0.001 TRP E 632 HIS 0.004 0.000 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00203 (26642) covalent geometry : angle 0.48551 (36022) hydrogen bonds : bond 0.03085 ( 1202) hydrogen bonds : angle 3.86598 ( 3498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.200 Fit side-chains REVERT: B 461 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: D 386 ASN cc_start: 0.7385 (m-40) cc_final: 0.7035 (t0) REVERT: D 472 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7379 (t80) REVERT: E 393 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8521 (mtp) REVERT: F 495 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.4734 (pt) REVERT: F 676 MET cc_start: 0.7067 (mmt) cc_final: 0.6588 (mmm) REVERT: G 615 LYS cc_start: 0.4387 (mtpt) cc_final: 0.4101 (ttpt) REVERT: G 705 ASN cc_start: 0.3993 (t0) cc_final: 0.3646 (p0) outliers start: 35 outliers final: 16 residues processed: 205 average time/residue: 0.1668 time to fit residues: 56.9746 Evaluate side-chains 183 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain G residue 610 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 311 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.154928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104186 restraints weight = 45480.045| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.50 r_work: 0.3172 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26642 Z= 0.121 Angle : 0.509 6.818 36022 Z= 0.255 Chirality : 0.040 0.147 4192 Planarity : 0.004 0.053 4614 Dihedral : 7.204 86.125 3846 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.38 % Allowed : 10.08 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3287 helix: 2.03 (0.13), residues: 1635 sheet: 1.18 (0.23), residues: 428 loop : -0.68 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 712 TYR 0.014 0.001 TYR E 280 PHE 0.014 0.001 PHE C 256 TRP 0.008 0.001 TRP E 632 HIS 0.004 0.001 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00286 (26642) covalent geometry : angle 0.50947 (36022) hydrogen bonds : bond 0.03830 ( 1202) hydrogen bonds : angle 3.93298 ( 3498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.119 Fit side-chains REVERT: A 441 MET cc_start: 0.7692 (ttm) cc_final: 0.7427 (mtp) REVERT: B 461 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: D 386 ASN cc_start: 0.7417 (m-40) cc_final: 0.6999 (t0) REVERT: D 525 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7271 (tm-30) REVERT: D 756 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6045 (mp10) REVERT: E 393 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8498 (mtp) REVERT: F 676 MET cc_start: 0.6856 (mmt) cc_final: 0.6611 (mmt) REVERT: G 615 LYS cc_start: 0.4318 (mtpt) cc_final: 0.4074 (ttpt) REVERT: G 705 ASN cc_start: 0.4062 (t0) cc_final: 0.3728 (p0) outliers start: 40 outliers final: 27 residues processed: 203 average time/residue: 0.1587 time to fit residues: 54.4002 Evaluate side-chains 195 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain G residue 586 ILE Chi-restraints excluded: chain G residue 610 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 215 optimal weight: 0.0060 chunk 187 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 259 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106125 restraints weight = 45404.141| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.47 r_work: 0.3209 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26642 Z= 0.091 Angle : 0.482 8.191 36022 Z= 0.239 Chirality : 0.039 0.147 4192 Planarity : 0.003 0.053 4614 Dihedral : 7.071 89.228 3846 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.17 % Allowed : 10.43 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.15), residues: 3287 helix: 2.14 (0.14), residues: 1638 sheet: 1.22 (0.22), residues: 428 loop : -0.63 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 292 TYR 0.011 0.001 TYR E 280 PHE 0.012 0.001 PHE C 256 TRP 0.006 0.001 TRP B 632 HIS 0.003 0.000 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00197 (26642) covalent geometry : angle 0.48234 (36022) hydrogen bonds : bond 0.02922 ( 1202) hydrogen bonds : angle 3.82748 ( 3498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.067 Fit side-chains REVERT: B 461 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: C 738 GLU cc_start: 0.8396 (tp30) cc_final: 0.8155 (tp30) REVERT: D 386 ASN cc_start: 0.7393 (m-40) cc_final: 0.6973 (t0) REVERT: D 756 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5980 (mp10) REVERT: E 393 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (mtp) REVERT: F 676 MET cc_start: 0.6953 (mmt) cc_final: 0.6745 (mmt) REVERT: G 615 LYS cc_start: 0.4687 (mtpt) cc_final: 0.4412 (tttt) REVERT: G 705 ASN cc_start: 0.3991 (t0) cc_final: 0.3629 (p0) outliers start: 34 outliers final: 25 residues processed: 203 average time/residue: 0.1568 time to fit residues: 53.3893 Evaluate side-chains 193 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 478 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain G residue 586 ILE Chi-restraints excluded: chain G residue 610 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 51 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 300 optimal weight: 0.3980 chunk 230 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 204 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105470 restraints weight = 45505.709| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.46 r_work: 0.3203 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26642 Z= 0.095 Angle : 0.487 7.808 36022 Z= 0.242 Chirality : 0.039 0.159 4192 Planarity : 0.003 0.053 4614 Dihedral : 6.989 88.057 3846 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.07 % Allowed : 10.53 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3287 helix: 2.13 (0.13), residues: 1644 sheet: 1.20 (0.22), residues: 428 loop : -0.60 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 712 TYR 0.012 0.001 TYR E 280 PHE 0.011 0.001 PHE C 256 TRP 0.006 0.001 TRP E 632 HIS 0.003 0.000 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00211 (26642) covalent geometry : angle 0.48721 (36022) hydrogen bonds : bond 0.03092 ( 1202) hydrogen bonds : angle 3.83215 ( 3498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.011 Fit side-chains REVERT: B 461 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: D 386 ASN cc_start: 0.7424 (m-40) cc_final: 0.7002 (t0) REVERT: D 525 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7303 (tm-30) REVERT: D 756 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6038 (mp10) REVERT: E 322 ASN cc_start: 0.8169 (m110) cc_final: 0.7904 (p0) REVERT: E 393 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (mtp) REVERT: G 615 LYS cc_start: 0.4735 (mtpt) cc_final: 0.4434 (tttt) REVERT: G 705 ASN cc_start: 0.4029 (t0) cc_final: 0.3656 (p0) outliers start: 31 outliers final: 25 residues processed: 197 average time/residue: 0.1548 time to fit residues: 51.4764 Evaluate side-chains 193 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain G residue 586 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 205 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.154184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103606 restraints weight = 45071.932| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.60 r_work: 0.3158 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26642 Z= 0.121 Angle : 0.519 8.043 36022 Z= 0.260 Chirality : 0.040 0.169 4192 Planarity : 0.004 0.054 4614 Dihedral : 7.059 83.205 3846 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.07 % Allowed : 10.70 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3287 helix: 2.04 (0.13), residues: 1644 sheet: 1.26 (0.22), residues: 416 loop : -0.65 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 547 TYR 0.015 0.001 TYR E 280 PHE 0.014 0.001 PHE E 585 TRP 0.009 0.001 TRP E 632 HIS 0.003 0.001 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00285 (26642) covalent geometry : angle 0.51930 (36022) hydrogen bonds : bond 0.03910 ( 1202) hydrogen bonds : angle 3.93631 ( 3498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.153 Fit side-chains REVERT: B 461 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: D 386 ASN cc_start: 0.7446 (m-40) cc_final: 0.6997 (t0) REVERT: D 525 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 756 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.5822 (mp10) REVERT: E 322 ASN cc_start: 0.8175 (m110) cc_final: 0.7921 (p0) REVERT: E 393 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (mtp) REVERT: G 615 LYS cc_start: 0.4816 (mtpt) cc_final: 0.4532 (ttpt) REVERT: G 705 ASN cc_start: 0.4064 (t0) cc_final: 0.3678 (p0) outliers start: 31 outliers final: 25 residues processed: 195 average time/residue: 0.1610 time to fit residues: 52.5300 Evaluate side-chains 198 residues out of total 2906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 472 PHE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 393 MET Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain G residue 586 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 135 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN E 548 GLN ** F 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097749 restraints weight = 45339.942| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.44 r_work: 0.3115 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26642 Z= 0.207 Angle : 0.615 8.110 36022 Z= 0.312 Chirality : 0.043 0.157 4192 Planarity : 0.004 0.056 4614 Dihedral : 7.614 80.613 3846 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.17 % Allowed : 10.84 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3287 helix: 1.71 (0.13), residues: 1626 sheet: 1.15 (0.23), residues: 398 loop : -0.86 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 406 TYR 0.019 0.002 TYR E 280 PHE 0.025 0.002 PHE E 585 TRP 0.012 0.002 TRP E 632 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00519 (26642) covalent geometry : angle 0.61494 (36022) hydrogen bonds : bond 0.05624 ( 1202) hydrogen bonds : angle 4.24712 ( 3498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6319.63 seconds wall clock time: 108 minutes 57.10 seconds (6537.10 seconds total)