Starting phenix.real_space_refine on Mon Jan 13 20:16:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.map" model { file = "/net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xon_38535/01_2025/8xon_38535.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 1.277 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 32 5.49 5 Mg 7 5.21 5 S 161 5.16 5 C 29666 2.51 5 N 8300 2.21 5 O 9243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47409 Number of models: 1 Model: "" Number of chains: 27 Chain: "S" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "R" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "Q" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "P" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "O" Number of atoms: 4640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4640 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 22, 'TRANS': 570} Chain breaks: 2 Chain: "T" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4632 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "B" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "E" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "H" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1371 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "I" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1399 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "M" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "N" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "S" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" 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: "P" 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: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" 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} Time building chain proxies: 20.30, per 1000 atoms: 0.43 Number of scatterers: 47409 At special positions: 0 Unit cell: (150.36, 138.6, 213.36, 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 161 16.00 P 32 15.00 Mg 7 11.99 O 9243 8.00 N 8300 7.00 C 29666 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: 9.20 Conformation dependent library (CDL) restraints added in 4.5 seconds 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11248 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 66 sheets defined 56.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'S' and resid 164 through 170 Processing helix chain 'S' and resid 174 through 179 Processing helix chain 'S' and resid 189 through 201 Processing helix chain 'S' and resid 217 through 232 removed outlier: 3.795A pdb=" N VAL S 222 " --> pdb=" O LYS S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 235 through 239 Processing helix chain 'S' and resid 247 through 253 Processing helix chain 'S' and resid 263 through 276 Processing helix chain 'S' and resid 300 through 311 Proline residue: S 306 - end of helix removed outlier: 3.725A pdb=" N ALA S 309 " --> pdb=" O LYS S 305 " (cutoff:3.500A) Processing helix chain 'S' and resid 320 through 327 Processing helix chain 'S' and resid 328 through 331 Processing helix chain 'S' and resid 333 through 337 Processing helix chain 'S' and resid 347 through 367 removed outlier: 4.577A pdb=" N ASP S 360 " --> pdb=" O LYS S 356 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG S 361 " --> pdb=" O GLY S 357 " (cutoff:3.500A) Processing helix chain 'S' and resid 371 through 386 removed outlier: 3.592A pdb=" N ILE S 386 " --> pdb=" O ALA S 382 " (cutoff:3.500A) Processing helix chain 'S' and resid 390 through 410 removed outlier: 3.705A pdb=" N ALA S 395 " --> pdb=" O LEU S 391 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE S 396 " --> pdb=" O PRO S 392 " (cutoff:3.500A) Processing helix chain 'S' and resid 476 through 489 Processing helix chain 'S' and resid 496 through 505 Processing helix chain 'S' and resid 505 through 512 Processing helix chain 'S' and resid 517 through 533 Processing helix chain 'S' and resid 554 through 568 removed outlier: 3.744A pdb=" N SER S 559 " --> pdb=" O LYS S 555 " (cutoff:3.500A) Processing helix chain 'S' and resid 569 through 573 removed outlier: 3.736A pdb=" N LEU S 573 " --> pdb=" O GLU S 570 " (cutoff:3.500A) Processing helix chain 'S' and resid 579 through 581 No H-bonds generated for 'chain 'S' and resid 579 through 581' Processing helix chain 'S' and resid 583 through 586 Processing helix chain 'S' and resid 587 through 592 Processing helix chain 'S' and resid 604 through 613 removed outlier: 3.528A pdb=" N LYS S 609 " --> pdb=" O GLN S 605 " (cutoff:3.500A) Processing helix chain 'S' and resid 622 through 626 removed outlier: 3.540A pdb=" N ALA S 626 " --> pdb=" O VAL S 623 " (cutoff:3.500A) Processing helix chain 'S' and resid 627 through 639 removed outlier: 4.224A pdb=" N PHE S 631 " --> pdb=" O HIS S 627 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN S 632 " --> pdb=" O PRO S 628 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER S 633 " --> pdb=" O ASP S 629 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU S 634 " --> pdb=" O ILE S 630 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN S 636 " --> pdb=" O ASN S 632 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE S 637 " --> pdb=" O SER S 633 " (cutoff:3.500A) Processing helix chain 'S' and resid 665 through 672 removed outlier: 3.898A pdb=" N ILE S 669 " --> pdb=" O GLY S 665 " (cutoff:3.500A) Processing helix chain 'S' and resid 682 through 702 Processing helix chain 'S' and resid 703 through 710 removed outlier: 3.526A pdb=" N VAL S 710 " --> pdb=" O PHE S 706 " (cutoff:3.500A) Processing helix chain 'S' and resid 720 through 741 removed outlier: 3.702A pdb=" N LEU S 725 " --> pdb=" O GLN S 721 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS S 726 " --> pdb=" O ALA S 722 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP S 741 " --> pdb=" O GLU S 737 " (cutoff:3.500A) Processing helix chain 'S' and resid 749 through 760 Processing helix chain 'S' and resid 767 through 778 Processing helix chain 'S' and resid 778 through 788 Processing helix chain 'S' and resid 804 through 808 removed outlier: 3.722A pdb=" N LYS S 808 " --> pdb=" O GLY S 805 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 170 removed outlier: 3.502A pdb=" N PHE R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 217 through 232 removed outlier: 3.840A pdb=" N VAL R 222 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 255 removed outlier: 4.231A pdb=" N GLY R 254 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 276 Processing helix chain 'R' and resid 284 through 288 Processing helix chain 'R' and resid 304 through 311 Processing helix chain 'R' and resid 320 through 327 Processing helix chain 'R' and resid 328 through 330 No H-bonds generated for 'chain 'R' and resid 328 through 330' Processing helix chain 'R' and resid 331 through 336 Processing helix chain 'R' and resid 347 through 367 removed outlier: 4.348A pdb=" N ASP R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG R 361 " --> pdb=" O GLY R 357 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA R 364 " --> pdb=" O ASP R 360 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS R 365 " --> pdb=" O ARG R 361 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS R 366 " --> pdb=" O TYR R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 386 removed outlier: 3.608A pdb=" N ILE R 386 " --> pdb=" O ALA R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 410 removed outlier: 3.514A pdb=" N LYS R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 396 " --> pdb=" O PRO R 392 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG R 410 " --> pdb=" O MET R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 476 through 489 Processing helix chain 'R' and resid 498 through 503 removed outlier: 3.664A pdb=" N ARG R 502 " --> pdb=" O GLU R 498 " (cutoff:3.500A) Processing helix chain 'R' and resid 505 through 512 Processing helix chain 'R' and resid 517 through 533 removed outlier: 3.643A pdb=" N VAL R 521 " --> pdb=" O GLN R 517 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 568 removed outlier: 3.603A pdb=" N SER R 559 " --> pdb=" O LYS R 555 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 573 removed outlier: 3.555A pdb=" N LEU R 573 " --> pdb=" O GLU R 570 " (cutoff:3.500A) Processing helix chain 'R' and resid 579 through 581 No H-bonds generated for 'chain 'R' and resid 579 through 581' Processing helix chain 'R' and resid 584 through 586 No H-bonds generated for 'chain 'R' and resid 584 through 586' Processing helix chain 'R' and resid 587 through 592 removed outlier: 3.515A pdb=" N PHE R 591 " --> pdb=" O VAL R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 604 through 613 Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.623A pdb=" N ALA R 626 " --> pdb=" O VAL R 623 " (cutoff:3.500A) Processing helix chain 'R' and resid 630 through 633 Processing helix chain 'R' and resid 634 through 640 Processing helix chain 'R' and resid 682 through 702 Processing helix chain 'R' and resid 703 through 709 Processing helix chain 'R' and resid 720 through 741 removed outlier: 4.245A pdb=" N ASP R 729 " --> pdb=" O LEU R 725 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU R 730 " --> pdb=" O LYS R 726 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP R 741 " --> pdb=" O GLU R 737 " (cutoff:3.500A) Processing helix chain 'R' and resid 749 through 759 Processing helix chain 'R' and resid 767 through 778 Processing helix chain 'R' and resid 778 through 789 Processing helix chain 'Q' and resid 165 through 170 removed outlier: 4.374A pdb=" N PHE Q 170 " --> pdb=" O VAL Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 180 Processing helix chain 'Q' and resid 189 through 201 Processing helix chain 'Q' and resid 217 through 230 removed outlier: 3.540A pdb=" N VAL Q 222 " --> pdb=" O LYS Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 275 Processing helix chain 'Q' and resid 285 through 289 removed outlier: 3.709A pdb=" N VAL Q 289 " --> pdb=" O HIS Q 286 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 311 Proline residue: Q 306 - end of helix removed outlier: 3.533A pdb=" N ARG Q 310 " --> pdb=" O PRO Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 327 Processing helix chain 'Q' and resid 328 through 330 No H-bonds generated for 'chain 'Q' and resid 328 through 330' Processing helix chain 'Q' and resid 331 through 336 Processing helix chain 'Q' and resid 347 through 367 removed outlier: 4.446A pdb=" N ASP Q 360 " --> pdb=" O LYS Q 356 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG Q 361 " --> pdb=" O GLY Q 357 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Q 364 " --> pdb=" O ASP Q 360 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS Q 365 " --> pdb=" O ARG Q 361 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS Q 366 " --> pdb=" O TYR Q 362 " (cutoff:3.500A) Processing helix chain 'Q' and resid 371 through 386 removed outlier: 3.755A pdb=" N LEU Q 375 " --> pdb=" O THR Q 371 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL Q 376 " --> pdb=" O ASP Q 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 410 removed outlier: 3.541A pdb=" N ALA Q 395 " --> pdb=" O LEU Q 391 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE Q 396 " --> pdb=" O PRO Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 476 through 489 removed outlier: 3.652A pdb=" N ILE Q 480 " --> pdb=" O ASP Q 476 " (cutoff:3.500A) Processing helix chain 'Q' and resid 496 through 505 Processing helix chain 'Q' and resid 505 through 511 Processing helix chain 'Q' and resid 517 through 534 Processing helix chain 'Q' and resid 554 through 567 removed outlier: 3.594A pdb=" N SER Q 559 " --> pdb=" O LYS Q 555 " (cutoff:3.500A) Processing helix chain 'Q' and resid 569 through 573 removed outlier: 3.836A pdb=" N ALA Q 572 " --> pdb=" O ASP Q 569 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Q 573 " --> pdb=" O GLU Q 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 569 through 573' Processing helix chain 'Q' and resid 579 through 581 No H-bonds generated for 'chain 'Q' and resid 579 through 581' Processing helix chain 'Q' and resid 583 through 586 Processing helix chain 'Q' and resid 587 through 592 Processing helix chain 'Q' and resid 604 through 613 removed outlier: 3.501A pdb=" N LYS Q 609 " --> pdb=" O GLN Q 605 " (cutoff:3.500A) Processing helix chain 'Q' and resid 622 through 626 Processing helix chain 'Q' and resid 629 through 633 Processing helix chain 'Q' and resid 634 through 639 Processing helix chain 'Q' and resid 685 through 702 removed outlier: 3.529A pdb=" N ARG Q 689 " --> pdb=" O SER Q 685 " (cutoff:3.500A) Processing helix chain 'Q' and resid 703 through 708 Processing helix chain 'Q' and resid 720 through 741 removed outlier: 3.805A pdb=" N ASP Q 729 " --> pdb=" O LEU Q 725 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Q 730 " --> pdb=" O LYS Q 726 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP Q 741 " --> pdb=" O GLU Q 737 " (cutoff:3.500A) Processing helix chain 'Q' and resid 749 through 760 Processing helix chain 'Q' and resid 767 through 789 removed outlier: 3.822A pdb=" N ASP Q 780 " --> pdb=" O ARG Q 776 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER Q 781 " --> pdb=" O GLU Q 777 " (cutoff:3.500A) Processing helix chain 'Q' and resid 804 through 808 removed outlier: 3.570A pdb=" N THR Q 807 " --> pdb=" O GLU Q 804 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS Q 808 " --> pdb=" O GLY Q 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 804 through 808' Processing helix chain 'P' and resid 165 through 170 Processing helix chain 'P' and resid 174 through 180 Processing helix chain 'P' and resid 189 through 201 Processing helix chain 'P' and resid 217 through 232 removed outlier: 3.679A pdb=" N VAL P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 removed outlier: 3.763A pdb=" N LEU P 251 " --> pdb=" O ASP P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 276 Processing helix chain 'P' and resid 285 through 290 removed outlier: 4.016A pdb=" N VAL P 289 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY P 290 " --> pdb=" O HIS P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 299 through 309 Proline residue: P 306 - end of helix removed outlier: 3.570A pdb=" N ALA P 309 " --> pdb=" O LYS P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 327 Processing helix chain 'P' and resid 328 through 330 No H-bonds generated for 'chain 'P' and resid 328 through 330' Processing helix chain 'P' and resid 331 through 336 Processing helix chain 'P' and resid 347 through 367 removed outlier: 4.546A pdb=" N ASP P 360 " --> pdb=" O LYS P 356 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG P 361 " --> pdb=" O GLY P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 386 removed outlier: 3.835A pdb=" N LEU P 375 " --> pdb=" O THR P 371 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL P 376 " --> pdb=" O ASP P 372 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE P 386 " --> pdb=" O ALA P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 390 through 410 removed outlier: 3.613A pdb=" N LEU P 398 " --> pdb=" O LYS P 394 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE P 399 " --> pdb=" O ALA P 395 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG P 410 " --> pdb=" O MET P 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 476 through 489 removed outlier: 3.557A pdb=" N ILE P 480 " --> pdb=" O ASP P 476 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 505 Processing helix chain 'P' and resid 505 through 512 removed outlier: 3.553A pdb=" N GLU P 509 " --> pdb=" O ARG P 505 " (cutoff:3.500A) Processing helix chain 'P' and resid 517 through 533 Processing helix chain 'P' and resid 554 through 567 Processing helix chain 'P' and resid 569 through 571 No H-bonds generated for 'chain 'P' and resid 569 through 571' Processing helix chain 'P' and resid 583 through 586 Processing helix chain 'P' and resid 587 through 592 removed outlier: 3.988A pdb=" N PHE P 591 " --> pdb=" O VAL P 587 " (cutoff:3.500A) Processing helix chain 'P' and resid 605 through 613 Processing helix chain 'P' and resid 627 through 632 removed outlier: 3.636A pdb=" N ASN P 632 " --> pdb=" O ASP P 629 " (cutoff:3.500A) Processing helix chain 'P' and resid 633 through 639 removed outlier: 4.336A pdb=" N ILE P 637 " --> pdb=" O SER P 633 " (cutoff:3.500A) Processing helix chain 'P' and resid 686 through 702 Processing helix chain 'P' and resid 703 through 708 Processing helix chain 'P' and resid 720 through 740 Processing helix chain 'P' and resid 741 through 743 No H-bonds generated for 'chain 'P' and resid 741 through 743' Processing helix chain 'P' and resid 749 through 760 removed outlier: 3.531A pdb=" N LYS P 753 " --> pdb=" O SER P 749 " (cutoff:3.500A) Processing helix chain 'P' and resid 767 through 777 removed outlier: 3.862A pdb=" N ARG P 772 " --> pdb=" O ARG P 768 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN P 775 " --> pdb=" O ARG P 771 " (cutoff:3.500A) Processing helix chain 'P' and resid 778 through 789 Processing helix chain 'P' and resid 804 through 808 removed outlier: 4.177A pdb=" N THR P 807 " --> pdb=" O GLU P 804 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 174 through 180 removed outlier: 3.602A pdb=" N GLU O 180 " --> pdb=" O GLN O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 201 Processing helix chain 'O' and resid 217 through 231 Processing helix chain 'O' and resid 257 through 276 removed outlier: 4.239A pdb=" N PHE O 261 " --> pdb=" O TYR O 257 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU O 262 " --> pdb=" O ARG O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 294 removed outlier: 3.873A pdb=" N ALA O 293 " --> pdb=" O GLY O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 310 Processing helix chain 'O' and resid 320 through 328 Processing helix chain 'O' and resid 331 through 337 Processing helix chain 'O' and resid 347 through 366 removed outlier: 4.035A pdb=" N ASP O 360 " --> pdb=" O LYS O 356 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 371 through 386 Processing helix chain 'O' and resid 390 through 410 removed outlier: 4.082A pdb=" N LYS O 394 " --> pdb=" O PHE O 390 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA O 395 " --> pdb=" O LEU O 391 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE O 396 " --> pdb=" O PRO O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 476 through 488 Processing helix chain 'O' and resid 492 through 496 Processing helix chain 'O' and resid 498 through 514 removed outlier: 3.827A pdb=" N GLU O 507 " --> pdb=" O LEU O 503 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP O 508 " --> pdb=" O LEU O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 533 Processing helix chain 'O' and resid 554 through 568 Processing helix chain 'O' and resid 584 through 586 No H-bonds generated for 'chain 'O' and resid 584 through 586' Processing helix chain 'O' and resid 587 through 592 removed outlier: 3.524A pdb=" N PHE O 591 " --> pdb=" O VAL O 587 " (cutoff:3.500A) Processing helix chain 'O' and resid 604 through 613 Processing helix chain 'O' and resid 622 through 626 Processing helix chain 'O' and resid 627 through 640 removed outlier: 4.389A pdb=" N PHE O 631 " --> pdb=" O HIS O 627 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN O 632 " --> pdb=" O PRO O 628 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER O 633 " --> pdb=" O ASP O 629 " (cutoff:3.500A) Processing helix chain 'O' and resid 665 through 671 removed outlier: 4.151A pdb=" N ILE O 669 " --> pdb=" O GLY O 665 " (cutoff:3.500A) Processing helix chain 'O' and resid 684 through 702 removed outlier: 6.748A pdb=" N LYS O 691 " --> pdb=" O TYR O 687 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN O 692 " --> pdb=" O GLU O 688 " (cutoff:3.500A) Processing helix chain 'O' and resid 703 through 710 Processing helix chain 'O' and resid 720 through 740 removed outlier: 3.704A pdb=" N ARG O 738 " --> pdb=" O LYS O 734 " (cutoff:3.500A) Processing helix chain 'O' and resid 749 through 760 Processing helix chain 'O' and resid 769 through 789 removed outlier: 3.590A pdb=" N GLN O 775 " --> pdb=" O ARG O 771 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU O 779 " --> pdb=" O GLN O 775 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP O 780 " --> pdb=" O ARG O 776 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER O 781 " --> pdb=" O GLU O 777 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU O 784 " --> pdb=" O ASP O 780 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY O 789 " --> pdb=" O LYS O 785 " (cutoff:3.500A) Processing helix chain 'O' and resid 804 through 808 Processing helix chain 'T' and resid 165 through 170 Processing helix chain 'T' and resid 174 through 181 Processing helix chain 'T' and resid 189 through 201 removed outlier: 3.770A pdb=" N SER T 201 " --> pdb=" O MET T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 217 through 232 removed outlier: 3.503A pdb=" N GLY T 232 " --> pdb=" O ALA T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 247 through 253 Processing helix chain 'T' and resid 257 through 276 removed outlier: 3.555A pdb=" N ARG T 264 " --> pdb=" O ASP T 260 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 290 removed outlier: 4.134A pdb=" N LEU T 288 " --> pdb=" O ALA T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 291 through 294 removed outlier: 3.724A pdb=" N ALA T 294 " --> pdb=" O ALA T 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 291 through 294' Processing helix chain 'T' and resid 300 through 310 removed outlier: 3.975A pdb=" N LEU T 304 " --> pdb=" O ALA T 300 " (cutoff:3.500A) Proline residue: T 306 - end of helix Processing helix chain 'T' and resid 321 through 328 Processing helix chain 'T' and resid 331 through 336 removed outlier: 3.599A pdb=" N GLU T 335 " --> pdb=" O ASP T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 367 removed outlier: 4.615A pdb=" N ASP T 360 " --> pdb=" O LYS T 356 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG T 361 " --> pdb=" O GLY T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 371 through 386 removed outlier: 3.552A pdb=" N ILE T 386 " --> pdb=" O ALA T 382 " (cutoff:3.500A) Processing helix chain 'T' and resid 390 through 410 removed outlier: 4.314A pdb=" N ILE T 396 " --> pdb=" O PRO T 392 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP T 397 " --> pdb=" O ASP T 393 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG T 410 " --> pdb=" O MET T 406 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 489 removed outlier: 4.244A pdb=" N LEU T 484 " --> pdb=" O ILE T 480 " (cutoff:3.500A) Processing helix chain 'T' and resid 496 through 504 removed outlier: 3.591A pdb=" N LEU T 503 " --> pdb=" O GLU T 499 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU T 504 " --> pdb=" O SER T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 505 through 511 removed outlier: 3.837A pdb=" N GLU T 509 " --> pdb=" O ARG T 505 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 533 Processing helix chain 'T' and resid 556 through 567 Processing helix chain 'T' and resid 583 through 591 removed outlier: 3.612A pdb=" N PHE T 591 " --> pdb=" O VAL T 587 " (cutoff:3.500A) Processing helix chain 'T' and resid 605 through 613 Processing helix chain 'T' and resid 629 through 639 removed outlier: 3.664A pdb=" N SER T 633 " --> pdb=" O ASP T 629 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU T 635 " --> pdb=" O PHE T 631 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN T 636 " --> pdb=" O ASN T 632 " (cutoff:3.500A) Processing helix chain 'T' and resid 685 through 702 Processing helix chain 'T' and resid 703 through 708 removed outlier: 3.830A pdb=" N LEU T 707 " --> pdb=" O ARG T 703 " (cutoff:3.500A) Processing helix chain 'T' and resid 723 through 742 removed outlier: 3.523A pdb=" N ILE T 727 " --> pdb=" O ASP T 723 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG T 742 " --> pdb=" O ARG T 738 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 760 Processing helix chain 'T' and resid 767 through 778 removed outlier: 3.678A pdb=" N ARG T 771 " --> pdb=" O ALA T 767 " (cutoff:3.500A) Processing helix chain 'T' and resid 778 through 789 Processing helix chain 'T' and resid 804 through 808 removed outlier: 3.721A pdb=" N LYS T 808 " --> pdb=" O GLY T 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.644A pdb=" N ALA A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 148 through 174 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.852A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 97 Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 148 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'E' and resid 32 through 44 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.541A pdb=" N ILE E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 186 removed outlier: 4.644A pdb=" N ARG E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.630A pdb=" N GLY G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 53 through 60 removed outlier: 3.648A pdb=" N GLU H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 88 Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.661A pdb=" N LEU H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.562A pdb=" N VAL H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 191 removed outlier: 3.510A pdb=" N HIS H 191 " --> pdb=" O MET H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 103 through 117 removed outlier: 3.521A pdb=" N LEU I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 139 Processing helix chain 'I' and resid 167 through 191 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 70 through 88 Processing helix chain 'J' and resid 104 through 117 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.814A pdb=" N VAL J 135 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 191 removed outlier: 3.504A pdb=" N HIS J 191 " --> pdb=" O MET J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 203 Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 53 through 61 Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'K' and resid 103 through 117 Processing helix chain 'K' and resid 131 through 139 removed outlier: 3.615A pdb=" N VAL K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 191 removed outlier: 3.561A pdb=" N HIS K 191 " --> pdb=" O MET K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 203 Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.505A pdb=" N ARG L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 88 Processing helix chain 'L' and resid 103 through 117 removed outlier: 3.619A pdb=" N VAL L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 167 through 191 Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 70 through 88 Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.538A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.583A pdb=" N VAL M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 191 Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 211 through 218 Processing helix chain 'N' and resid 53 through 60 Processing helix chain 'N' and resid 70 through 88 Processing helix chain 'N' and resid 103 through 117 Processing helix chain 'N' and resid 131 through 139 Processing helix chain 'N' and resid 167 through 191 Processing helix chain 'N' and resid 195 through 203 Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'S' and resid 171 through 173 removed outlier: 6.083A pdb=" N HIS S 242 " --> pdb=" O ILE S 279 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE S 281 " --> pdb=" O HIS S 242 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR S 244 " --> pdb=" O PHE S 281 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP S 283 " --> pdb=" O TYR S 244 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU S 246 " --> pdb=" O ASP S 283 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ILE S 316 " --> pdb=" O ILE S 278 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU S 280 " --> pdb=" O ILE S 316 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ALA S 318 " --> pdb=" O LEU S 280 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE S 282 " --> pdb=" O ALA S 318 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR S 319 " --> pdb=" O PRO S 208 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU S 210 " --> pdb=" O THR S 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 369 through 370 removed outlier: 6.973A pdb=" N SER S 369 " --> pdb=" O VAL S 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'S' and resid 574 through 577 removed outlier: 6.609A pdb=" N ILE S 574 " --> pdb=" O LEU S 619 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP S 621 " --> pdb=" O ILE S 574 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU S 576 " --> pdb=" O ASP S 621 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY S 543 " --> pdb=" O ILE S 658 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N MET S 660 " --> pdb=" O GLY S 543 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE S 545 " --> pdb=" O MET S 660 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER S 544 " --> pdb=" O ASP S 712 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL S 714 " --> pdb=" O SER S 544 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE S 546 " --> pdb=" O VAL S 714 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 642 through 644 Processing sheet with id=AA5, first strand: chain 'S' and resid 744 through 748 removed outlier: 6.483A pdb=" N GLY S 745 " --> pdb=" O VAL S 797 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL S 799 " --> pdb=" O GLY S 745 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU S 747 " --> pdb=" O VAL S 799 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N THR S 801 " --> pdb=" O GLU S 747 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 171 through 173 removed outlier: 6.586A pdb=" N HIS R 242 " --> pdb=" O ILE R 279 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE R 281 " --> pdb=" O HIS R 242 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR R 244 " --> pdb=" O PHE R 281 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA R 318 " --> pdb=" O ILE R 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 369 through 370 removed outlier: 6.674A pdb=" N SER R 369 " --> pdb=" O VAL R 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 574 through 577 removed outlier: 6.455A pdb=" N ILE R 574 " --> pdb=" O LEU R 619 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP R 621 " --> pdb=" O ILE R 574 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU R 576 " --> pdb=" O ASP R 621 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL R 618 " --> pdb=" O ILE R 659 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR R 661 " --> pdb=" O VAL R 618 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE R 620 " --> pdb=" O THR R 661 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY R 543 " --> pdb=" O ILE R 658 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N MET R 660 " --> pdb=" O GLY R 543 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE R 545 " --> pdb=" O MET R 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 642 through 644 Processing sheet with id=AB1, first strand: chain 'R' and resid 744 through 746 removed outlier: 6.629A pdb=" N GLY R 745 " --> pdb=" O VAL R 797 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL R 799 " --> pdb=" O GLY R 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 172 through 173 removed outlier: 6.252A pdb=" N HIS Q 242 " --> pdb=" O ILE Q 279 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE Q 281 " --> pdb=" O HIS Q 242 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR Q 244 " --> pdb=" O PHE Q 281 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASP Q 283 " --> pdb=" O TYR Q 244 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR Q 319 " --> pdb=" O PRO Q 208 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU Q 210 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 341 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL Q 343 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE Q 211 " --> pdb=" O VAL Q 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 574 through 577 removed outlier: 6.420A pdb=" N ILE Q 574 " --> pdb=" O LEU Q 619 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP Q 621 " --> pdb=" O ILE Q 574 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU Q 576 " --> pdb=" O ASP Q 621 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY Q 543 " --> pdb=" O ILE Q 658 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N MET Q 660 " --> pdb=" O GLY Q 543 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE Q 545 " --> pdb=" O MET Q 660 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR Q 662 " --> pdb=" O PHE Q 545 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE Q 547 " --> pdb=" O THR Q 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 642 through 644 Processing sheet with id=AB5, first strand: chain 'Q' and resid 746 through 748 removed outlier: 6.574A pdb=" N GLU Q 747 " --> pdb=" O VAL Q 799 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR Q 801 " --> pdb=" O GLU Q 747 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 171 through 173 removed outlier: 6.544A pdb=" N HIS P 242 " --> pdb=" O ILE P 279 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE P 281 " --> pdb=" O HIS P 242 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR P 244 " --> pdb=" O PHE P 281 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASP P 283 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU P 246 " --> pdb=" O ASP P 283 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA P 318 " --> pdb=" O ILE P 282 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY P 212 " --> pdb=" O THR P 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 369 through 370 removed outlier: 6.738A pdb=" N SER P 369 " --> pdb=" O VAL P 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'P' and resid 573 through 577 removed outlier: 7.126A pdb=" N SER P 616 " --> pdb=" O VAL P 657 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE P 659 " --> pdb=" O SER P 616 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL P 618 " --> pdb=" O ILE P 659 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR P 661 " --> pdb=" O VAL P 618 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE P 620 " --> pdb=" O THR P 661 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY P 543 " --> pdb=" O ILE P 658 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N MET P 660 " --> pdb=" O GLY P 543 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE P 545 " --> pdb=" O MET P 660 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR P 662 " --> pdb=" O PHE P 545 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE P 547 " --> pdb=" O THR P 662 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER P 544 " --> pdb=" O ASP P 712 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL P 714 " --> pdb=" O SER P 544 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE P 546 " --> pdb=" O VAL P 714 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 642 through 644 Processing sheet with id=AC1, first strand: chain 'P' and resid 747 through 748 Processing sheet with id=AC2, first strand: chain 'O' and resid 171 through 173 removed outlier: 6.935A pdb=" N ILE O 278 " --> pdb=" O GLN O 314 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N ILE O 316 " --> pdb=" O ILE O 278 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU O 280 " --> pdb=" O ILE O 316 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ALA O 318 " --> pdb=" O LEU O 280 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL O 209 " --> pdb=" O ILE O 341 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 368 through 370 removed outlier: 6.483A pdb=" N SER O 369 " --> pdb=" O VAL O 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'O' and resid 573 through 577 removed outlier: 6.416A pdb=" N ILE O 574 " --> pdb=" O LEU O 619 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP O 621 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU O 576 " --> pdb=" O ASP O 621 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL O 618 " --> pdb=" O ILE O 659 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR O 661 " --> pdb=" O VAL O 618 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE O 620 " --> pdb=" O THR O 661 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY O 543 " --> pdb=" O ILE O 658 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N MET O 660 " --> pdb=" O GLY O 543 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE O 545 " --> pdb=" O MET O 660 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR O 662 " --> pdb=" O PHE O 545 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE O 547 " --> pdb=" O THR O 662 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER O 544 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL O 714 " --> pdb=" O SER O 544 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE O 546 " --> pdb=" O VAL O 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'O' and resid 642 through 644 Processing sheet with id=AC6, first strand: chain 'O' and resid 744 through 748 removed outlier: 5.999A pdb=" N GLY O 745 " --> pdb=" O VAL O 797 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL O 799 " --> pdb=" O GLY O 745 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU O 747 " --> pdb=" O VAL O 799 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR O 801 " --> pdb=" O GLU O 747 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 171 through 173 removed outlier: 5.300A pdb=" N ASP T 283 " --> pdb=" O LEU T 246 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ILE T 316 " --> pdb=" O ILE T 278 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU T 280 " --> pdb=" O ILE T 316 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ALA T 318 " --> pdb=" O LEU T 280 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE T 282 " --> pdb=" O ALA T 318 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N THR T 320 " --> pdb=" O ILE T 282 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 368 through 370 Processing sheet with id=AC9, first strand: chain 'T' and resid 576 through 577 removed outlier: 6.657A pdb=" N VAL T 618 " --> pdb=" O ILE T 659 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N THR T 661 " --> pdb=" O VAL T 618 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE T 620 " --> pdb=" O THR T 661 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY T 543 " --> pdb=" O ILE T 658 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N MET T 660 " --> pdb=" O GLY T 543 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE T 545 " --> pdb=" O MET T 660 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER T 544 " --> pdb=" O ASP T 712 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL T 714 " --> pdb=" O SER T 544 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE T 546 " --> pdb=" O VAL T 714 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 744 through 748 removed outlier: 6.822A pdb=" N GLY T 745 " --> pdb=" O VAL T 797 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL T 799 " --> pdb=" O GLY T 745 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLU T 747 " --> pdb=" O VAL T 799 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N THR T 801 " --> pdb=" O GLU T 747 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.371A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.371A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG A 127 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AD5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AD6, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.597A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.597A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.704A pdb=" N GLY B 146 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 45 through 48 removed outlier: 4.198A pdb=" N LEU C 48 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 129 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AE4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.825A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 134 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.825A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AE8, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.680A pdb=" N ASN E 80 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 135 " --> pdb=" O PHE E 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 45 through 48 removed outlier: 3.680A pdb=" N ASN E 80 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 129 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 141 through 147 removed outlier: 6.797A pdb=" N ALA E 142 " --> pdb=" O ARG M 164 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG M 164 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.286A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG F 127 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AF4, first strand: chain 'F' and resid 141 through 147 removed outlier: 6.654A pdb=" N ALA F 142 " --> pdb=" O ARG N 164 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG N 164 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU F 144 " --> pdb=" O THR N 162 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 46 through 48 removed outlier: 6.798A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE G 75 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE G 106 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU G 77 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET G 108 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE G 79 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU G 110 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU G 134 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 46 through 48 removed outlier: 6.798A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE G 75 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE G 106 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU G 77 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET G 108 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE G 79 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU G 110 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG G 127 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 141 through 147 removed outlier: 6.702A pdb=" N ALA G 142 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG H 164 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU G 144 " --> pdb=" O THR H 162 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.540A pdb=" N ILE H 63 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 128 through 130 removed outlier: 6.492A pdb=" N ALA H 129 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 62 through 65 removed outlier: 8.137A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 128 through 129 removed outlier: 6.328A pdb=" N ALA I 129 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 62 through 65 removed outlier: 3.538A pdb=" N ALA J 147 " --> pdb=" O GLN J 222 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 128 through 130 Processing sheet with id=AG5, first strand: chain 'K' and resid 62 through 65 removed outlier: 6.282A pdb=" N ILE K 93 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL K 124 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL K 95 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA K 147 " --> pdb=" O GLN K 222 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 128 through 130 removed outlier: 6.402A pdb=" N ALA K 129 " --> pdb=" O LEU K 154 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 62 through 65 removed outlier: 8.134A pdb=" N MET L 146 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THR L 123 " --> pdb=" O MET L 146 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 128 through 130 Processing sheet with id=AG9, first strand: chain 'M' and resid 62 through 65 removed outlier: 8.104A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 147 " --> pdb=" O GLN M 222 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 129 through 130 removed outlier: 6.693A pdb=" N ALA M 129 " --> pdb=" O LEU M 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.586A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N MET N 146 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR N 123 " --> pdb=" O MET N 146 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 128 through 130 removed outlier: 6.309A pdb=" N ALA N 129 " --> pdb=" O LEU N 154 " (cutoff:3.500A) 2437 hydrogen bonds defined for protein. 7083 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: 17.56 Time building geometry restraints manager: 10.76 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: 16149 1.34 - 1.46: 6655 1.46 - 1.58: 24923 1.58 - 1.69: 53 1.69 - 1.81: 308 Bond restraints: 48088 Sorted by residual: bond pdb=" CA GLU F 72 " pdb=" CB GLU F 72 " ideal model delta sigma weight residual 1.531 1.602 -0.072 3.12e-02 1.03e+03 5.28e+00 bond pdb=" CA PRO O 594 " pdb=" C PRO O 594 " ideal model delta sigma weight residual 1.514 1.507 0.008 5.50e-03 3.31e+04 1.87e+00 bond pdb=" C LYS T 305 " pdb=" N PRO T 306 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.30e-02 5.92e+03 1.79e+00 bond pdb=" C VAL L 117 " pdb=" N LYS L 118 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.50e-02 4.44e+03 1.46e+00 bond pdb=" N THR C 207 " pdb=" CA THR C 207 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 ... (remaining 48083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 64611 2.88 - 5.77: 343 5.77 - 8.65: 17 8.65 - 11.53: 3 11.53 - 14.41: 1 Bond angle restraints: 64975 Sorted by residual: angle pdb=" C GLY A 49 " pdb=" N GLN A 50 " pdb=" CA GLN A 50 " ideal model delta sigma weight residual 122.56 133.97 -11.41 1.58e+00 4.01e-01 5.22e+01 angle pdb=" C THR P 683 " pdb=" CA THR P 683 " pdb=" CB THR P 683 " ideal model delta sigma weight residual 116.63 110.16 6.47 1.16e+00 7.43e-01 3.11e+01 angle pdb=" N GLN A 50 " pdb=" CA GLN A 50 " pdb=" C GLN A 50 " ideal model delta sigma weight residual 108.13 103.20 4.93 9.00e-01 1.23e+00 3.01e+01 angle pdb=" C THR T 237 " pdb=" N LEU T 238 " pdb=" CA LEU T 238 " ideal model delta sigma weight residual 126.32 134.30 -7.98 1.74e+00 3.30e-01 2.11e+01 angle pdb=" C GLU K 60 " pdb=" N ARG K 61 " pdb=" CA ARG K 61 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 ... (remaining 64970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 29227 35.86 - 71.71: 461 71.71 - 107.57: 50 107.57 - 143.43: 7 143.43 - 179.29: 4 Dihedral angle restraints: 29749 sinusoidal: 12323 harmonic: 17426 Sorted by residual: dihedral pdb=" C5' ADP P 901 " pdb=" O5' ADP P 901 " pdb=" PA ADP P 901 " pdb=" O2A ADP P 901 " ideal model delta sinusoidal sigma weight residual -60.00 119.29 -179.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP O 901 " pdb=" O5' ADP O 901 " pdb=" PA ADP O 901 " pdb=" O2A ADP O 901 " ideal model delta sinusoidal sigma weight residual 300.00 125.94 174.06 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP T 901 " pdb=" O5' ADP T 901 " pdb=" PA ADP T 901 " pdb=" O2A ADP T 901 " ideal model delta sinusoidal sigma weight residual -60.00 94.99 -154.99 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 29746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5775 0.044 - 0.088: 1225 0.088 - 0.133: 468 0.133 - 0.177: 12 0.177 - 0.221: 2 Chirality restraints: 7482 Sorted by residual: chirality pdb=" CB VAL O 492 " pdb=" CA VAL O 492 " pdb=" CG1 VAL O 492 " pdb=" CG2 VAL O 492 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU T 576 " pdb=" CB LEU T 576 " pdb=" CD1 LEU T 576 " pdb=" CD2 LEU T 576 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CG LEU H 57 " pdb=" CB LEU H 57 " pdb=" CD1 LEU H 57 " pdb=" CD2 LEU H 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 7479 not shown) Planarity restraints: 8435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 213 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO T 214 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO T 214 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO T 214 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 70 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO F 71 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 234 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO S 235 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO S 235 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 235 " 0.027 5.00e-02 4.00e+02 ... (remaining 8432 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 399 2.60 - 3.17: 41135 3.17 - 3.75: 72837 3.75 - 4.32: 99135 4.32 - 4.90: 168402 Nonbonded interactions: 381908 Sorted by model distance: nonbonded pdb=" O1B ATP P 902 " pdb="MG MG P 903 " model vdw 2.025 2.170 nonbonded pdb=" O2B ATP S 902 " pdb="MG MG S 904 " model vdw 2.053 2.170 nonbonded pdb=" O2G ATP S 902 " pdb="MG MG S 904 " model vdw 2.059 2.170 nonbonded pdb=" O1B ATP T 902 " pdb="MG MG T 903 " model vdw 2.063 2.170 nonbonded pdb=" O3B ATP S 901 " pdb="MG MG S 903 " model vdw 2.064 2.170 ... (remaining 381903 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' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 52 through 227) selection = (chain 'I' and resid 52 through 227) selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 52 through 227) selection = (chain 'M' and resid 52 through 227) selection = (chain 'N' and resid 52 through 227) } ncs_group { reference = (chain 'O' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 410 or resid 472 through 816 o \ r resid 902)) selection = (chain 'P' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 816 or resid 902)) selection = (chain 'Q' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 816 or resid 902)) selection = (chain 'R' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 816 or resid 902)) selection = (chain 'S' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 816 or resid 902)) selection = (chain 'T' and (resid 164 through 816 or resid 902)) } 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: 2.140 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: 0.040 Extract box with map and model: 1.340 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 80.430 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.220 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:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.003 0.072 48088 Z= 0.176 Angle : 0.569 14.414 64975 Z= 0.307 Chirality : 0.041 0.221 7482 Planarity : 0.004 0.070 8435 Dihedral : 14.065 179.286 18501 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 5991 helix: 1.62 (0.10), residues: 3119 sheet: 0.36 (0.18), residues: 759 loop : -0.74 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 189 HIS 0.009 0.001 HIS O 327 PHE 0.028 0.001 PHE P 631 TYR 0.019 0.001 TYR O 324 ARG 0.004 0.000 ARG K 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1237 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 170 PHE cc_start: 0.7948 (m-10) cc_final: 0.7728 (m-10) REVERT: S 183 LEU cc_start: 0.8004 (mt) cc_final: 0.7699 (mp) REVERT: S 206 ASN cc_start: 0.7053 (p0) cc_final: 0.6597 (p0) REVERT: S 211 ILE cc_start: 0.7974 (mm) cc_final: 0.7759 (mp) REVERT: S 233 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7258 (mp0) REVERT: S 267 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7995 (ptmm) REVERT: S 270 LYS cc_start: 0.7892 (tmmt) cc_final: 0.7388 (tmmm) REVERT: S 313 LEU cc_start: 0.6936 (mm) cc_final: 0.6448 (tm) REVERT: S 345 GLU cc_start: 0.8551 (tt0) cc_final: 0.8138 (tt0) REVERT: S 397 ASP cc_start: 0.7073 (m-30) cc_final: 0.6613 (m-30) REVERT: S 407 ARG cc_start: 0.7611 (ttt90) cc_final: 0.7357 (tmm-80) REVERT: S 476 ASP cc_start: 0.6147 (p0) cc_final: 0.5609 (p0) REVERT: S 512 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8461 (mtpp) REVERT: S 539 LYS cc_start: 0.8285 (mppt) cc_final: 0.7917 (mtpp) REVERT: S 571 ASP cc_start: 0.7549 (m-30) cc_final: 0.7071 (m-30) REVERT: S 584 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8281 (ptpp) REVERT: S 609 LYS cc_start: 0.8439 (mttt) cc_final: 0.8234 (mtmm) REVERT: S 663 ASN cc_start: 0.8166 (t0) cc_final: 0.7567 (t0) REVERT: S 671 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8108 (tmmt) REVERT: S 688 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7422 (mp0) REVERT: S 693 LYS cc_start: 0.8084 (tppp) cc_final: 0.7822 (tptp) REVERT: S 697 GLU cc_start: 0.8056 (tp30) cc_final: 0.7735 (tt0) REVERT: S 712 ASP cc_start: 0.7333 (m-30) cc_final: 0.6976 (m-30) REVERT: S 743 ASP cc_start: 0.7794 (t0) cc_final: 0.7038 (t0) REVERT: S 758 LYS cc_start: 0.8500 (tttm) cc_final: 0.8149 (mmpt) REVERT: R 170 PHE cc_start: 0.7580 (m-10) cc_final: 0.7267 (m-80) REVERT: R 179 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8262 (ttp-170) REVERT: R 244 TYR cc_start: 0.8075 (m-80) cc_final: 0.7860 (m-80) REVERT: R 258 ARG cc_start: 0.7392 (tmm-80) cc_final: 0.7000 (tmm-80) REVERT: R 373 GLU cc_start: 0.7526 (mp0) cc_final: 0.7245 (mp0) REVERT: R 494 LYS cc_start: 0.8382 (ttpp) cc_final: 0.7971 (ttpp) REVERT: R 499 GLU cc_start: 0.7611 (pt0) cc_final: 0.7269 (pp20) REVERT: R 584 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7985 (mtpm) REVERT: R 640 ASP cc_start: 0.7732 (t0) cc_final: 0.6575 (t0) REVERT: R 642 ARG cc_start: 0.8129 (ptt-90) cc_final: 0.7674 (ptt180) REVERT: R 647 GLN cc_start: 0.8712 (mt0) cc_final: 0.8401 (mt0) REVERT: R 649 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7858 (ttm-80) REVERT: R 754 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7298 (tp30) REVERT: R 804 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7205 (mm-30) REVERT: Q 192 GLU cc_start: 0.7797 (mp0) cc_final: 0.7345 (mp0) REVERT: Q 310 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6667 (ttp80) REVERT: Q 312 GLU cc_start: 0.7515 (mp0) cc_final: 0.6874 (mp0) REVERT: Q 322 ASP cc_start: 0.7883 (m-30) cc_final: 0.7680 (m-30) REVERT: Q 325 ARG cc_start: 0.8192 (tmm160) cc_final: 0.7692 (ptm-80) REVERT: Q 326 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7992 (ttpt) REVERT: Q 495 LEU cc_start: 0.8587 (mt) cc_final: 0.8384 (mt) REVERT: Q 509 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7797 (mm-30) REVERT: Q 584 LYS cc_start: 0.8808 (pptt) cc_final: 0.8576 (pttp) REVERT: Q 697 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7717 (mp0) REVERT: P 172 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6733 (ptm160) REVERT: P 182 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8214 (mptt) REVERT: P 211 ILE cc_start: 0.8258 (pt) cc_final: 0.7755 (pt) REVERT: P 273 ARG cc_start: 0.8469 (ttt90) cc_final: 0.8003 (tpm170) REVERT: P 329 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7796 (mm-30) REVERT: P 342 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7933 (mm-40) REVERT: P 388 ASP cc_start: 0.6296 (p0) cc_final: 0.6055 (p0) REVERT: P 401 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7956 (mm-30) REVERT: P 405 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7482 (mtp180) REVERT: P 406 MET cc_start: 0.8039 (tpp) cc_final: 0.7766 (tpt) REVERT: P 478 GLU cc_start: 0.7818 (tt0) cc_final: 0.7493 (tm-30) REVERT: P 492 VAL cc_start: 0.7902 (t) cc_final: 0.7576 (m) REVERT: P 505 ARG cc_start: 0.7493 (ptt90) cc_final: 0.7206 (ptt-90) REVERT: P 509 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7466 (mm-30) REVERT: P 557 GLU cc_start: 0.7813 (tp30) cc_final: 0.7252 (tp30) REVERT: P 560 LYS cc_start: 0.7718 (mttm) cc_final: 0.7352 (mmmm) REVERT: P 608 GLU cc_start: 0.7006 (mp0) cc_final: 0.6544 (mp0) REVERT: P 621 ASP cc_start: 0.8154 (m-30) cc_final: 0.7807 (m-30) REVERT: P 625 LYS cc_start: 0.8189 (mttm) cc_final: 0.7878 (mttm) REVERT: P 652 ASP cc_start: 0.8407 (p0) cc_final: 0.8057 (p0) REVERT: P 703 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7202 (mmt180) REVERT: P 712 ASP cc_start: 0.7211 (m-30) cc_final: 0.6819 (t0) REVERT: P 744 MET cc_start: 0.7022 (mtt) cc_final: 0.6341 (mmm) REVERT: O 267 LYS cc_start: 0.8443 (mmpt) cc_final: 0.8074 (mtmt) REVERT: O 310 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7418 (tpp-160) REVERT: O 328 LEU cc_start: 0.7404 (mm) cc_final: 0.6827 (tm) REVERT: O 401 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7551 (tm-30) REVERT: O 504 LEU cc_start: 0.8580 (mm) cc_final: 0.8304 (pp) REVERT: O 584 LYS cc_start: 0.8316 (tppt) cc_final: 0.7734 (pptt) REVERT: O 635 LEU cc_start: 0.8268 (tp) cc_final: 0.7790 (tp) REVERT: O 690 MET cc_start: 0.7850 (ptp) cc_final: 0.7209 (pmm) REVERT: O 788 PHE cc_start: 0.8009 (t80) cc_final: 0.7306 (t80) REVERT: T 198 GLN cc_start: 0.5934 (pt0) cc_final: 0.5716 (pt0) REVERT: T 384 ARG cc_start: 0.6273 (ptm160) cc_final: 0.5978 (tpm170) REVERT: T 589 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7501 (ttm110) REVERT: T 806 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7709 (tm-30) REVERT: A 39 ARG cc_start: 0.8394 (mtm180) cc_final: 0.8105 (mtp180) REVERT: A 54 ASP cc_start: 0.7410 (m-30) cc_final: 0.7196 (m-30) REVERT: A 73 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7713 (mtmm) REVERT: A 76 TYR cc_start: 0.8374 (m-80) cc_final: 0.8159 (m-80) REVERT: A 141 SER cc_start: 0.8821 (p) cc_final: 0.8534 (t) REVERT: A 164 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7974 (tpt170) REVERT: B 187 ASP cc_start: 0.8190 (m-30) cc_final: 0.7794 (m-30) REVERT: C 59 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7840 (ttmm) REVERT: D 76 TYR cc_start: 0.8341 (m-80) cc_final: 0.8042 (m-80) REVERT: D 150 ASP cc_start: 0.7589 (m-30) cc_final: 0.7339 (m-30) REVERT: E 59 LYS cc_start: 0.8286 (tttt) cc_final: 0.8036 (ttmm) REVERT: E 72 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7410 (mp0) REVERT: E 96 MET cc_start: 0.7947 (mtp) cc_final: 0.7615 (mtp) REVERT: E 98 TYR cc_start: 0.8660 (t80) cc_final: 0.8409 (t80) REVERT: E 102 ASP cc_start: 0.7855 (m-30) cc_final: 0.7576 (m-30) REVERT: E 165 MET cc_start: 0.8299 (tpp) cc_final: 0.7988 (tpp) REVERT: E 178 GLU cc_start: 0.8121 (mp0) cc_final: 0.7917 (mp0) REVERT: E 179 GLN cc_start: 0.7515 (tp40) cc_final: 0.6920 (tp40) REVERT: E 182 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7299 (mtm-85) REVERT: E 205 MET cc_start: 0.7860 (ttm) cc_final: 0.7483 (ttp) REVERT: F 36 VAL cc_start: 0.7470 (t) cc_final: 0.7258 (m) REVERT: F 69 SER cc_start: 0.8681 (m) cc_final: 0.8408 (p) REVERT: F 102 ASP cc_start: 0.8243 (m-30) cc_final: 0.7827 (m-30) REVERT: G 39 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7565 (mtp85) REVERT: G 55 ASP cc_start: 0.8059 (t70) cc_final: 0.7732 (t0) REVERT: G 139 GLN cc_start: 0.8485 (pt0) cc_final: 0.8247 (pt0) REVERT: H 154 LEU cc_start: 0.8848 (tt) cc_final: 0.8637 (tp) REVERT: H 171 GLU cc_start: 0.7474 (tt0) cc_final: 0.7230 (tt0) REVERT: H 175 ASN cc_start: 0.8195 (m-40) cc_final: 0.7862 (m-40) REVERT: H 212 GLU cc_start: 0.7282 (pm20) cc_final: 0.6979 (pm20) REVERT: I 76 ASP cc_start: 0.7753 (m-30) cc_final: 0.7517 (m-30) REVERT: I 166 GLN cc_start: 0.8699 (mt0) cc_final: 0.8490 (mt0) REVERT: J 60 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7847 (mm-30) REVERT: J 112 ASP cc_start: 0.7930 (m-30) cc_final: 0.7689 (m-30) REVERT: J 113 THR cc_start: 0.8287 (m) cc_final: 0.7908 (m) REVERT: J 227 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6912 (ttp-170) REVERT: K 161 GLU cc_start: 0.8083 (pt0) cc_final: 0.7849 (pt0) REVERT: K 164 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7632 (ttm110) REVERT: K 198 LYS cc_start: 0.7816 (tttm) cc_final: 0.7300 (tttt) REVERT: L 76 ASP cc_start: 0.7406 (m-30) cc_final: 0.7086 (m-30) REVERT: M 60 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7483 (mp0) REVERT: M 76 ASP cc_start: 0.7647 (m-30) cc_final: 0.7424 (m-30) REVERT: M 160 SER cc_start: 0.8493 (t) cc_final: 0.8190 (p) REVERT: M 182 SER cc_start: 0.7865 (t) cc_final: 0.7569 (m) REVERT: N 91 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7062 (mmm-85) REVERT: N 161 GLU cc_start: 0.7818 (pp20) cc_final: 0.7062 (tm-30) REVERT: N 180 MET cc_start: 0.7619 (mtt) cc_final: 0.7297 (mmm) outliers start: 0 outliers final: 1 residues processed: 1237 average time/residue: 1.6148 time to fit residues: 2380.2590 Evaluate side-chains 983 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 982 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 74 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 502 optimal weight: 2.9990 chunk 450 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 466 optimal weight: 0.0770 chunk 180 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 347 optimal weight: 5.9990 chunk 540 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 339 GLN S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 647 GLN S 674 ASN ** R 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 HIS R 674 ASN Q 227 GLN Q 795 HIS P 173 ASN P 314 GLN P 692 ASN ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 HIS T 366 HIS T 721 GLN A 42 ASN A 101 ASN A 132 ASN B 58 ASN B 63 GLN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN E 97 GLN E 139 GLN E 154 HIS E 171 GLN F 38 ASN F 101 ASN I 122 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN L 122 GLN L 157 GLN L 222 GLN M 150 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.122202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.093263 restraints weight = 79106.492| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.79 r_work: 0.3510 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 48088 Z= 0.321 Angle : 0.644 10.857 64975 Z= 0.331 Chirality : 0.045 0.224 7482 Planarity : 0.004 0.041 8435 Dihedral : 9.072 174.773 6910 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 2.52 % Allowed : 11.25 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.11), residues: 5991 helix: 1.60 (0.09), residues: 3156 sheet: 0.39 (0.18), residues: 793 loop : -0.74 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 189 HIS 0.008 0.001 HIS S 511 PHE 0.022 0.002 PHE O 677 TYR 0.024 0.002 TYR S 600 ARG 0.011 0.001 ARG P 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1023 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7841 (p0) cc_final: 0.7300 (p0) REVERT: S 270 LYS cc_start: 0.8383 (tmmt) cc_final: 0.7954 (tppt) REVERT: S 397 ASP cc_start: 0.7967 (m-30) cc_final: 0.7670 (m-30) REVERT: S 684 LYS cc_start: 0.8213 (tptm) cc_final: 0.7543 (mmmm) REVERT: S 743 ASP cc_start: 0.8164 (t0) cc_final: 0.7877 (OUTLIER) REVERT: R 258 ARG cc_start: 0.8311 (tmm-80) cc_final: 0.8070 (ttp80) REVERT: R 263 GLU cc_start: 0.7874 (tt0) cc_final: 0.7495 (tt0) REVERT: R 804 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7091 (mm-30) REVERT: Q 310 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7409 (ttm110) REVERT: Q 326 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8502 (ttmm) REVERT: P 165 LEU cc_start: 0.7888 (pt) cc_final: 0.7570 (tt) REVERT: P 505 ARG cc_start: 0.8030 (ptt90) cc_final: 0.7418 (ptt-90) REVERT: P 608 GLU cc_start: 0.7904 (mp0) cc_final: 0.7566 (mp0) REVERT: P 744 MET cc_start: 0.7301 (mtt) cc_final: 0.7085 (mmm) REVERT: P 775 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7591 (tp-100) REVERT: P 779 GLU cc_start: 0.7416 (pt0) cc_final: 0.7157 (pm20) REVERT: O 211 ILE cc_start: 0.8228 (pt) cc_final: 0.8012 (pp) REVERT: O 267 LYS cc_start: 0.8359 (mmpt) cc_final: 0.8053 (tptp) REVERT: O 270 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8312 (pttm) REVERT: O 401 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7282 (tm-30) REVERT: O 584 LYS cc_start: 0.8550 (tppt) cc_final: 0.7863 (pptt) REVERT: O 660 MET cc_start: 0.8267 (mtm) cc_final: 0.7757 (mtm) REVERT: O 740 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7950 (mmmm) REVERT: O 788 PHE cc_start: 0.7681 (t80) cc_final: 0.7152 (t80) REVERT: T 198 GLN cc_start: 0.6193 (pt0) cc_final: 0.5970 (pt0) REVERT: T 384 ARG cc_start: 0.6354 (ptm160) cc_final: 0.6144 (tpm170) REVERT: T 480 ILE cc_start: 0.8494 (tp) cc_final: 0.8221 (tp) REVERT: T 531 THR cc_start: 0.7718 (m) cc_final: 0.7271 (p) REVERT: T 564 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8024 (tm-30) REVERT: T 636 GLN cc_start: 0.8045 (mp10) cc_final: 0.7678 (mp10) REVERT: T 765 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 35 GLN cc_start: 0.8059 (mp10) cc_final: 0.7770 (mp10) REVERT: C 164 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8077 (mmp-170) REVERT: D 188 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7892 (ttt-90) REVERT: E 96 MET cc_start: 0.8821 (mtp) cc_final: 0.8410 (mtp) REVERT: H 175 ASN cc_start: 0.8711 (m-40) cc_final: 0.8506 (m-40) REVERT: K 115 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: M 212 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: N 161 GLU cc_start: 0.8104 (pp20) cc_final: 0.7831 (tm-30) outliers start: 127 outliers final: 50 residues processed: 1085 average time/residue: 1.6668 time to fit residues: 2148.0511 Evaluate side-chains 1003 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 948 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 809 THR Chi-restraints excluded: chain R residue 646 SER Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 388 ASP Chi-restraints excluded: chain Q residue 405 ARG Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 270 LYS Chi-restraints excluded: chain O residue 321 LEU Chi-restraints excluded: chain O residue 698 LEU Chi-restraints excluded: chain T residue 408 ILE Chi-restraints excluded: chain T residue 569 ASP Chi-restraints excluded: chain T residue 635 LEU Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 212 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 32 optimal weight: 2.9990 chunk 475 optimal weight: 0.7980 chunk 270 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 342 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 479 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 647 GLN R 198 GLN R 674 ASN R 692 ASN R 775 GLN Q 795 HIS P 173 ASN P 692 ASN ** P 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 HIS O 795 HIS A 42 ASN B 58 ASN B 101 ASN C 139 GLN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 97 GLN E 171 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN I 231 ASN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN M 150 ASN N 222 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.122240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093248 restraints weight = 79222.126| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.81 r_work: 0.3505 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 48088 Z= 0.267 Angle : 0.609 14.172 64975 Z= 0.309 Chirality : 0.043 0.214 7482 Planarity : 0.004 0.062 8435 Dihedral : 8.877 175.284 6910 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.41 % Favored : 95.44 % Rotamer: Outliers : 2.82 % Allowed : 14.99 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5991 helix: 1.69 (0.09), residues: 3158 sheet: 0.42 (0.18), residues: 767 loop : -0.76 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.006 0.001 HIS A 138 PHE 0.022 0.002 PHE P 631 TYR 0.018 0.002 TYR L 159 ARG 0.014 0.001 ARG R 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 980 time to evaluate : 4.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7885 (p0) cc_final: 0.7360 (p0) REVERT: S 256 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7928 (ppp80) REVERT: S 270 LYS cc_start: 0.8437 (tmmt) cc_final: 0.8024 (tppt) REVERT: S 397 ASP cc_start: 0.8021 (m-30) cc_final: 0.7707 (m-30) REVERT: S 684 LYS cc_start: 0.8147 (tptm) cc_final: 0.7559 (mmmm) REVERT: S 688 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: S 743 ASP cc_start: 0.8174 (t0) cc_final: 0.7871 (OUTLIER) REVERT: R 258 ARG cc_start: 0.8343 (tmm-80) cc_final: 0.8109 (ttp80) REVERT: R 804 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7172 (mm-30) REVERT: Q 231 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7424 (ttpp) REVERT: Q 310 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7265 (ttp80) REVERT: Q 312 GLU cc_start: 0.8009 (mp0) cc_final: 0.7432 (mp0) REVERT: Q 326 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8473 (ttmm) REVERT: Q 505 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7789 (mtm110) REVERT: Q 743 ASP cc_start: 0.7707 (t0) cc_final: 0.7303 (t70) REVERT: P 564 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: P 608 GLU cc_start: 0.7936 (mp0) cc_final: 0.7631 (mp0) REVERT: P 771 ARG cc_start: 0.7496 (tpm-80) cc_final: 0.7219 (tpm-80) REVERT: P 775 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7263 (tp-100) REVERT: P 779 GLU cc_start: 0.7483 (pt0) cc_final: 0.7164 (pm20) REVERT: O 211 ILE cc_start: 0.8213 (pt) cc_final: 0.7967 (pp) REVERT: O 270 LYS cc_start: 0.8587 (pttt) cc_final: 0.8356 (pptt) REVERT: O 401 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7336 (tm-30) REVERT: O 406 MET cc_start: 0.8220 (mmm) cc_final: 0.7463 (pp-130) REVERT: O 482 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7516 (tm-30) REVERT: O 584 LYS cc_start: 0.8526 (tppt) cc_final: 0.7795 (pttp) REVERT: O 734 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8466 (mmpt) REVERT: O 740 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7954 (mmmm) REVERT: O 788 PHE cc_start: 0.7710 (t80) cc_final: 0.7201 (t80) REVERT: T 198 GLN cc_start: 0.6249 (pt0) cc_final: 0.5764 (pt0) REVERT: T 384 ARG cc_start: 0.6372 (ptm160) cc_final: 0.6171 (tpm170) REVERT: T 564 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7966 (tm-30) REVERT: T 636 GLN cc_start: 0.7950 (mp10) cc_final: 0.7637 (mp10) REVERT: T 765 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 35 GLN cc_start: 0.8102 (mp10) cc_final: 0.7842 (mp10) REVERT: B 38 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8453 (m-40) REVERT: B 73 LYS cc_start: 0.8258 (mmpt) cc_final: 0.8005 (mppt) REVERT: B 108 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8654 (ptt) REVERT: C 164 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8063 (mmp-170) REVERT: D 188 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7791 (ttt-90) REVERT: E 96 MET cc_start: 0.8853 (mtp) cc_final: 0.8482 (mtp) REVERT: F 186 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7031 (mpt90) REVERT: H 175 ASN cc_start: 0.8779 (m-40) cc_final: 0.8577 (m-40) REVERT: K 115 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: L 76 ASP cc_start: 0.8198 (m-30) cc_final: 0.7978 (m-30) REVERT: L 197 GLU cc_start: 0.8183 (mp0) cc_final: 0.7980 (mp0) REVERT: M 212 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: N 161 GLU cc_start: 0.8089 (pp20) cc_final: 0.7777 (tm-30) outliers start: 142 outliers final: 60 residues processed: 1051 average time/residue: 1.6500 time to fit residues: 2061.0334 Evaluate side-chains 1006 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 935 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 388 ASP Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 700 GLN Chi-restraints excluded: chain P residue 753 LYS Chi-restraints excluded: chain P residue 773 THR Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 321 LEU Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 698 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 210 LEU Chi-restraints excluded: chain T residue 408 ILE Chi-restraints excluded: chain T residue 544 SER Chi-restraints excluded: chain T residue 569 ASP Chi-restraints excluded: chain T residue 629 ASP Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 180 MET Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 457 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 318 optimal weight: 9.9990 chunk 358 optimal weight: 1.9990 chunk 486 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 273 optimal weight: 0.0010 chunk 444 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN R 692 ASN Q 700 GLN Q 795 HIS P 692 ASN P 721 GLN ** O 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN A 132 ASN B 58 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 97 GLN E 179 GLN F 35 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN I 231 ASN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN N 222 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.122991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094123 restraints weight = 78621.296| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.80 r_work: 0.3524 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 48088 Z= 0.207 Angle : 0.576 12.383 64975 Z= 0.292 Chirality : 0.042 0.218 7482 Planarity : 0.004 0.061 8435 Dihedral : 8.629 169.835 6910 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 2.64 % Allowed : 16.50 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.11), residues: 5991 helix: 1.79 (0.09), residues: 3165 sheet: 0.44 (0.18), residues: 763 loop : -0.75 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.012 0.001 HIS T 627 PHE 0.019 0.001 PHE P 631 TYR 0.020 0.001 TYR L 159 ARG 0.013 0.000 ARG P 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 960 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7871 (p0) cc_final: 0.7337 (p0) REVERT: S 239 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7671 (ttmt) REVERT: S 270 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8010 (tppt) REVERT: S 338 PHE cc_start: 0.8801 (m-10) cc_final: 0.8257 (m-80) REVERT: S 712 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: S 743 ASP cc_start: 0.8191 (t0) cc_final: 0.7859 (OUTLIER) REVERT: R 258 ARG cc_start: 0.8313 (tmm-80) cc_final: 0.8095 (ttp80) REVERT: R 267 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8161 (mmtt) REVERT: R 499 GLU cc_start: 0.7985 (pt0) cc_final: 0.7754 (pp20) REVERT: R 640 ASP cc_start: 0.7726 (t0) cc_final: 0.7228 (t0) REVERT: R 804 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7118 (mm-30) REVERT: Q 231 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7279 (ttpp) REVERT: Q 310 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7434 (ttp80) REVERT: Q 312 GLU cc_start: 0.8014 (mp0) cc_final: 0.7664 (mp0) REVERT: Q 326 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8461 (ttmm) REVERT: Q 478 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: Q 505 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7618 (mtm110) REVERT: Q 509 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: Q 743 ASP cc_start: 0.7756 (t0) cc_final: 0.7324 (t70) REVERT: P 165 LEU cc_start: 0.8051 (pt) cc_final: 0.7755 (tt) REVERT: P 509 GLU cc_start: 0.8083 (mp0) cc_final: 0.7871 (mp0) REVERT: P 564 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: P 608 GLU cc_start: 0.7958 (mp0) cc_final: 0.7629 (mp0) REVERT: P 775 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7250 (tp-100) REVERT: P 779 GLU cc_start: 0.7496 (pt0) cc_final: 0.7147 (pm20) REVERT: O 267 LYS cc_start: 0.8330 (mmpt) cc_final: 0.8028 (tptp) REVERT: O 270 LYS cc_start: 0.8553 (pttt) cc_final: 0.8301 (pttt) REVERT: O 401 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7351 (tm-30) REVERT: O 406 MET cc_start: 0.8235 (mmm) cc_final: 0.7515 (pp-130) REVERT: O 584 LYS cc_start: 0.8488 (tppt) cc_final: 0.7839 (pptt) REVERT: O 587 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7742 (t) REVERT: O 660 MET cc_start: 0.8299 (mtm) cc_final: 0.7754 (ttm) REVERT: O 740 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7960 (mmmm) REVERT: O 788 PHE cc_start: 0.7728 (t80) cc_final: 0.7206 (t80) REVERT: T 198 GLN cc_start: 0.6202 (pt0) cc_final: 0.5952 (pt0) REVERT: T 564 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7976 (tm-30) REVERT: T 569 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7080 (t70) REVERT: T 660 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8250 (mmp) REVERT: T 693 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8191 (mtmt) REVERT: T 737 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8219 (tm-30) REVERT: T 765 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7786 (mt) REVERT: T 806 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8011 (tm-30) REVERT: A 164 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8638 (mmp-170) REVERT: B 35 GLN cc_start: 0.8083 (mp10) cc_final: 0.7812 (mp10) REVERT: B 38 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8460 (m-40) REVERT: B 108 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8705 (ptt) REVERT: C 164 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8036 (mmp-170) REVERT: C 167 GLU cc_start: 0.8173 (tp30) cc_final: 0.7914 (tp30) REVERT: D 188 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7659 (ttt-90) REVERT: E 157 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7757 (tpt170) REVERT: F 186 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.6977 (mpt90) REVERT: H 175 ASN cc_start: 0.8804 (m-40) cc_final: 0.8589 (m-40) REVERT: N 161 GLU cc_start: 0.8078 (pp20) cc_final: 0.7758 (tm-30) outliers start: 133 outliers final: 59 residues processed: 1035 average time/residue: 1.6617 time to fit residues: 2042.1077 Evaluate side-chains 1000 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 927 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 753 LYS Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 321 LEU Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 408 ILE Chi-restraints excluded: chain T residue 544 SER Chi-restraints excluded: chain T residue 569 ASP Chi-restraints excluded: chain T residue 587 VAL Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 455 optimal weight: 0.5980 chunk 289 optimal weight: 7.9990 chunk 493 optimal weight: 0.0770 chunk 372 optimal weight: 3.9990 chunk 488 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 461 optimal weight: 3.9990 chunk 504 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 309 optimal weight: 0.5980 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 674 ASN R 692 ASN Q 700 GLN Q 795 HIS P 173 ASN P 692 ASN O 286 HIS T 627 HIS T 636 GLN A 42 ASN A 132 ASN B 58 ASN C 80 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 171 GLN E 179 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 116 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.122403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093334 restraints weight = 79156.227| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.80 r_work: 0.3509 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 48088 Z= 0.256 Angle : 0.594 16.557 64975 Z= 0.302 Chirality : 0.043 0.242 7482 Planarity : 0.004 0.084 8435 Dihedral : 8.506 162.861 6908 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.49 % Favored : 95.36 % Rotamer: Outliers : 2.88 % Allowed : 17.43 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5991 helix: 1.78 (0.09), residues: 3165 sheet: 0.44 (0.18), residues: 761 loop : -0.78 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 189 HIS 0.006 0.001 HIS A 138 PHE 0.027 0.001 PHE P 261 TYR 0.019 0.001 TYR H 159 ARG 0.015 0.000 ARG R 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 954 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7850 (p0) cc_final: 0.7298 (p0) REVERT: S 270 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8007 (tppt) REVERT: S 273 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7461 (tmm-80) REVERT: S 338 PHE cc_start: 0.8793 (m-10) cc_final: 0.8245 (m-80) REVERT: S 743 ASP cc_start: 0.8185 (t0) cc_final: 0.7852 (OUTLIER) REVERT: R 258 ARG cc_start: 0.8375 (tmm-80) cc_final: 0.8016 (tmm-80) REVERT: R 499 GLU cc_start: 0.7923 (pt0) cc_final: 0.7691 (pp20) REVERT: R 640 ASP cc_start: 0.7714 (t0) cc_final: 0.7010 (t0) REVERT: R 804 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Q 310 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.7246 (ttp80) REVERT: Q 312 GLU cc_start: 0.8016 (mp0) cc_final: 0.7555 (mp0) REVERT: Q 326 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8474 (ttmm) REVERT: Q 478 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: Q 505 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7646 (mtm110) REVERT: Q 509 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: Q 734 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8324 (mmtt) REVERT: Q 743 ASP cc_start: 0.7748 (t0) cc_final: 0.7318 (t70) REVERT: P 410 ARG cc_start: 0.7767 (tpm170) cc_final: 0.7540 (tpm170) REVERT: P 564 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: P 608 GLU cc_start: 0.7940 (mp0) cc_final: 0.7578 (mp0) REVERT: P 775 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7299 (tp-100) REVERT: P 779 GLU cc_start: 0.7455 (pt0) cc_final: 0.7138 (pm20) REVERT: O 267 LYS cc_start: 0.8325 (mmpt) cc_final: 0.8005 (tptp) REVERT: O 270 LYS cc_start: 0.8549 (pttt) cc_final: 0.8252 (pttt) REVERT: O 279 ILE cc_start: 0.8769 (mt) cc_final: 0.8549 (mp) REVERT: O 342 GLN cc_start: 0.8376 (mp10) cc_final: 0.8141 (mp10) REVERT: O 401 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7309 (tm-30) REVERT: O 406 MET cc_start: 0.8285 (mmm) cc_final: 0.8073 (mmm) REVERT: O 584 LYS cc_start: 0.8469 (tppt) cc_final: 0.7917 (tmmt) REVERT: O 587 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7806 (t) REVERT: O 640 ASP cc_start: 0.8427 (m-30) cc_final: 0.8129 (m-30) REVERT: O 660 MET cc_start: 0.8300 (mtm) cc_final: 0.7761 (ttm) REVERT: O 734 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8440 (mmpt) REVERT: O 740 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7954 (mmmm) REVERT: O 788 PHE cc_start: 0.7723 (t80) cc_final: 0.7212 (t80) REVERT: T 197 MET cc_start: 0.6923 (ppp) cc_final: 0.6718 (ppp) REVERT: T 198 GLN cc_start: 0.6271 (pt0) cc_final: 0.5891 (pt0) REVERT: T 223 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: T 319 THR cc_start: 0.5468 (OUTLIER) cc_final: 0.5128 (p) REVERT: T 480 ILE cc_start: 0.8347 (tp) cc_final: 0.8088 (tp) REVERT: T 564 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8022 (tm-30) REVERT: T 660 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8162 (mmp) REVERT: T 693 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8168 (mtmt) REVERT: T 765 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7860 (mt) REVERT: T 806 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7972 (tm-30) REVERT: A 164 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8639 (mmp-170) REVERT: B 35 GLN cc_start: 0.8063 (mp10) cc_final: 0.7842 (mp10) REVERT: B 38 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8482 (m-40) REVERT: B 108 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8727 (ptt) REVERT: B 165 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.7887 (mpt) REVERT: C 164 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8018 (mmp-170) REVERT: C 167 GLU cc_start: 0.8201 (tp30) cc_final: 0.7942 (tp30) REVERT: D 188 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7746 (ttt-90) REVERT: E 157 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7736 (tpt170) REVERT: E 205 MET cc_start: 0.8521 (ttp) cc_final: 0.8236 (ptm) REVERT: F 186 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.6973 (mpt90) REVERT: H 175 ASN cc_start: 0.8803 (m-40) cc_final: 0.8590 (m-40) REVERT: K 115 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: L 115 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8708 (mp10) REVERT: M 212 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: N 161 GLU cc_start: 0.8051 (pp20) cc_final: 0.7718 (tm-30) REVERT: N 190 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (tttp) outliers start: 145 outliers final: 76 residues processed: 1035 average time/residue: 1.6680 time to fit residues: 2051.7649 Evaluate side-chains 1025 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 931 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 303 ILE Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 729 ASP Chi-restraints excluded: chain Q residue 256 ARG Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 753 LYS Chi-restraints excluded: chain P residue 773 THR Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 408 ILE Chi-restraints excluded: chain T residue 410 ARG Chi-restraints excluded: chain T residue 544 SER Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 629 ASP Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 673 PHE Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 180 MET Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 180 MET Chi-restraints excluded: chain N residue 190 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 405 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 464 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 473 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 427 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 692 ASN Q 700 GLN Q 795 HIS P 692 ASN O 511 HIS ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 58 ASN C 80 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 97 GLN E 171 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.123748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.094854 restraints weight = 78912.671| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.80 r_work: 0.3533 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 48088 Z= 0.186 Angle : 0.579 15.795 64975 Z= 0.292 Chirality : 0.042 0.238 7482 Planarity : 0.004 0.173 8435 Dihedral : 8.339 156.178 6908 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 2.36 % Allowed : 18.13 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 5991 helix: 1.87 (0.10), residues: 3162 sheet: 0.52 (0.18), residues: 757 loop : -0.70 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.004 0.001 HIS T 627 PHE 0.041 0.001 PHE O 565 TYR 0.019 0.001 TYR S 600 ARG 0.023 0.000 ARG T 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 973 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7879 (p0) cc_final: 0.7337 (p0) REVERT: S 239 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7730 (ttmt) REVERT: S 270 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8003 (tppt) REVERT: S 273 ARG cc_start: 0.7867 (tmm-80) cc_final: 0.7443 (tmm-80) REVERT: S 303 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8372 (mp) REVERT: S 338 PHE cc_start: 0.8784 (m-10) cc_final: 0.8208 (m-80) REVERT: S 688 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: S 712 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: S 743 ASP cc_start: 0.8188 (t0) cc_final: 0.7842 (OUTLIER) REVERT: R 499 GLU cc_start: 0.7888 (pt0) cc_final: 0.7651 (pp20) REVERT: R 640 ASP cc_start: 0.7624 (t0) cc_final: 0.7216 (t0) REVERT: R 804 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7088 (mm-30) REVERT: Q 231 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7208 (ttpp) REVERT: Q 310 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.7239 (ttm110) REVERT: Q 312 GLU cc_start: 0.7992 (mp0) cc_final: 0.7602 (mp0) REVERT: Q 326 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8472 (ttmm) REVERT: Q 478 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: Q 509 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: Q 743 ASP cc_start: 0.7702 (t0) cc_final: 0.7291 (t70) REVERT: P 342 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8084 (mm-40) REVERT: P 505 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7818 (ptt-90) REVERT: P 564 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: P 608 GLU cc_start: 0.7829 (mp0) cc_final: 0.7494 (mp0) REVERT: P 775 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7370 (tp-100) REVERT: P 779 GLU cc_start: 0.7483 (pt0) cc_final: 0.7136 (pm20) REVERT: O 267 LYS cc_start: 0.8332 (mmpt) cc_final: 0.7991 (tptp) REVERT: O 270 LYS cc_start: 0.8569 (pttt) cc_final: 0.8245 (pttt) REVERT: O 342 GLN cc_start: 0.8385 (mp10) cc_final: 0.8132 (mp10) REVERT: O 401 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7365 (tm-30) REVERT: O 406 MET cc_start: 0.8175 (mmm) cc_final: 0.7933 (mmm) REVERT: O 584 LYS cc_start: 0.8467 (tppt) cc_final: 0.7926 (tmmt) REVERT: O 587 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7804 (t) REVERT: O 640 ASP cc_start: 0.8386 (m-30) cc_final: 0.8103 (m-30) REVERT: O 660 MET cc_start: 0.8298 (mtm) cc_final: 0.7751 (ttm) REVERT: O 713 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8263 (t) REVERT: O 734 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8429 (mmpt) REVERT: O 740 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7929 (mmmm) REVERT: O 788 PHE cc_start: 0.7699 (t80) cc_final: 0.7194 (t80) REVERT: T 197 MET cc_start: 0.6973 (ppp) cc_final: 0.6754 (ppp) REVERT: T 198 GLN cc_start: 0.6205 (pt0) cc_final: 0.5800 (pt0) REVERT: T 223 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: T 480 ILE cc_start: 0.8373 (tp) cc_final: 0.8089 (tp) REVERT: T 564 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7896 (pp20) REVERT: T 660 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7902 (mmp) REVERT: T 693 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8142 (mtmt) REVERT: T 765 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7894 (mt) REVERT: T 806 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7978 (tm-30) REVERT: A 97 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: B 35 GLN cc_start: 0.8081 (mp10) cc_final: 0.7836 (mp10) REVERT: B 38 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8462 (m-40) REVERT: B 108 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8680 (ptt) REVERT: C 164 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7918 (mmp-170) REVERT: D 188 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7768 (ttt-90) REVERT: E 101 ASN cc_start: 0.8379 (m-40) cc_final: 0.8105 (m-40) REVERT: E 157 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7741 (tpt170) REVERT: E 205 MET cc_start: 0.8452 (ttp) cc_final: 0.8188 (ptm) REVERT: F 186 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.6942 (mpt90) REVERT: G 100 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8183 (tttm) REVERT: H 175 ASN cc_start: 0.8745 (m-40) cc_final: 0.8533 (m-40) REVERT: K 115 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: L 87 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7053 (mpp) REVERT: M 212 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: N 161 GLU cc_start: 0.8064 (pp20) cc_final: 0.7666 (tm-30) REVERT: N 190 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8686 (tttp) REVERT: N 207 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8383 (tttm) outliers start: 119 outliers final: 58 residues processed: 1038 average time/residue: 1.7118 time to fit residues: 2104.4872 Evaluate side-chains 1023 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 942 time to evaluate : 4.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 303 ILE Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 729 ASP Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 256 ARG Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 700 GLN Chi-restraints excluded: chain P residue 753 LYS Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 713 VAL Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 618 VAL Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 521 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 584 optimal weight: 4.9990 chunk 591 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 273 optimal weight: 0.0570 chunk 354 optimal weight: 8.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 692 ASN R 718 GLN Q 795 HIS P 173 ASN P 692 ASN T 636 GLN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 154 HIS E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.123617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094533 restraints weight = 78400.741| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.84 r_work: 0.3527 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48088 Z= 0.204 Angle : 0.597 15.830 64975 Z= 0.301 Chirality : 0.042 0.250 7482 Planarity : 0.004 0.081 8435 Dihedral : 8.179 145.637 6908 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 2.68 % Allowed : 18.86 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 5991 helix: 1.85 (0.09), residues: 3164 sheet: 0.57 (0.18), residues: 752 loop : -0.71 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 189 HIS 0.004 0.001 HIS A 138 PHE 0.032 0.001 PHE O 565 TYR 0.018 0.001 TYR I 159 ARG 0.019 0.000 ARG R 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 954 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7896 (p0) cc_final: 0.7408 (p0) REVERT: S 239 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7745 (ttmt) REVERT: S 270 LYS cc_start: 0.8421 (tmmt) cc_final: 0.8022 (tppt) REVERT: S 273 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7504 (tmm-80) REVERT: S 303 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8379 (mp) REVERT: S 305 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8318 (tppt) REVERT: S 338 PHE cc_start: 0.8781 (m-10) cc_final: 0.8374 (m-80) REVERT: S 612 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7777 (mpt180) REVERT: S 712 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: S 743 ASP cc_start: 0.8216 (t0) cc_final: 0.7888 (OUTLIER) REVERT: R 499 GLU cc_start: 0.7906 (pt0) cc_final: 0.7684 (pp20) REVERT: R 640 ASP cc_start: 0.7459 (t0) cc_final: 0.7189 (t0) REVERT: R 744 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8802 (mtp) REVERT: R 804 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Q 231 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7293 (ttpp) REVERT: Q 310 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7333 (ttm110) REVERT: Q 312 GLU cc_start: 0.7987 (mp0) cc_final: 0.7778 (mp0) REVERT: Q 326 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8494 (ttmm) REVERT: Q 478 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: Q 509 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: Q 743 ASP cc_start: 0.7730 (t0) cc_final: 0.7349 (t70) REVERT: P 367 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7987 (tmm-80) REVERT: P 405 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7895 (ttp-170) REVERT: P 505 ARG cc_start: 0.8079 (ptt-90) cc_final: 0.7800 (ptt-90) REVERT: P 564 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: P 608 GLU cc_start: 0.7863 (mp0) cc_final: 0.7523 (mp0) REVERT: P 771 ARG cc_start: 0.7820 (mmm160) cc_final: 0.7395 (tpt90) REVERT: P 775 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7421 (tp-100) REVERT: P 779 GLU cc_start: 0.7529 (pt0) cc_final: 0.7264 (pm20) REVERT: O 267 LYS cc_start: 0.8334 (mmtt) cc_final: 0.8008 (tptp) REVERT: O 270 LYS cc_start: 0.8575 (pttt) cc_final: 0.8239 (pttt) REVERT: O 279 ILE cc_start: 0.8750 (mt) cc_final: 0.8535 (mp) REVERT: O 342 GLN cc_start: 0.8384 (mp10) cc_final: 0.8117 (mp10) REVERT: O 401 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7353 (tm-30) REVERT: O 584 LYS cc_start: 0.8468 (tppt) cc_final: 0.7910 (tmmt) REVERT: O 587 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7967 (t) REVERT: O 640 ASP cc_start: 0.8403 (m-30) cc_final: 0.8116 (m-30) REVERT: O 660 MET cc_start: 0.8320 (mtm) cc_final: 0.7783 (ttm) REVERT: O 734 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8429 (mmpt) REVERT: O 740 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7888 (mmmm) REVERT: O 788 PHE cc_start: 0.7723 (t80) cc_final: 0.7211 (t80) REVERT: T 197 MET cc_start: 0.6947 (ppp) cc_final: 0.6728 (ppp) REVERT: T 198 GLN cc_start: 0.6200 (pt0) cc_final: 0.5782 (pt0) REVERT: T 223 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8189 (mm-30) REVERT: T 348 LEU cc_start: 0.8144 (pp) cc_final: 0.7753 (tt) REVERT: T 480 ILE cc_start: 0.8386 (tp) cc_final: 0.8095 (tp) REVERT: T 564 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7892 (pp20) REVERT: T 660 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8052 (mmp) REVERT: T 693 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8139 (mtmt) REVERT: T 765 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7970 (mt) REVERT: T 806 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7977 (tm-30) REVERT: B 35 GLN cc_start: 0.8101 (mp10) cc_final: 0.7858 (mp10) REVERT: B 38 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (m-40) REVERT: B 108 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8652 (ptt) REVERT: D 188 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7848 (ttt-90) REVERT: E 101 ASN cc_start: 0.8344 (m-40) cc_final: 0.8049 (m-40) REVERT: E 157 ARG cc_start: 0.8038 (tpp-160) cc_final: 0.7718 (tpt170) REVERT: E 205 MET cc_start: 0.8454 (ttp) cc_final: 0.8221 (ptm) REVERT: F 186 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.6958 (mpt90) REVERT: I 179 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8713 (ttp80) REVERT: K 115 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: L 87 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7140 (mpp) REVERT: L 197 GLU cc_start: 0.8249 (mp0) cc_final: 0.8034 (mp0) REVERT: M 212 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: N 190 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8673 (tttp) REVERT: N 207 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8388 (tttm) outliers start: 135 outliers final: 70 residues processed: 1023 average time/residue: 1.6697 time to fit residues: 2030.4911 Evaluate side-chains 1030 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 939 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 287 THR Chi-restraints excluded: chain S residue 303 ILE Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain R residue 744 MET Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 256 ARG Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 367 ARG Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 700 GLN Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 673 PHE Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 334 optimal weight: 6.9990 chunk 499 optimal weight: 1.9990 chunk 419 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 273 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 506 optimal weight: 5.9990 chunk 393 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 647 GLN R 692 ASN Q 700 GLN Q 795 HIS P 692 ASN T 511 HIS T 636 GLN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 58 ASN C 80 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN E 38 ASN E 97 GLN E 154 HIS E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN H 175 ASN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095382 restraints weight = 78613.239| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.85 r_work: 0.3541 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 48088 Z= 0.181 Angle : 0.597 15.228 64975 Z= 0.300 Chirality : 0.042 0.257 7482 Planarity : 0.004 0.086 8435 Dihedral : 8.034 137.252 6908 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 2.46 % Allowed : 19.73 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 5991 helix: 1.88 (0.10), residues: 3165 sheet: 0.53 (0.18), residues: 757 loop : -0.67 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.003 0.001 HIS A 138 PHE 0.029 0.001 PHE P 261 TYR 0.021 0.001 TYR H 159 ARG 0.020 0.000 ARG R 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 943 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7876 (p0) cc_final: 0.7414 (p0) REVERT: S 239 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7762 (ttmt) REVERT: S 270 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8010 (tppt) REVERT: S 273 ARG cc_start: 0.7930 (tmm-80) cc_final: 0.7560 (tmm-80) REVERT: S 338 PHE cc_start: 0.8802 (m-10) cc_final: 0.8227 (m-80) REVERT: S 612 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7783 (mpt180) REVERT: S 684 LYS cc_start: 0.8052 (tppp) cc_final: 0.6974 (tppp) REVERT: S 688 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: S 743 ASP cc_start: 0.8233 (t0) cc_final: 0.7920 (OUTLIER) REVERT: R 499 GLU cc_start: 0.7863 (pt0) cc_final: 0.7642 (pp20) REVERT: R 642 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8552 (ptp-170) REVERT: R 804 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7046 (mm-30) REVERT: Q 231 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7230 (ttpp) REVERT: Q 310 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7377 (ttm110) REVERT: Q 312 GLU cc_start: 0.8037 (mp0) cc_final: 0.7799 (mp0) REVERT: Q 326 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8538 (ttmm) REVERT: Q 478 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: Q 509 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: Q 743 ASP cc_start: 0.7810 (t0) cc_final: 0.7401 (t70) REVERT: P 367 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7988 (tmm-80) REVERT: P 405 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7819 (ttp-170) REVERT: P 564 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: P 608 GLU cc_start: 0.7902 (mp0) cc_final: 0.7602 (mp0) REVERT: P 771 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7462 (tpm-80) REVERT: P 775 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7507 (tp-100) REVERT: P 779 GLU cc_start: 0.7546 (pt0) cc_final: 0.7295 (pm20) REVERT: O 267 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7991 (tptp) REVERT: O 270 LYS cc_start: 0.8573 (pttt) cc_final: 0.8211 (pttt) REVERT: O 342 GLN cc_start: 0.8401 (mp10) cc_final: 0.8192 (mp10) REVERT: O 401 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7405 (tm-30) REVERT: O 406 MET cc_start: 0.8224 (mmm) cc_final: 0.7438 (pp-130) REVERT: O 584 LYS cc_start: 0.8471 (tppt) cc_final: 0.7921 (tmmt) REVERT: O 587 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (t) REVERT: O 640 ASP cc_start: 0.8412 (m-30) cc_final: 0.8107 (m-30) REVERT: O 660 MET cc_start: 0.8326 (mtm) cc_final: 0.7827 (ttm) REVERT: O 734 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8475 (mmpt) REVERT: O 740 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7913 (mmmm) REVERT: O 788 PHE cc_start: 0.7777 (t80) cc_final: 0.7236 (t80) REVERT: T 198 GLN cc_start: 0.6239 (pt0) cc_final: 0.5819 (pt0) REVERT: T 223 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: T 348 LEU cc_start: 0.8151 (pp) cc_final: 0.7778 (tt) REVERT: T 480 ILE cc_start: 0.8440 (tp) cc_final: 0.8141 (tp) REVERT: T 564 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7882 (pp20) REVERT: T 660 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8064 (mmp) REVERT: T 693 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8142 (mtmt) REVERT: T 765 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7983 (mt) REVERT: T 806 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7982 (tm-30) REVERT: A 97 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 35 GLN cc_start: 0.8098 (mp10) cc_final: 0.7843 (mp10) REVERT: B 38 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8483 (m-40) REVERT: B 108 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8676 (ptt) REVERT: B 165 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7617 (mpt) REVERT: D 188 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7850 (ttt-90) REVERT: E 101 ASN cc_start: 0.8333 (m-40) cc_final: 0.8011 (m-40) REVERT: E 157 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7729 (tpt170) REVERT: E 205 MET cc_start: 0.8511 (ttp) cc_final: 0.8274 (ptm) REVERT: F 186 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.6909 (mpt90) REVERT: H 85 GLU cc_start: 0.8877 (tt0) cc_final: 0.8528 (tt0) REVERT: K 115 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: L 87 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: L 197 GLU cc_start: 0.8242 (mp0) cc_final: 0.8001 (mp0) REVERT: N 207 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8232 (ttmm) outliers start: 124 outliers final: 69 residues processed: 1008 average time/residue: 1.6588 time to fit residues: 1986.7998 Evaluate side-chains 1023 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 934 time to evaluate : 3.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 287 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 503 LEU Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 642 ARG Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 256 ARG Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 367 ARG Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 700 GLN Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 164 ARG Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 165 optimal weight: 0.6980 chunk 589 optimal weight: 0.4980 chunk 375 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 462 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 541 optimal weight: 0.5980 chunk 394 optimal weight: 1.9990 chunk 560 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 647 GLN S 686 ASN R 692 ASN Q 327 HIS Q 700 GLN Q 795 HIS P 173 ASN P 692 ASN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 58 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN G 50 GLN H 175 ASN K 222 GLN L 75 ASN N 222 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.131606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102957 restraints weight = 77904.860| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.83 r_work: 0.3550 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 48088 Z= 0.184 Angle : 0.609 14.955 64975 Z= 0.306 Chirality : 0.042 0.266 7482 Planarity : 0.004 0.089 8435 Dihedral : 7.931 128.671 6908 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 2.26 % Allowed : 20.21 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 5991 helix: 1.89 (0.10), residues: 3164 sheet: 0.58 (0.18), residues: 737 loop : -0.66 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.003 0.001 HIS A 138 PHE 0.030 0.001 PHE S 673 TYR 0.020 0.001 TYR L 159 ARG 0.020 0.000 ARG R 502 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 953 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 173 ASN cc_start: 0.8515 (t0) cc_final: 0.8308 (t0) REVERT: S 206 ASN cc_start: 0.7857 (p0) cc_final: 0.6607 (p0) REVERT: S 239 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7771 (ttmt) REVERT: S 270 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7987 (tppt) REVERT: S 273 ARG cc_start: 0.7925 (tmm-80) cc_final: 0.7572 (tmm-80) REVERT: S 338 PHE cc_start: 0.8781 (m-10) cc_final: 0.8231 (m-80) REVERT: S 612 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7795 (mpt180) REVERT: S 684 LYS cc_start: 0.8037 (tppp) cc_final: 0.7005 (tppp) REVERT: S 688 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: S 693 LYS cc_start: 0.8710 (tppt) cc_final: 0.8476 (ttpt) REVERT: S 712 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: S 743 ASP cc_start: 0.8208 (t0) cc_final: 0.7908 (OUTLIER) REVERT: R 640 ASP cc_start: 0.7943 (p0) cc_final: 0.7631 (p0) REVERT: R 642 ARG cc_start: 0.8613 (ptp-170) cc_final: 0.8377 (ptp90) REVERT: R 804 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6991 (mm-30) REVERT: Q 231 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7237 (ttpp) REVERT: Q 326 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8499 (ttmm) REVERT: Q 478 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: Q 509 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: Q 743 ASP cc_start: 0.7801 (t0) cc_final: 0.7430 (t70) REVERT: P 367 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (tmm-80) REVERT: P 564 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: P 608 GLU cc_start: 0.7846 (mp0) cc_final: 0.7569 (mp0) REVERT: P 775 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7388 (tp-100) REVERT: P 779 GLU cc_start: 0.7543 (pt0) cc_final: 0.7301 (pm20) REVERT: O 267 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8005 (tptp) REVERT: O 270 LYS cc_start: 0.8579 (pttt) cc_final: 0.8274 (pttt) REVERT: O 342 GLN cc_start: 0.8403 (mp10) cc_final: 0.8133 (mp10) REVERT: O 401 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7345 (tm-30) REVERT: O 406 MET cc_start: 0.8203 (mmm) cc_final: 0.7750 (mmp) REVERT: O 501 SER cc_start: 0.7656 (p) cc_final: 0.7232 (p) REVERT: O 526 LYS cc_start: 0.8935 (mmpt) cc_final: 0.8593 (mmpt) REVERT: O 584 LYS cc_start: 0.8475 (tppt) cc_final: 0.7928 (tmmt) REVERT: O 587 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (t) REVERT: O 640 ASP cc_start: 0.8383 (m-30) cc_final: 0.8083 (m-30) REVERT: O 660 MET cc_start: 0.8258 (mtm) cc_final: 0.7752 (ttm) REVERT: O 734 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8438 (mmpt) REVERT: O 740 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7896 (mmmm) REVERT: O 788 PHE cc_start: 0.7691 (t80) cc_final: 0.7174 (t80) REVERT: T 223 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: T 348 LEU cc_start: 0.8076 (pp) cc_final: 0.7729 (tt) REVERT: T 480 ILE cc_start: 0.8480 (tp) cc_final: 0.8200 (tp) REVERT: T 564 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7915 (pp20) REVERT: T 660 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8257 (mmp) REVERT: T 693 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8112 (mtmt) REVERT: T 765 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8011 (mt) REVERT: T 806 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7989 (tm-30) REVERT: B 35 GLN cc_start: 0.8056 (mp10) cc_final: 0.7825 (mp10) REVERT: B 38 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: B 108 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8602 (ptt) REVERT: D 188 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7854 (ttt-90) REVERT: E 101 ASN cc_start: 0.8295 (m-40) cc_final: 0.7970 (m-40) REVERT: E 157 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7714 (tpt170) REVERT: E 205 MET cc_start: 0.8381 (ttp) cc_final: 0.8156 (ptm) REVERT: F 186 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.6965 (mpt90) REVERT: H 85 GLU cc_start: 0.8841 (tt0) cc_final: 0.8494 (tt0) REVERT: K 115 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: L 197 GLU cc_start: 0.8243 (mp0) cc_final: 0.7989 (mp0) REVERT: N 207 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8209 (ttmm) outliers start: 114 outliers final: 69 residues processed: 1017 average time/residue: 1.6684 time to fit residues: 2015.2235 Evaluate side-chains 1018 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 932 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 287 THR Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 256 ARG Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 493 PHE Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 367 ARG Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 587 VAL Chi-restraints excluded: chain T residue 629 ASP Chi-restraints excluded: chain T residue 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 164 ARG Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 444 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 440 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN ** S 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 647 GLN S 686 ASN R 692 ASN Q 700 GLN Q 795 HIS P 339 GLN P 692 ASN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN D 80 ASN E 97 GLN E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.123526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.094671 restraints weight = 78975.491| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.81 r_work: 0.3535 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 48088 Z= 0.234 Angle : 0.642 14.653 64975 Z= 0.323 Chirality : 0.043 0.259 7482 Planarity : 0.004 0.095 8435 Dihedral : 7.940 122.092 6908 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.64 % Favored : 95.23 % Rotamer: Outliers : 2.12 % Allowed : 20.86 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.11), residues: 5991 helix: 1.84 (0.09), residues: 3156 sheet: 0.57 (0.18), residues: 737 loop : -0.69 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 189 HIS 0.005 0.001 HIS A 138 PHE 0.035 0.001 PHE S 673 TYR 0.024 0.001 TYR S 600 ARG 0.020 0.001 ARG P 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 942 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7842 (p0) cc_final: 0.6549 (p0) REVERT: S 256 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8054 (ptm-80) REVERT: S 264 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7959 (mtp180) REVERT: S 270 LYS cc_start: 0.8416 (tmmt) cc_final: 0.7997 (tppt) REVERT: S 273 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7596 (tmm-80) REVERT: S 338 PHE cc_start: 0.8811 (m-10) cc_final: 0.8244 (m-80) REVERT: S 612 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7841 (mpt180) REVERT: S 668 ASP cc_start: 0.7749 (p0) cc_final: 0.7501 (p0) REVERT: S 684 LYS cc_start: 0.8042 (tppp) cc_final: 0.6960 (tppp) REVERT: S 688 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: S 712 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: S 743 ASP cc_start: 0.8300 (t0) cc_final: 0.7969 (t0) REVERT: R 499 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: R 640 ASP cc_start: 0.7980 (p0) cc_final: 0.7773 (p0) REVERT: R 804 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7058 (mm-30) REVERT: Q 231 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7264 (ttpp) REVERT: Q 310 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7286 (ttm110) REVERT: Q 312 GLU cc_start: 0.8060 (mp0) cc_final: 0.7652 (mp0) REVERT: Q 326 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8543 (ttmm) REVERT: Q 478 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: Q 509 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: Q 743 ASP cc_start: 0.7785 (t0) cc_final: 0.7369 (t70) REVERT: P 564 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8400 (tm-30) REVERT: P 608 GLU cc_start: 0.7873 (mp0) cc_final: 0.7542 (mp0) REVERT: P 771 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7383 (tpm-80) REVERT: P 775 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7332 (tp-100) REVERT: P 779 GLU cc_start: 0.7530 (pt0) cc_final: 0.7250 (pm20) REVERT: O 267 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8008 (tptp) REVERT: O 270 LYS cc_start: 0.8572 (pttt) cc_final: 0.8220 (pttt) REVERT: O 342 GLN cc_start: 0.8400 (mp10) cc_final: 0.8141 (mp10) REVERT: O 401 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7337 (tm-30) REVERT: O 406 MET cc_start: 0.8232 (mmm) cc_final: 0.7380 (pp-130) REVERT: O 501 SER cc_start: 0.7707 (p) cc_final: 0.7298 (p) REVERT: O 526 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8585 (mmpt) REVERT: O 584 LYS cc_start: 0.8466 (tppt) cc_final: 0.7915 (tmmt) REVERT: O 587 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7951 (t) REVERT: O 640 ASP cc_start: 0.8399 (m-30) cc_final: 0.8111 (m-30) REVERT: O 660 MET cc_start: 0.8315 (mtm) cc_final: 0.7796 (ttm) REVERT: O 734 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8440 (mmpt) REVERT: O 740 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7927 (mmmm) REVERT: O 788 PHE cc_start: 0.7725 (t80) cc_final: 0.7208 (t80) REVERT: T 223 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: T 348 LEU cc_start: 0.8089 (pp) cc_final: 0.7738 (tt) REVERT: T 480 ILE cc_start: 0.8469 (tp) cc_final: 0.8184 (tp) REVERT: T 564 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7857 (pp20) REVERT: T 660 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8266 (mmp) REVERT: T 664 LEU cc_start: 0.8612 (pp) cc_final: 0.8401 (mp) REVERT: T 693 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8118 (mtmt) REVERT: T 765 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8026 (mt) REVERT: T 806 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7992 (tm-30) REVERT: A 97 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: B 35 GLN cc_start: 0.8091 (mp10) cc_final: 0.7880 (mp10) REVERT: B 38 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8466 (m-40) REVERT: B 108 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8708 (ptt) REVERT: D 188 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7911 (ttt-90) REVERT: E 157 ARG cc_start: 0.8092 (tpp-160) cc_final: 0.7772 (tpt170) REVERT: E 205 MET cc_start: 0.8509 (ttp) cc_final: 0.8268 (ptm) REVERT: F 50 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: F 186 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.6905 (mpt90) REVERT: K 115 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: N 207 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8385 (tttm) outliers start: 107 outliers final: 71 residues processed: 998 average time/residue: 1.7706 time to fit residues: 2121.6882 Evaluate side-chains 1024 residues out of total 5043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 932 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain S residue 287 THR Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 688 GLU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 499 GLU Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 645 ASP Chi-restraints excluded: chain R residue 697 GLU Chi-restraints excluded: chain R residue 729 ASP Chi-restraints excluded: chain Q residue 231 LYS Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 493 PHE Chi-restraints excluded: chain Q residue 509 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 564 GLU Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 238 LEU Chi-restraints excluded: chain T residue 319 THR Chi-restraints excluded: chain T residue 587 VAL Chi-restraints excluded: chain T residue 629 ASP Chi-restraints excluded: chain T residue 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 224 ILE Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 164 ARG Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 469 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 chunk 419 optimal weight: 1.9990 chunk 367 optimal weight: 0.9990 chunk 402 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 500 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 342 GLN S 632 ASN S 647 GLN S 686 ASN R 692 ASN Q 700 GLN Q 795 HIS P 692 ASN T 636 GLN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN C 179 GLN E 154 HIS E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN K 222 GLN N 222 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.124282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095593 restraints weight = 78346.083| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.81 r_work: 0.3547 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 48088 Z= 0.195 Angle : 0.635 15.278 64975 Z= 0.319 Chirality : 0.042 0.264 7482 Planarity : 0.004 0.084 8435 Dihedral : 7.871 115.999 6908 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 2.00 % Allowed : 21.06 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 5991 helix: 1.87 (0.10), residues: 3149 sheet: 0.60 (0.18), residues: 738 loop : -0.68 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.005 0.001 HIS T 627 PHE 0.033 0.001 PHE S 673 TYR 0.020 0.001 TYR L 159 ARG 0.019 0.000 ARG R 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 60127.96 seconds wall clock time: 1019 minutes 4.68 seconds (61144.68 seconds total)