Starting phenix.real_space_refine on Wed Oct 9 16:25:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_38535.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_38535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_38535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_38535.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xon_38535/10_2024/8xon_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 20.05, per 1000 atoms: 0.42 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: 8.44 Conformation dependent library (CDL) restraints added in 4.4 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: 4.66 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: 18.33 Time building geometry restraints manager: 9.95 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.340 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 79.730 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.280 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:9.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.110 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 1237 time to evaluate : 3.984 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: 1.6182 time to fit residues: 2376.2010 Evaluate side-chains 983 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 982 time to evaluate : 3.996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 fitting. rotamer outliers: 127 poor density : 1023 time to evaluate : 4.095 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: 0.7075 (p0) cc_final: 0.6545 (p0) REVERT: S 213 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7424 (mm-30) REVERT: S 233 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7327 (mm-30) REVERT: S 267 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8109 (ptmm) REVERT: S 270 LYS cc_start: 0.7977 (tmmt) cc_final: 0.7383 (tppt) REVERT: S 304 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (tp) REVERT: S 345 GLU cc_start: 0.8590 (tt0) cc_final: 0.8281 (tt0) REVERT: S 367 ARG cc_start: 0.7517 (tpt90) cc_final: 0.7127 (tmm-80) REVERT: S 397 ASP cc_start: 0.7068 (m-30) cc_final: 0.6457 (m-30) REVERT: S 407 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7490 (tmm-80) REVERT: S 498 GLU cc_start: 0.7135 (pm20) cc_final: 0.6914 (pm20) REVERT: S 539 LYS cc_start: 0.8370 (mppt) cc_final: 0.8037 (mtpp) REVERT: S 571 ASP cc_start: 0.7741 (m-30) cc_final: 0.7330 (m-30) REVERT: S 584 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8319 (ptpp) REVERT: S 608 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7215 (mm-30) REVERT: S 609 LYS cc_start: 0.8229 (mttt) cc_final: 0.8028 (mttm) REVERT: S 636 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7346 (mp10) REVERT: S 639 GLU cc_start: 0.8182 (tp30) cc_final: 0.7892 (tp30) REVERT: S 668 ASP cc_start: 0.8335 (t0) cc_final: 0.7825 (p0) REVERT: S 669 ILE cc_start: 0.8346 (mp) cc_final: 0.7879 (mp) REVERT: S 671 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8074 (tmmt) REVERT: S 684 LYS cc_start: 0.8061 (tptm) cc_final: 0.7083 (mmmm) REVERT: S 688 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7359 (mp0) REVERT: S 693 LYS cc_start: 0.8177 (tppp) cc_final: 0.7964 (tppp) REVERT: S 699 LYS cc_start: 0.8375 (tppt) cc_final: 0.8141 (mmtt) REVERT: S 743 ASP cc_start: 0.7845 (t0) cc_final: 0.7111 (OUTLIER) REVERT: S 754 GLU cc_start: 0.7809 (tp30) cc_final: 0.7481 (mp0) REVERT: S 758 LYS cc_start: 0.8433 (tttm) cc_final: 0.8198 (mptp) REVERT: S 815 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5873 (mm-30) REVERT: R 244 TYR cc_start: 0.8161 (m-80) cc_final: 0.7884 (m-80) REVERT: R 263 GLU cc_start: 0.7557 (tt0) cc_final: 0.6889 (tt0) REVERT: R 307 MET cc_start: 0.8090 (mtm) cc_final: 0.7843 (mtm) REVERT: R 499 GLU cc_start: 0.7601 (pt0) cc_final: 0.7382 (pp20) REVERT: R 584 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8118 (mtpm) REVERT: R 640 ASP cc_start: 0.7820 (t0) cc_final: 0.7247 (t0) REVERT: R 645 ASP cc_start: 0.7735 (t0) cc_final: 0.7464 (t0) REVERT: R 647 GLN cc_start: 0.8681 (mt0) cc_final: 0.8465 (mt0) REVERT: R 736 ASP cc_start: 0.8548 (t70) cc_final: 0.8192 (t70) REVERT: R 754 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7449 (tp30) REVERT: R 790 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7679 (tm-30) REVERT: R 804 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7235 (mm-30) REVERT: Q 231 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7157 (ttpp) REVERT: Q 264 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7404 (mtt90) REVERT: Q 310 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6782 (ttm110) REVERT: Q 312 GLU cc_start: 0.7557 (mp0) cc_final: 0.6945 (mp0) REVERT: Q 322 ASP cc_start: 0.7930 (m-30) cc_final: 0.7647 (m-30) REVERT: Q 325 ARG cc_start: 0.8222 (tmm160) cc_final: 0.7783 (ptm-80) REVERT: Q 326 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7966 (ttmm) REVERT: Q 367 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.7365 (mtm-85) REVERT: Q 482 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7153 (tp30) REVERT: Q 509 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7830 (mm-30) REVERT: Q 682 ASP cc_start: 0.7476 (t70) cc_final: 0.7093 (t70) REVERT: Q 697 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7729 (mp0) REVERT: Q 747 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7494 (tp30) REVERT: P 165 LEU cc_start: 0.7892 (pt) cc_final: 0.7464 (tt) REVERT: P 170 PHE cc_start: 0.8067 (m-10) cc_final: 0.7862 (m-80) REVERT: P 182 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8237 (mptt) REVERT: P 223 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: P 240 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: P 273 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8083 (tpm170) REVERT: P 326 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8203 (ttpp) REVERT: P 329 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7493 (mm-30) REVERT: P 342 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7896 (mm-40) REVERT: P 389 ARG cc_start: 0.7796 (ptp90) cc_final: 0.7292 (mtm-85) REVERT: P 401 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8019 (mm-30) REVERT: P 478 GLU cc_start: 0.7827 (tt0) cc_final: 0.7570 (pp20) REVERT: P 492 VAL cc_start: 0.8078 (t) cc_final: 0.7789 (m) REVERT: P 497 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7615 (mp0) REVERT: P 505 ARG cc_start: 0.7523 (ptt90) cc_final: 0.6386 (ptt-90) REVERT: P 509 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7622 (mp0) REVERT: P 557 GLU cc_start: 0.7808 (tp30) cc_final: 0.7281 (tp30) REVERT: P 560 LYS cc_start: 0.7764 (mttm) cc_final: 0.7428 (mmmm) REVERT: P 608 GLU cc_start: 0.7114 (mp0) cc_final: 0.6485 (mp0) REVERT: P 652 ASP cc_start: 0.8446 (p0) cc_final: 0.8072 (p0) REVERT: P 663 ASN cc_start: 0.7950 (m110) cc_final: 0.7690 (m-40) REVERT: P 703 ARG cc_start: 0.7370 (mmt180) cc_final: 0.7102 (mmt180) REVERT: P 712 ASP cc_start: 0.7809 (m-30) cc_final: 0.7464 (t0) REVERT: P 744 MET cc_start: 0.7260 (mtt) cc_final: 0.6683 (mmm) REVERT: P 771 ARG cc_start: 0.8140 (ttt90) cc_final: 0.7511 (tpm-80) REVERT: P 779 GLU cc_start: 0.7172 (pt0) cc_final: 0.6819 (pm20) REVERT: O 211 ILE cc_start: 0.7467 (pt) cc_final: 0.7257 (pp) REVERT: O 267 LYS cc_start: 0.8363 (mmpt) cc_final: 0.8044 (tptp) REVERT: O 270 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8230 (pttm) REVERT: O 310 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7553 (tpp-160) REVERT: O 401 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7429 (tm-30) REVERT: O 578 MET cc_start: 0.7194 (mpp) cc_final: 0.6913 (mpp) REVERT: O 584 LYS cc_start: 0.8276 (tppt) cc_final: 0.7695 (pptt) REVERT: O 660 MET cc_start: 0.7538 (mtm) cc_final: 0.6993 (mtm) REVERT: O 690 MET cc_start: 0.7691 (ptp) cc_final: 0.7460 (pmm) REVERT: O 740 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7968 (mmmm) REVERT: O 788 PHE cc_start: 0.7982 (t80) cc_final: 0.7306 (t80) REVERT: T 480 ILE cc_start: 0.8188 (tp) cc_final: 0.7931 (tp) REVERT: T 531 THR cc_start: 0.7205 (m) cc_final: 0.6598 (p) REVERT: T 564 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7808 (tm-30) REVERT: T 636 GLN cc_start: 0.7459 (mp10) cc_final: 0.7198 (mp10) REVERT: T 765 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 54 ASP cc_start: 0.7472 (m-30) cc_final: 0.7178 (m-30) REVERT: A 73 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8102 (mttp) REVERT: A 97 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: B 35 GLN cc_start: 0.7723 (mp10) cc_final: 0.7134 (mp10) REVERT: B 73 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7549 (mmpt) REVERT: B 182 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7663 (ttm110) REVERT: B 187 ASP cc_start: 0.8142 (m-30) cc_final: 0.7745 (m-30) REVERT: C 42 ASN cc_start: 0.8486 (m-40) cc_final: 0.8238 (m-40) REVERT: C 59 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7832 (ttmm) REVERT: C 164 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7127 (mmp-170) REVERT: C 167 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7105 (tp30) REVERT: D 76 TYR cc_start: 0.8414 (m-80) cc_final: 0.8053 (m-80) REVERT: D 150 ASP cc_start: 0.7684 (m-30) cc_final: 0.7478 (m-30) REVERT: D 163 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7813 (ttpt) REVERT: D 188 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6711 (ttt-90) REVERT: E 59 LYS cc_start: 0.8281 (tttt) cc_final: 0.8071 (ttmm) REVERT: E 72 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7613 (mp0) REVERT: E 96 MET cc_start: 0.7980 (mtp) cc_final: 0.7431 (mtp) REVERT: E 102 ASP cc_start: 0.8103 (m-30) cc_final: 0.7821 (m-30) REVERT: E 178 GLU cc_start: 0.8153 (mp0) cc_final: 0.7694 (mp0) REVERT: E 182 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7735 (mtm110) REVERT: E 205 MET cc_start: 0.7872 (ttm) cc_final: 0.7488 (ttp) REVERT: F 167 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7322 (mt-10) REVERT: G 39 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7576 (mtp85) REVERT: G 55 ASP cc_start: 0.8061 (t70) cc_final: 0.7720 (t0) REVERT: H 76 ASP cc_start: 0.7977 (m-30) cc_final: 0.7585 (m-30) REVERT: H 154 LEU cc_start: 0.8933 (tt) cc_final: 0.8667 (tp) REVERT: H 171 GLU cc_start: 0.7739 (tt0) cc_final: 0.7498 (tt0) REVERT: H 175 ASN cc_start: 0.8243 (m-40) cc_final: 0.7878 (m-40) REVERT: H 201 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7414 (mt-10) REVERT: I 76 ASP cc_start: 0.7804 (m-30) cc_final: 0.7587 (m-30) REVERT: I 176 GLU cc_start: 0.7996 (tp30) cc_final: 0.7683 (tm-30) REVERT: K 103 SER cc_start: 0.8203 (t) cc_final: 0.7959 (t) REVERT: K 115 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: K 161 GLU cc_start: 0.8048 (pt0) cc_final: 0.7785 (pm20) REVERT: K 164 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7708 (ttm110) REVERT: K 176 GLU cc_start: 0.8192 (tp30) cc_final: 0.7922 (tm-30) REVERT: K 185 GLU cc_start: 0.6862 (tp30) cc_final: 0.6453 (mp0) REVERT: L 76 ASP cc_start: 0.7622 (m-30) cc_final: 0.7279 (m-30) REVERT: M 60 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7487 (mp0) REVERT: M 73 SER cc_start: 0.7516 (m) cc_final: 0.7186 (p) REVERT: M 99 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8874 (t) REVERT: M 160 SER cc_start: 0.8515 (t) cc_final: 0.8313 (t) REVERT: M 182 SER cc_start: 0.7625 (t) cc_final: 0.7216 (m) REVERT: M 186 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: M 212 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: N 91 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7146 (mmm-85) REVERT: N 161 GLU cc_start: 0.7878 (pp20) cc_final: 0.7183 (tm-30) REVERT: N 177 ILE cc_start: 0.8184 (mm) cc_final: 0.7950 (mt) REVERT: N 180 MET cc_start: 0.7714 (mtt) cc_final: 0.7427 (mmm) outliers start: 127 outliers final: 50 residues processed: 1085 average time/residue: 1.6471 time to fit residues: 2118.0489 Evaluate side-chains 1023 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 960 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 304 LEU 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 223 GLU Chi-restraints excluded: chain P residue 240 ASP Chi-restraints excluded: chain P residue 326 LYS 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 97 GLN 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 163 LYS 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 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 186 ASP 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 300 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 449 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 541 optimal weight: 2.9990 chunk 584 optimal weight: 0.8980 chunk 482 optimal weight: 3.9990 chunk 536 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 434 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 692 ASN R 775 GLN Q 795 HIS P 173 ASN P 692 ASN P 721 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 48088 Z= 0.238 Angle : 0.584 13.997 64975 Z= 0.296 Chirality : 0.043 0.214 7482 Planarity : 0.004 0.063 8435 Dihedral : 8.833 175.428 6910 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 2.58 % Allowed : 14.36 % Favored : 83.06 % 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: 1.09 (0.11), residues: 5991 helix: 1.74 (0.09), residues: 3160 sheet: 0.45 (0.18), residues: 758 loop : -0.73 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 189 HIS 0.005 0.001 HIS A 138 PHE 0.020 0.001 PHE P 631 TYR 0.019 0.001 TYR L 159 ARG 0.013 0.000 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 1125 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 995 time to evaluate : 3.943 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: 0.7138 (p0) cc_final: 0.6622 (p0) REVERT: S 256 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7338 (ppp80) REVERT: S 270 LYS cc_start: 0.7999 (tmmt) cc_final: 0.7478 (tppt) REVERT: S 345 GLU cc_start: 0.8552 (tt0) cc_final: 0.8295 (tt0) REVERT: S 373 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: S 397 ASP cc_start: 0.7150 (m-30) cc_final: 0.6568 (m-30) REVERT: S 407 ARG cc_start: 0.7811 (ttt90) cc_final: 0.7453 (tmm-80) REVERT: S 478 GLU cc_start: 0.7039 (pm20) cc_final: 0.6837 (pm20) REVERT: S 539 LYS cc_start: 0.8412 (mppt) cc_final: 0.8080 (mtpp) REVERT: S 560 LYS cc_start: 0.8313 (mttt) cc_final: 0.8089 (mttm) REVERT: S 571 ASP cc_start: 0.7766 (m-30) cc_final: 0.7314 (m-30) REVERT: S 584 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8307 (ptpp) REVERT: S 636 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7375 (mp10) REVERT: S 660 MET cc_start: 0.8785 (mtm) cc_final: 0.8535 (mtm) REVERT: S 668 ASP cc_start: 0.8394 (t0) cc_final: 0.7804 (p0) REVERT: S 669 ILE cc_start: 0.8288 (mp) cc_final: 0.7775 (mp) REVERT: S 671 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8104 (tmmt) REVERT: S 684 LYS cc_start: 0.7885 (tptm) cc_final: 0.7616 (mmmm) REVERT: S 688 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7621 (mm-30) REVERT: S 693 LYS cc_start: 0.8181 (tppp) cc_final: 0.7943 (tppp) REVERT: S 699 LYS cc_start: 0.8378 (tppt) cc_final: 0.8169 (mmtt) REVERT: S 743 ASP cc_start: 0.7889 (t0) cc_final: 0.7138 (OUTLIER) REVERT: S 754 GLU cc_start: 0.7794 (tp30) cc_final: 0.7498 (mp0) REVERT: S 758 LYS cc_start: 0.8399 (tttm) cc_final: 0.8168 (mptp) REVERT: S 815 GLU cc_start: 0.6256 (mm-30) cc_final: 0.5931 (mm-30) REVERT: R 170 PHE cc_start: 0.7787 (m-80) cc_final: 0.7532 (m-80) REVERT: R 244 TYR cc_start: 0.8196 (m-80) cc_final: 0.7891 (m-80) REVERT: R 263 GLU cc_start: 0.7357 (tt0) cc_final: 0.7075 (tt0) REVERT: R 267 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6923 (mmtt) REVERT: R 307 MET cc_start: 0.8083 (mtm) cc_final: 0.7842 (mtm) REVERT: R 407 ARG cc_start: 0.7510 (tpm170) cc_final: 0.7276 (tpm170) REVERT: R 499 GLU cc_start: 0.7637 (pt0) cc_final: 0.7320 (pp20) REVERT: R 584 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8133 (mtpm) REVERT: R 640 ASP cc_start: 0.7818 (t0) cc_final: 0.7219 (t0) REVERT: R 645 ASP cc_start: 0.7694 (t0) cc_final: 0.7393 (t0) REVERT: R 712 ASP cc_start: 0.7801 (m-30) cc_final: 0.7591 (m-30) REVERT: R 736 ASP cc_start: 0.8568 (t70) cc_final: 0.8243 (t70) REVERT: R 758 LYS cc_start: 0.8464 (tptp) cc_final: 0.8226 (tppp) REVERT: R 775 GLN cc_start: 0.8181 (tt0) cc_final: 0.7856 (tt0) REVERT: R 790 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7630 (tm-30) REVERT: R 804 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7238 (mm-30) REVERT: Q 192 GLU cc_start: 0.7836 (mp0) cc_final: 0.7627 (mp0) REVERT: Q 264 ARG cc_start: 0.7708 (mtt90) cc_final: 0.7337 (mtt90) REVERT: Q 310 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6781 (ttm110) REVERT: Q 312 GLU cc_start: 0.7538 (mp0) cc_final: 0.6929 (mp0) REVERT: Q 322 ASP cc_start: 0.7940 (m-30) cc_final: 0.7642 (m-30) REVERT: Q 325 ARG cc_start: 0.8217 (tmm160) cc_final: 0.7770 (ptm-80) REVERT: Q 326 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7984 (ttmm) REVERT: Q 367 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7465 (mtm-85) REVERT: Q 509 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7652 (mp0) REVERT: Q 564 GLU cc_start: 0.7893 (tt0) cc_final: 0.7600 (tt0) REVERT: Q 608 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: Q 697 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7660 (mp0) REVERT: Q 743 ASP cc_start: 0.7170 (t0) cc_final: 0.6480 (t70) REVERT: Q 747 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7548 (tm-30) REVERT: P 170 PHE cc_start: 0.8080 (m-10) cc_final: 0.7811 (m-80) REVERT: P 182 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8223 (mptt) REVERT: P 240 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: P 273 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8088 (tpm170) REVERT: P 310 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7773 (mmm160) REVERT: P 326 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8204 (ttpp) REVERT: P 329 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7458 (mm-30) REVERT: P 389 ARG cc_start: 0.8138 (ptp90) cc_final: 0.7382 (mtm-85) REVERT: P 401 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7980 (mm-30) REVERT: P 406 MET cc_start: 0.7914 (tpt) cc_final: 0.7714 (tpt) REVERT: P 478 GLU cc_start: 0.7799 (tt0) cc_final: 0.7550 (pp20) REVERT: P 492 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7760 (m) REVERT: P 505 ARG cc_start: 0.7489 (ptt90) cc_final: 0.6717 (ptt-90) REVERT: P 509 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7558 (mm-30) REVERT: P 557 GLU cc_start: 0.7751 (tp30) cc_final: 0.7304 (tp30) REVERT: P 560 LYS cc_start: 0.7733 (mttm) cc_final: 0.7417 (mmmm) REVERT: P 578 MET cc_start: 0.8389 (mmp) cc_final: 0.8121 (mmp) REVERT: P 584 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8311 (mmmt) REVERT: P 608 GLU cc_start: 0.7104 (mp0) cc_final: 0.6526 (mp0) REVERT: P 625 LYS cc_start: 0.8566 (mttm) cc_final: 0.8284 (mtmt) REVERT: P 652 ASP cc_start: 0.8473 (p0) cc_final: 0.8050 (p0) REVERT: P 663 ASN cc_start: 0.7993 (m110) cc_final: 0.7764 (m-40) REVERT: P 703 ARG cc_start: 0.7339 (mmt180) cc_final: 0.7019 (mmm-85) REVERT: P 712 ASP cc_start: 0.7815 (m-30) cc_final: 0.7528 (t0) REVERT: P 744 MET cc_start: 0.7345 (mtt) cc_final: 0.6801 (mmm) REVERT: P 771 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7417 (tpm-80) REVERT: P 779 GLU cc_start: 0.7206 (pt0) cc_final: 0.6930 (pm20) REVERT: O 270 LYS cc_start: 0.8499 (pttt) cc_final: 0.8294 (pptt) REVERT: O 310 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7329 (tpm170) REVERT: O 401 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7506 (tm-30) REVERT: O 406 MET cc_start: 0.8162 (mmm) cc_final: 0.7398 (pp-130) REVERT: O 522 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8700 (ptpt) REVERT: O 578 MET cc_start: 0.7243 (mpp) cc_final: 0.6973 (mpp) REVERT: O 584 LYS cc_start: 0.8247 (tppt) cc_final: 0.7624 (pttp) REVERT: O 660 MET cc_start: 0.7622 (mtm) cc_final: 0.7023 (ttm) REVERT: O 690 MET cc_start: 0.7688 (ptp) cc_final: 0.7467 (pmm) REVERT: O 734 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8542 (mmpt) REVERT: O 740 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7962 (mmmm) REVERT: O 788 PHE cc_start: 0.7992 (t80) cc_final: 0.7347 (t80) REVERT: T 197 MET cc_start: 0.6833 (ppp) cc_final: 0.6628 (ppp) REVERT: T 410 ARG cc_start: 0.5613 (ptp90) cc_final: 0.5323 (ptp90) REVERT: T 480 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (tp) REVERT: T 564 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7714 (tm-30) REVERT: T 636 GLN cc_start: 0.7452 (mp10) cc_final: 0.7220 (mp10) REVERT: T 765 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7182 (mt) REVERT: A 54 ASP cc_start: 0.7502 (m-30) cc_final: 0.7180 (m-30) REVERT: A 73 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8052 (mttp) REVERT: B 35 GLN cc_start: 0.7745 (mp10) cc_final: 0.7204 (mp10) REVERT: B 38 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7748 (m-40) REVERT: B 108 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8281 (ptt) REVERT: B 182 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7665 (ttm110) REVERT: B 185 ASP cc_start: 0.8520 (t70) cc_final: 0.8302 (t0) REVERT: B 187 ASP cc_start: 0.8114 (m-30) cc_final: 0.7733 (m-30) REVERT: C 42 ASN cc_start: 0.8443 (m-40) cc_final: 0.8174 (m-40) REVERT: C 59 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7828 (ttmm) REVERT: C 164 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7015 (mmp-170) REVERT: C 167 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7109 (tp30) REVERT: D 39 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7559 (mtp85) REVERT: D 76 TYR cc_start: 0.8417 (m-80) cc_final: 0.8098 (m-80) REVERT: D 163 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7731 (ttpt) REVERT: D 188 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6614 (ttt-90) REVERT: E 72 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7573 (mp0) REVERT: E 96 MET cc_start: 0.7968 (mtp) cc_final: 0.7506 (mtp) REVERT: E 102 ASP cc_start: 0.8110 (m-30) cc_final: 0.7823 (m-30) REVERT: E 178 GLU cc_start: 0.8140 (mp0) cc_final: 0.7673 (mp0) REVERT: E 205 MET cc_start: 0.7912 (ttm) cc_final: 0.7522 (ttp) REVERT: F 114 MET cc_start: 0.8301 (mmm) cc_final: 0.8073 (tpt) REVERT: F 167 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7297 (mt-10) REVERT: F 186 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6500 (mpt90) REVERT: G 55 ASP cc_start: 0.8016 (t70) cc_final: 0.7664 (t0) REVERT: G 165 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7864 (mmm) REVERT: H 76 ASP cc_start: 0.7991 (m-30) cc_final: 0.7601 (m-30) REVERT: H 90 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7490 (OUTLIER) REVERT: H 154 LEU cc_start: 0.8901 (tt) cc_final: 0.8629 (tp) REVERT: H 161 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7500 (tm-30) REVERT: H 171 GLU cc_start: 0.7655 (tt0) cc_final: 0.7424 (tt0) REVERT: H 175 ASN cc_start: 0.8265 (m-40) cc_final: 0.7914 (m-40) REVERT: I 76 ASP cc_start: 0.7818 (m-30) cc_final: 0.7559 (m-30) REVERT: I 176 GLU cc_start: 0.8084 (tp30) cc_final: 0.7688 (tm-30) REVERT: K 161 GLU cc_start: 0.8038 (pt0) cc_final: 0.7795 (pm20) REVERT: K 164 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7686 (ttm110) REVERT: K 176 GLU cc_start: 0.8171 (tp30) cc_final: 0.7933 (tm-30) REVERT: K 185 GLU cc_start: 0.6923 (tp30) cc_final: 0.6540 (mp0) REVERT: L 76 ASP cc_start: 0.7584 (m-30) cc_final: 0.7259 (m-30) REVERT: L 144 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8293 (ptmt) REVERT: L 146 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8431 (ptp) REVERT: M 60 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7502 (mp0) REVERT: M 85 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8015 (tt0) REVERT: M 99 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8854 (t) REVERT: M 160 SER cc_start: 0.8530 (t) cc_final: 0.8306 (t) REVERT: M 182 SER cc_start: 0.7570 (t) cc_final: 0.7366 (m) REVERT: M 212 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: N 91 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7118 (mmm-85) REVERT: N 180 MET cc_start: 0.7711 (mtt) cc_final: 0.7429 (mmm) outliers start: 130 outliers final: 52 residues processed: 1061 average time/residue: 1.6446 time to fit residues: 2068.7882 Evaluate side-chains 1027 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 957 time to evaluate : 4.043 ------------------------------------------------------------------------------- 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 373 GLU Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain R residue 646 SER Chi-restraints excluded: chain Q residue 388 ASP Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 608 GLU Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 240 ASP Chi-restraints excluded: chain P residue 246 LEU Chi-restraints excluded: chain P residue 326 LYS Chi-restraints excluded: chain P residue 492 VAL Chi-restraints excluded: chain P residue 501 SER 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 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 480 ILE 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 163 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 188 ARG 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 165 MET 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 K residue 64 PHE 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 144 LYS Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain M residue 99 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 534 optimal weight: 0.6980 chunk 406 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 543 optimal weight: 0.6980 chunk 575 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 514 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 HIS 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 F 35 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 116 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 48088 Z= 0.277 Angle : 0.592 12.639 64975 Z= 0.302 Chirality : 0.043 0.220 7482 Planarity : 0.004 0.059 8435 Dihedral : 8.663 167.924 6910 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 2.92 % Allowed : 15.47 % Favored : 81.61 % 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: 1.06 (0.11), residues: 5991 helix: 1.73 (0.09), residues: 3165 sheet: 0.40 (0.18), residues: 758 loop : -0.76 (0.14), residues: 2068 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 0.001 PHE P 631 TYR 0.016 0.001 TYR T 362 ARG 0.009 0.000 ARG G 39 *********************** 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 1119 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 972 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7197 (p0) cc_final: 0.6683 (p0) REVERT: S 239 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7303 (ttmt) REVERT: S 256 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7421 (ppp80) REVERT: S 270 LYS cc_start: 0.8019 (tmmt) cc_final: 0.7519 (tppt) REVERT: S 345 GLU cc_start: 0.8498 (tt0) cc_final: 0.8249 (tt0) REVERT: S 373 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7153 (pp20) REVERT: S 397 ASP cc_start: 0.7177 (m-30) cc_final: 0.6585 (m-30) REVERT: S 407 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7395 (tmm-80) REVERT: S 478 GLU cc_start: 0.7068 (pm20) cc_final: 0.6855 (pm20) REVERT: S 514 VAL cc_start: 0.8216 (t) cc_final: 0.7966 (p) REVERT: S 539 LYS cc_start: 0.8429 (mppt) cc_final: 0.8123 (mtpp) REVERT: S 560 LYS cc_start: 0.8326 (mttt) cc_final: 0.8109 (mttm) REVERT: S 571 ASP cc_start: 0.7785 (m-30) cc_final: 0.7329 (m-30) REVERT: S 584 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8327 (ptpp) REVERT: S 636 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7408 (mp10) REVERT: S 639 GLU cc_start: 0.8199 (tp30) cc_final: 0.7872 (tp30) REVERT: S 668 ASP cc_start: 0.8359 (t70) cc_final: 0.7789 (p0) REVERT: S 669 ILE cc_start: 0.8318 (mp) cc_final: 0.7748 (mp) REVERT: S 684 LYS cc_start: 0.7860 (tptm) cc_final: 0.7567 (mmmm) REVERT: S 688 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7641 (mm-30) REVERT: S 693 LYS cc_start: 0.8177 (tppp) cc_final: 0.7951 (tppp) REVERT: S 712 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: S 743 ASP cc_start: 0.7895 (t0) cc_final: 0.7126 (OUTLIER) REVERT: S 754 GLU cc_start: 0.7790 (tp30) cc_final: 0.7512 (mp0) REVERT: S 758 LYS cc_start: 0.8375 (tttm) cc_final: 0.8138 (mttp) REVERT: S 779 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7252 (mt-10) REVERT: S 815 GLU cc_start: 0.6245 (mm-30) cc_final: 0.5862 (mm-30) REVERT: R 194 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7006 (tm-30) REVERT: R 244 TYR cc_start: 0.8170 (m-80) cc_final: 0.7883 (m-80) REVERT: R 263 GLU cc_start: 0.7354 (tt0) cc_final: 0.7015 (tt0) REVERT: R 267 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6849 (mmtt) REVERT: R 307 MET cc_start: 0.8070 (mtm) cc_final: 0.7827 (mtm) REVERT: R 499 GLU cc_start: 0.7663 (pt0) cc_final: 0.7377 (pp20) REVERT: R 584 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8150 (mtpm) REVERT: R 640 ASP cc_start: 0.7813 (t0) cc_final: 0.6673 (t0) REVERT: R 642 ARG cc_start: 0.8268 (ptt-90) cc_final: 0.7877 (ptt180) REVERT: R 645 ASP cc_start: 0.7673 (t0) cc_final: 0.7342 (t0) REVERT: R 736 ASP cc_start: 0.8589 (t70) cc_final: 0.8280 (t70) REVERT: R 775 GLN cc_start: 0.8188 (tt0) cc_final: 0.7826 (tt0) REVERT: R 777 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: R 790 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7595 (tm-30) REVERT: R 804 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7214 (mm-30) REVERT: Q 192 GLU cc_start: 0.7826 (mp0) cc_final: 0.7616 (mp0) REVERT: Q 264 ARG cc_start: 0.7758 (mtt90) cc_final: 0.7401 (mtt90) REVERT: Q 310 ARG cc_start: 0.6997 (ttp-110) cc_final: 0.6787 (ttm110) REVERT: Q 312 GLU cc_start: 0.7547 (mp0) cc_final: 0.7043 (mp0) REVERT: Q 322 ASP cc_start: 0.7947 (m-30) cc_final: 0.7644 (m-30) REVERT: Q 325 ARG cc_start: 0.8200 (tmm160) cc_final: 0.7743 (ptm-80) REVERT: Q 326 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8035 (ttmm) REVERT: Q 367 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.6581 (mtm-85) REVERT: Q 478 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: Q 509 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7675 (mp0) REVERT: Q 564 GLU cc_start: 0.7868 (tt0) cc_final: 0.7550 (tt0) REVERT: Q 608 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: Q 743 ASP cc_start: 0.7248 (t0) cc_final: 0.6547 (t70) REVERT: Q 747 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7603 (tm-30) REVERT: P 182 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8226 (mptt) REVERT: P 240 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: P 273 ARG cc_start: 0.8498 (ttt90) cc_final: 0.8123 (tpm170) REVERT: P 310 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7747 (mmm160) REVERT: P 326 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8227 (ttpp) REVERT: P 329 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7375 (mm-30) REVERT: P 389 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7451 (mtm-85) REVERT: P 401 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7971 (mm-30) REVERT: P 478 GLU cc_start: 0.7789 (tt0) cc_final: 0.7536 (pp20) REVERT: P 492 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7779 (m) REVERT: P 505 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6321 (ptt-90) REVERT: P 509 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7661 (mp0) REVERT: P 557 GLU cc_start: 0.7743 (tp30) cc_final: 0.7328 (tp30) REVERT: P 560 LYS cc_start: 0.7722 (mttm) cc_final: 0.7406 (mmmm) REVERT: P 578 MET cc_start: 0.8374 (mmp) cc_final: 0.8141 (mmp) REVERT: P 601 GLU cc_start: 0.7835 (mp0) cc_final: 0.7522 (mp0) REVERT: P 605 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7238 (mt0) REVERT: P 608 GLU cc_start: 0.7115 (mp0) cc_final: 0.6524 (mp0) REVERT: P 625 LYS cc_start: 0.8603 (mttm) cc_final: 0.8303 (mtmt) REVERT: P 652 ASP cc_start: 0.8489 (p0) cc_final: 0.8067 (p0) REVERT: P 663 ASN cc_start: 0.8030 (m110) cc_final: 0.7808 (m-40) REVERT: P 703 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6971 (mmm-85) REVERT: P 712 ASP cc_start: 0.7820 (m-30) cc_final: 0.7565 (t0) REVERT: P 744 MET cc_start: 0.7406 (mtt) cc_final: 0.6847 (mmm) REVERT: P 771 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7495 (tpm-80) REVERT: P 779 GLU cc_start: 0.7170 (pt0) cc_final: 0.6818 (pm20) REVERT: O 270 LYS cc_start: 0.8466 (pttt) cc_final: 0.8225 (pptt) REVERT: O 401 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7487 (tm-30) REVERT: O 578 MET cc_start: 0.7354 (mpp) cc_final: 0.7025 (mpp) REVERT: O 584 LYS cc_start: 0.8233 (tppt) cc_final: 0.7639 (pttt) REVERT: O 587 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7435 (t) REVERT: O 690 MET cc_start: 0.7678 (ptp) cc_final: 0.7465 (pmm) REVERT: O 734 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8528 (mmpt) REVERT: O 788 PHE cc_start: 0.7992 (t80) cc_final: 0.7349 (t80) REVERT: T 499 GLU cc_start: 0.7912 (tt0) cc_final: 0.7511 (pp20) REVERT: T 564 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7755 (tm-30) REVERT: T 569 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7006 (t70) REVERT: T 636 GLN cc_start: 0.7483 (mp10) cc_final: 0.7241 (mp10) REVERT: T 660 MET cc_start: 0.7869 (mmp) cc_final: 0.7415 (mmp) REVERT: T 693 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8113 (mtmt) REVERT: T 765 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7262 (mt) REVERT: T 806 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7889 (tm-30) REVERT: A 54 ASP cc_start: 0.7502 (m-30) cc_final: 0.7016 (m-30) REVERT: A 58 ASN cc_start: 0.8502 (m110) cc_final: 0.8264 (m110) REVERT: A 73 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8074 (mttp) REVERT: A 97 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: A 164 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8104 (mmp-170) REVERT: B 35 GLN cc_start: 0.7740 (mp10) cc_final: 0.7187 (mp10) REVERT: B 38 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: B 73 LYS cc_start: 0.8293 (mmmm) cc_final: 0.7780 (mmpt) REVERT: B 108 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8323 (ptt) REVERT: B 182 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7656 (ttm110) REVERT: B 187 ASP cc_start: 0.8097 (m-30) cc_final: 0.7692 (m-30) REVERT: C 42 ASN cc_start: 0.8481 (m-40) cc_final: 0.8214 (m-40) REVERT: C 59 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7850 (ttmm) REVERT: C 164 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7068 (mmp-170) REVERT: C 167 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7096 (tp30) REVERT: D 163 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: D 188 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6574 (ttt-90) REVERT: E 72 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7700 (mp0) REVERT: E 102 ASP cc_start: 0.8158 (m-30) cc_final: 0.7855 (m-30) REVERT: E 157 ARG cc_start: 0.7283 (tpp-160) cc_final: 0.6653 (tpt170) REVERT: E 178 GLU cc_start: 0.8084 (mp0) cc_final: 0.7709 (mp0) REVERT: E 205 MET cc_start: 0.7902 (ttm) cc_final: 0.7508 (ttp) REVERT: F 167 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7313 (mt-10) REVERT: F 186 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6443 (mpt90) REVERT: G 55 ASP cc_start: 0.8012 (t70) cc_final: 0.7648 (t0) REVERT: G 165 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7866 (mmm) REVERT: H 60 GLU cc_start: 0.7942 (mp0) cc_final: 0.7488 (mp0) REVERT: H 76 ASP cc_start: 0.7998 (m-30) cc_final: 0.7588 (m-30) REVERT: H 161 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7526 (tm-30) REVERT: H 171 GLU cc_start: 0.7678 (tt0) cc_final: 0.7442 (tt0) REVERT: H 175 ASN cc_start: 0.8279 (m-40) cc_final: 0.7926 (m-40) REVERT: I 76 ASP cc_start: 0.7839 (m-30) cc_final: 0.7566 (m-30) REVERT: I 176 GLU cc_start: 0.8094 (tp30) cc_final: 0.7678 (tm-30) REVERT: K 115 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: K 161 GLU cc_start: 0.8044 (pt0) cc_final: 0.7830 (pm20) REVERT: K 164 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7626 (ttm110) REVERT: K 176 GLU cc_start: 0.8171 (tp30) cc_final: 0.7939 (tm-30) REVERT: K 185 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: L 76 ASP cc_start: 0.7596 (m-30) cc_final: 0.7265 (m-30) REVERT: L 146 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8368 (ptp) REVERT: M 60 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7548 (mp0) REVERT: M 67 VAL cc_start: 0.8674 (p) cc_final: 0.8449 (m) REVERT: M 85 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8000 (tt0) REVERT: M 99 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8871 (t) REVERT: M 160 SER cc_start: 0.8513 (t) cc_final: 0.8268 (t) REVERT: M 198 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7594 (tppt) REVERT: M 212 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: N 91 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7151 (mmm-85) REVERT: N 180 MET cc_start: 0.7690 (mtt) cc_final: 0.7375 (mmm) outliers start: 147 outliers final: 66 residues processed: 1052 average time/residue: 1.6819 time to fit residues: 2094.1462 Evaluate side-chains 1038 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 946 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 531 THR Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 666 THR Chi-restraints excluded: chain R residue 777 GLU Chi-restraints excluded: chain Q residue 388 ASP Chi-restraints excluded: chain Q residue 478 GLU Chi-restraints excluded: chain Q residue 582 SER Chi-restraints excluded: chain Q residue 584 LYS Chi-restraints excluded: chain Q residue 608 GLU 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 729 ASP Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 240 ASP Chi-restraints excluded: chain P residue 245 THR Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN 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 197 MET 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 410 ARG 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 765 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 97 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 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 163 LYS 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 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 165 MET Chi-restraints excluded: chain G residue 170 SER 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 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 115 GLN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 185 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 146 MET Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 99 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 478 optimal weight: 0.5980 chunk 326 optimal weight: 20.0000 chunk 8 optimal weight: 0.1980 chunk 428 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 490 optimal weight: 2.9990 chunk 397 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 516 optimal weight: 0.0030 chunk 145 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 S 718 GLN R 692 ASN Q 795 HIS P 173 ASN P 692 ASN O 286 HIS 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 171 GLN F 38 ASN F 58 ASN F 171 GLN I 231 ASN K 222 GLN N 222 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 48088 Z= 0.161 Angle : 0.560 15.921 64975 Z= 0.282 Chirality : 0.041 0.229 7482 Planarity : 0.004 0.137 8435 Dihedral : 8.397 161.754 6910 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 2.42 % Allowed : 16.98 % Favored : 80.60 % 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: 1.90 (0.10), residues: 3166 sheet: 0.53 (0.18), residues: 746 loop : -0.69 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 189 HIS 0.003 0.001 HIS O 242 PHE 0.040 0.001 PHE O 565 TYR 0.017 0.001 TYR I 159 ARG 0.014 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 1105 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 983 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7232 (p0) cc_final: 0.6702 (p0) REVERT: S 256 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7379 (ptm-80) REVERT: S 270 LYS cc_start: 0.8025 (tmmt) cc_final: 0.7450 (tppt) REVERT: S 273 ARG cc_start: 0.7904 (tmm-80) cc_final: 0.7254 (tmm-80) REVERT: S 338 PHE cc_start: 0.7595 (m-10) cc_final: 0.7240 (m-80) REVERT: S 345 GLU cc_start: 0.8517 (tt0) cc_final: 0.8285 (tt0) REVERT: S 407 ARG cc_start: 0.7757 (ttt90) cc_final: 0.7339 (tmm-80) REVERT: S 478 GLU cc_start: 0.7056 (pm20) cc_final: 0.6807 (pm20) REVERT: S 514 VAL cc_start: 0.8193 (t) cc_final: 0.7962 (p) REVERT: S 539 LYS cc_start: 0.8453 (mppt) cc_final: 0.8152 (mtpp) REVERT: S 571 ASP cc_start: 0.7743 (m-30) cc_final: 0.7295 (m-30) REVERT: S 584 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8313 (ptpp) REVERT: S 639 GLU cc_start: 0.8130 (tp30) cc_final: 0.7842 (tp30) REVERT: S 668 ASP cc_start: 0.8355 (t70) cc_final: 0.8035 (p0) REVERT: S 669 ILE cc_start: 0.8387 (mp) cc_final: 0.7840 (mp) REVERT: S 696 ASP cc_start: 0.7793 (t0) cc_final: 0.7543 (t0) REVERT: S 743 ASP cc_start: 0.7903 (t0) cc_final: 0.7155 (OUTLIER) REVERT: S 754 GLU cc_start: 0.7766 (tp30) cc_final: 0.7495 (mp0) REVERT: S 758 LYS cc_start: 0.8370 (tttm) cc_final: 0.8155 (mptp) REVERT: S 813 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7449 (ttp-170) REVERT: S 815 GLU cc_start: 0.6238 (mm-30) cc_final: 0.5909 (mm-30) REVERT: R 244 TYR cc_start: 0.8171 (m-80) cc_final: 0.7845 (m-80) REVERT: R 258 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7166 (tmm-80) REVERT: R 267 LYS cc_start: 0.7217 (mmtt) cc_final: 0.6950 (mmtt) REVERT: R 307 MET cc_start: 0.8039 (mtm) cc_final: 0.7761 (mtm) REVERT: R 407 ARG cc_start: 0.7528 (tpm170) cc_final: 0.7226 (tpm170) REVERT: R 499 GLU cc_start: 0.7618 (pt0) cc_final: 0.7388 (pp20) REVERT: R 584 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8149 (mtpm) REVERT: R 640 ASP cc_start: 0.7786 (t0) cc_final: 0.6740 (t0) REVERT: R 642 ARG cc_start: 0.8237 (ptt-90) cc_final: 0.7750 (ptt180) REVERT: R 645 ASP cc_start: 0.7642 (t0) cc_final: 0.7320 (t0) REVERT: R 712 ASP cc_start: 0.7841 (m-30) cc_final: 0.7626 (m-30) REVERT: R 736 ASP cc_start: 0.8579 (t70) cc_final: 0.8291 (t70) REVERT: R 775 GLN cc_start: 0.8143 (tt0) cc_final: 0.7861 (tt0) REVERT: R 777 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: R 790 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7678 (tm-30) REVERT: R 804 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7221 (mm-30) REVERT: Q 192 GLU cc_start: 0.7784 (mp0) cc_final: 0.7542 (mp0) REVERT: Q 231 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7092 (ttpt) REVERT: Q 256 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7125 (tpp80) REVERT: Q 264 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7354 (mtt90) REVERT: Q 310 ARG cc_start: 0.6938 (ttp-110) cc_final: 0.6724 (ttm110) REVERT: Q 312 GLU cc_start: 0.7580 (mp0) cc_final: 0.7050 (mp0) REVERT: Q 325 ARG cc_start: 0.8186 (tmm160) cc_final: 0.7729 (ptm-80) REVERT: Q 326 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8044 (ttmm) REVERT: Q 367 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.7371 (mtm-85) REVERT: Q 478 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: Q 482 GLU cc_start: 0.7422 (tp30) cc_final: 0.7186 (tm-30) REVERT: Q 499 GLU cc_start: 0.7465 (mp0) cc_final: 0.7208 (mp0) REVERT: Q 509 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7586 (mp0) REVERT: Q 564 GLU cc_start: 0.7842 (tt0) cc_final: 0.7597 (tt0) REVERT: Q 608 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: Q 734 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7788 (mmtt) REVERT: Q 743 ASP cc_start: 0.7281 (t0) cc_final: 0.6554 (t70) REVERT: Q 747 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7567 (tm-30) REVERT: P 182 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8210 (mptt) REVERT: P 223 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: P 273 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8086 (tpm170) REVERT: P 307 MET cc_start: 0.8680 (ptp) cc_final: 0.8442 (pmm) REVERT: P 310 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7708 (mmm160) REVERT: P 329 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7525 (mm-30) REVERT: P 389 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7337 (mtm-85) REVERT: P 401 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7975 (mm-30) REVERT: P 478 GLU cc_start: 0.7788 (tt0) cc_final: 0.7550 (pp20) REVERT: P 492 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7730 (m) REVERT: P 505 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6727 (ptt-90) REVERT: P 509 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7607 (mm-30) REVERT: P 557 GLU cc_start: 0.7759 (tp30) cc_final: 0.7324 (tp30) REVERT: P 560 LYS cc_start: 0.7716 (mttm) cc_final: 0.7421 (mtpp) REVERT: P 578 MET cc_start: 0.8328 (mmp) cc_final: 0.8095 (mmp) REVERT: P 584 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8313 (mmmt) REVERT: P 601 GLU cc_start: 0.7830 (mp0) cc_final: 0.7474 (mp0) REVERT: P 608 GLU cc_start: 0.7154 (mp0) cc_final: 0.6504 (mp0) REVERT: P 625 LYS cc_start: 0.8516 (mttm) cc_final: 0.8221 (mtmt) REVERT: P 629 ASP cc_start: 0.7872 (m-30) cc_final: 0.7635 (m-30) REVERT: P 652 ASP cc_start: 0.8454 (p0) cc_final: 0.8025 (p0) REVERT: P 663 ASN cc_start: 0.8049 (m110) cc_final: 0.7838 (m-40) REVERT: P 703 ARG cc_start: 0.7296 (mmt180) cc_final: 0.6961 (mmm-85) REVERT: P 712 ASP cc_start: 0.7823 (m-30) cc_final: 0.7591 (t0) REVERT: P 744 MET cc_start: 0.7400 (mtt) cc_final: 0.6842 (mmm) REVERT: P 771 ARG cc_start: 0.8059 (ttt90) cc_final: 0.7464 (tpm-80) REVERT: P 779 GLU cc_start: 0.7231 (pt0) cc_final: 0.6891 (pm20) REVERT: O 267 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7948 (tptp) REVERT: O 270 LYS cc_start: 0.8458 (pttt) cc_final: 0.8166 (pttt) REVERT: O 305 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (mttm) REVERT: O 342 GLN cc_start: 0.8284 (mp10) cc_final: 0.8009 (mp10) REVERT: O 401 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7479 (tm-30) REVERT: O 406 MET cc_start: 0.8155 (mmm) cc_final: 0.7387 (pp-130) REVERT: O 578 MET cc_start: 0.7300 (mpp) cc_final: 0.7084 (mpp) REVERT: O 584 LYS cc_start: 0.8201 (tppt) cc_final: 0.7606 (pttp) REVERT: O 587 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7480 (t) REVERT: O 660 MET cc_start: 0.7643 (mtm) cc_final: 0.7051 (ttm) REVERT: O 690 MET cc_start: 0.7670 (ptp) cc_final: 0.7458 (pmm) REVERT: O 734 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8530 (mmpt) REVERT: O 788 PHE cc_start: 0.7987 (t80) cc_final: 0.7359 (t80) REVERT: T 197 MET cc_start: 0.6873 (ppp) cc_final: 0.6656 (ppp) REVERT: T 223 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: T 564 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7667 (pp20) REVERT: T 569 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6999 (t70) REVERT: T 636 GLN cc_start: 0.7625 (mt0) cc_final: 0.7344 (mp10) REVERT: T 660 MET cc_start: 0.7902 (mmp) cc_final: 0.7352 (mmp) REVERT: T 693 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8094 (mtmt) REVERT: T 765 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7278 (mt) REVERT: T 806 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7913 (tm-30) REVERT: A 54 ASP cc_start: 0.7449 (m-30) cc_final: 0.6951 (m-30) REVERT: A 58 ASN cc_start: 0.8458 (m110) cc_final: 0.8199 (m110) REVERT: A 73 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8144 (mttp) REVERT: A 97 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: A 164 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8045 (mmp-170) REVERT: B 35 GLN cc_start: 0.7765 (mp10) cc_final: 0.7255 (mp10) REVERT: B 38 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: B 182 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7618 (ttm110) REVERT: B 187 ASP cc_start: 0.8096 (m-30) cc_final: 0.7676 (m-30) REVERT: C 59 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7804 (ttmm) REVERT: C 80 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7961 (p0) REVERT: C 164 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6926 (mmp-170) REVERT: C 167 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7081 (tp30) REVERT: D 136 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8042 (tp) REVERT: D 188 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6213 (ttt-90) REVERT: E 72 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7708 (mp0) REVERT: E 102 ASP cc_start: 0.8102 (m-30) cc_final: 0.7808 (m-30) REVERT: E 157 ARG cc_start: 0.7212 (tpp-160) cc_final: 0.6709 (tpt170) REVERT: E 167 GLU cc_start: 0.7276 (tp30) cc_final: 0.7069 (tp30) REVERT: E 178 GLU cc_start: 0.8072 (mp0) cc_final: 0.7689 (mp0) REVERT: E 205 MET cc_start: 0.7886 (ttm) cc_final: 0.7491 (ttp) REVERT: F 186 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.6440 (mpt90) REVERT: G 55 ASP cc_start: 0.7955 (t70) cc_final: 0.7628 (t0) REVERT: H 60 GLU cc_start: 0.7908 (mp0) cc_final: 0.7520 (mp0) REVERT: H 76 ASP cc_start: 0.7988 (m-30) cc_final: 0.7643 (m-30) REVERT: H 161 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7479 (tm-30) REVERT: H 171 GLU cc_start: 0.7524 (tt0) cc_final: 0.7285 (tt0) REVERT: H 175 ASN cc_start: 0.8229 (m-40) cc_final: 0.7877 (m-40) REVERT: I 76 ASP cc_start: 0.7830 (m-30) cc_final: 0.7557 (m-30) REVERT: I 176 GLU cc_start: 0.8074 (tp30) cc_final: 0.7677 (tm-30) REVERT: K 161 GLU cc_start: 0.8024 (pt0) cc_final: 0.7787 (pt0) REVERT: K 164 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7603 (ttm110) REVERT: K 176 GLU cc_start: 0.8137 (tp30) cc_final: 0.7910 (tm-30) REVERT: K 185 GLU cc_start: 0.6911 (tp30) cc_final: 0.6495 (mp0) REVERT: L 76 ASP cc_start: 0.7574 (m-30) cc_final: 0.7255 (m-30) REVERT: L 146 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8301 (ptp) REVERT: M 85 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7966 (tt0) REVERT: M 99 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8865 (t) REVERT: M 157 GLN cc_start: 0.8823 (pt0) cc_final: 0.8557 (pt0) REVERT: M 198 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7606 (tppt) REVERT: N 91 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7147 (mmm-85) REVERT: N 166 GLN cc_start: 0.8112 (mt0) cc_final: 0.7855 (mt0) REVERT: N 180 MET cc_start: 0.7691 (mtt) cc_final: 0.7396 (mmm) REVERT: N 207 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7749 (tttm) outliers start: 122 outliers final: 49 residues processed: 1049 average time/residue: 1.6586 time to fit residues: 2060.8747 Evaluate side-chains 1023 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 950 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 777 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 582 SER Chi-restraints excluded: chain Q residue 608 GLU Chi-restraints excluded: chain Q residue 633 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain P residue 223 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 388 ASP Chi-restraints excluded: chain P residue 389 ARG Chi-restraints excluded: chain P residue 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER 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 305 LYS 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 544 SER Chi-restraints excluded: chain T residue 569 ASP 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 765 LEU Chi-restraints excluded: chain A residue 97 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 C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain F residue 52 VAL 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 59 GLU 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 64 PHE Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain M residue 99 SER 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 207 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 193 optimal weight: 6.9990 chunk 517 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 337 optimal weight: 30.0000 chunk 141 optimal weight: 0.6980 chunk 575 optimal weight: 0.5980 chunk 477 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 190 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 700 GLN Q 795 HIS P 173 ASN P 692 ASN A 132 ASN B 58 ASN C 80 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 97 GLN E 154 HIS E 171 GLN E 179 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 48088 Z= 0.317 Angle : 0.616 15.577 64975 Z= 0.313 Chirality : 0.044 0.243 7482 Planarity : 0.004 0.085 8435 Dihedral : 8.389 152.846 6908 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.01 % Favored : 94.84 % Rotamer: Outliers : 3.07 % Allowed : 17.18 % Favored : 79.75 % 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: 1.77 (0.09), residues: 3164 sheet: 0.46 (0.18), residues: 751 loop : -0.76 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 189 HIS 0.008 0.001 HIS A 138 PHE 0.033 0.002 PHE O 565 TYR 0.023 0.002 TYR S 600 ARG 0.017 0.001 ARG R 502 *********************** 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 1122 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 967 time to evaluate : 4.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 206 ASN cc_start: 0.7238 (p0) cc_final: 0.6715 (p0) REVERT: S 239 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7346 (ttmt) REVERT: S 256 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7478 (ppp80) REVERT: S 270 LYS cc_start: 0.8036 (tmmt) cc_final: 0.7482 (tppt) REVERT: S 273 ARG cc_start: 0.7978 (tmm-80) cc_final: 0.7446 (tmm-80) REVERT: S 373 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: S 407 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7399 (tmm-80) REVERT: S 514 VAL cc_start: 0.8228 (t) cc_final: 0.8002 (p) REVERT: S 539 LYS cc_start: 0.8441 (mppt) cc_final: 0.8137 (mtpp) REVERT: S 571 ASP cc_start: 0.7802 (m-30) cc_final: 0.7344 (m-30) REVERT: S 584 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8316 (ptpp) REVERT: S 668 ASP cc_start: 0.8337 (t70) cc_final: 0.7890 (p0) REVERT: S 669 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7863 (mp) REVERT: S 693 LYS cc_start: 0.8146 (tppt) cc_final: 0.7804 (tppp) REVERT: S 696 ASP cc_start: 0.7838 (t0) cc_final: 0.7364 (m-30) REVERT: S 712 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: S 743 ASP cc_start: 0.7926 (t0) cc_final: 0.7162 (OUTLIER) REVERT: S 754 GLU cc_start: 0.7797 (tp30) cc_final: 0.7526 (mp0) REVERT: S 758 LYS cc_start: 0.8371 (tttm) cc_final: 0.8145 (mttp) REVERT: S 784 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7009 (mm-30) REVERT: S 813 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7484 (ttp-170) REVERT: S 815 GLU cc_start: 0.6303 (mm-30) cc_final: 0.6003 (mm-30) REVERT: R 194 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6987 (tm-30) REVERT: R 273 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.7177 (ttm110) REVERT: R 307 MET cc_start: 0.8023 (mtm) cc_final: 0.7804 (mtm) REVERT: R 406 MET cc_start: 0.8189 (tpt) cc_final: 0.7941 (tpt) REVERT: R 407 ARG cc_start: 0.7539 (tpm170) cc_final: 0.7329 (tpm170) REVERT: R 499 GLU cc_start: 0.7630 (pt0) cc_final: 0.7378 (pp20) REVERT: R 584 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8184 (mtpm) REVERT: R 640 ASP cc_start: 0.7796 (t0) cc_final: 0.6732 (t0) REVERT: R 642 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7823 (ptt180) REVERT: R 645 ASP cc_start: 0.7741 (t0) cc_final: 0.7414 (t0) REVERT: R 712 ASP cc_start: 0.7902 (m-30) cc_final: 0.7677 (m-30) REVERT: R 736 ASP cc_start: 0.8574 (t70) cc_final: 0.8275 (t70) REVERT: R 775 GLN cc_start: 0.8149 (tt0) cc_final: 0.7850 (tt0) REVERT: R 790 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7655 (tm-30) REVERT: R 804 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7283 (mm-30) REVERT: Q 192 GLU cc_start: 0.7833 (mp0) cc_final: 0.7626 (mp0) REVERT: Q 231 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7159 (ttpt) REVERT: Q 236 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8028 (mp0) REVERT: Q 312 GLU cc_start: 0.7568 (mp0) cc_final: 0.7313 (mp0) REVERT: Q 322 ASP cc_start: 0.7953 (m-30) cc_final: 0.7718 (m-30) REVERT: Q 325 ARG cc_start: 0.8192 (tmm160) cc_final: 0.7956 (ttp80) REVERT: Q 326 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8036 (ttmm) REVERT: Q 478 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: Q 482 GLU cc_start: 0.7436 (tp30) cc_final: 0.7187 (tm-30) REVERT: Q 499 GLU cc_start: 0.7520 (mp0) cc_final: 0.7191 (mp0) REVERT: Q 509 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7670 (mp0) REVERT: Q 564 GLU cc_start: 0.7861 (tt0) cc_final: 0.7596 (tt0) REVERT: Q 734 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7760 (mmtt) REVERT: Q 743 ASP cc_start: 0.7236 (t0) cc_final: 0.6528 (t70) REVERT: Q 747 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7620 (tm-30) REVERT: P 182 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8233 (mptt) REVERT: P 223 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: P 273 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8192 (tpm170) REVERT: P 310 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7727 (mmm160) REVERT: P 329 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7276 (mm-30) REVERT: P 389 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7423 (mtm-85) REVERT: P 401 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7971 (mm-30) REVERT: P 478 GLU cc_start: 0.7738 (tt0) cc_final: 0.7519 (pp20) REVERT: P 492 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7816 (m) REVERT: P 505 ARG cc_start: 0.7475 (ptt90) cc_final: 0.6368 (ptt-90) REVERT: P 509 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7654 (mp0) REVERT: P 557 GLU cc_start: 0.7705 (tp30) cc_final: 0.7242 (tp30) REVERT: P 560 LYS cc_start: 0.7732 (mttm) cc_final: 0.7443 (mtpp) REVERT: P 584 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8329 (mmmt) REVERT: P 601 GLU cc_start: 0.7875 (mp0) cc_final: 0.7529 (mp0) REVERT: P 605 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: P 608 GLU cc_start: 0.7074 (mp0) cc_final: 0.6431 (mp0) REVERT: P 625 LYS cc_start: 0.8625 (mttm) cc_final: 0.8313 (mtmt) REVERT: P 629 ASP cc_start: 0.7868 (m-30) cc_final: 0.7639 (m-30) REVERT: P 652 ASP cc_start: 0.8501 (p0) cc_final: 0.8066 (p0) REVERT: P 663 ASN cc_start: 0.8049 (m110) cc_final: 0.7847 (m-40) REVERT: P 703 ARG cc_start: 0.7387 (mmt180) cc_final: 0.7049 (mmm-85) REVERT: P 712 ASP cc_start: 0.7829 (m-30) cc_final: 0.7615 (t0) REVERT: P 744 MET cc_start: 0.7479 (mtt) cc_final: 0.6927 (mmm) REVERT: P 771 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7514 (tpm-80) REVERT: P 779 GLU cc_start: 0.7209 (pt0) cc_final: 0.6891 (pm20) REVERT: O 205 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7824 (ttmm) REVERT: O 267 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7974 (tptp) REVERT: O 270 LYS cc_start: 0.8463 (pttt) cc_final: 0.8168 (pttt) REVERT: O 342 GLN cc_start: 0.8307 (mp10) cc_final: 0.8017 (mp10) REVERT: O 401 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7501 (tm-30) REVERT: O 578 MET cc_start: 0.7376 (mpp) cc_final: 0.7095 (mpp) REVERT: O 584 LYS cc_start: 0.8210 (tppt) cc_final: 0.7629 (pptt) REVERT: O 587 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7525 (t) REVERT: O 660 MET cc_start: 0.7675 (mtm) cc_final: 0.7088 (ttm) REVERT: O 690 MET cc_start: 0.7730 (ptp) cc_final: 0.7497 (pmm) REVERT: O 734 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8561 (mmpt) REVERT: O 788 PHE cc_start: 0.8002 (t80) cc_final: 0.7377 (t80) REVERT: T 197 MET cc_start: 0.6797 (ppp) cc_final: 0.6540 (ppp) REVERT: T 223 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: T 348 LEU cc_start: 0.8223 (pp) cc_final: 0.7879 (tt) REVERT: T 564 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7687 (pp20) REVERT: T 569 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7135 (t70) REVERT: T 636 GLN cc_start: 0.7635 (mt0) cc_final: 0.7371 (mp10) REVERT: T 660 MET cc_start: 0.7917 (mmp) cc_final: 0.7218 (mmp) REVERT: T 693 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8087 (mtmt) REVERT: T 765 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7378 (mt) REVERT: T 806 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7908 (tm-30) REVERT: A 54 ASP cc_start: 0.7512 (m-30) cc_final: 0.7025 (m-30) REVERT: A 58 ASN cc_start: 0.8448 (m110) cc_final: 0.8208 (m110) REVERT: A 73 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8090 (mttp) REVERT: B 35 GLN cc_start: 0.7771 (mp10) cc_final: 0.7242 (mp10) REVERT: B 38 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7775 (m-40) REVERT: B 108 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8313 (ptt) REVERT: B 165 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.6912 (mpt) REVERT: B 182 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7660 (ttm110) REVERT: B 187 ASP cc_start: 0.8079 (m-30) cc_final: 0.7675 (m-30) REVERT: C 42 ASN cc_start: 0.8503 (m-40) cc_final: 0.8157 (m-40) REVERT: C 59 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7851 (ttmm) REVERT: C 164 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7028 (mmp-170) REVERT: C 167 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7073 (tp30) REVERT: D 136 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8094 (tp) REVERT: D 163 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: D 188 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6298 (ttt-90) REVERT: E 72 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7779 (mp0) REVERT: E 102 ASP cc_start: 0.8168 (m-30) cc_final: 0.7856 (m-30) REVERT: E 157 ARG cc_start: 0.7256 (tpp-160) cc_final: 0.6673 (tpt170) REVERT: E 178 GLU cc_start: 0.8058 (mp0) cc_final: 0.7662 (mp0) REVERT: E 205 MET cc_start: 0.7889 (ttm) cc_final: 0.7491 (ttp) REVERT: F 114 MET cc_start: 0.8254 (mmm) cc_final: 0.7981 (tpt) REVERT: F 186 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6470 (mpt90) REVERT: G 55 ASP cc_start: 0.8018 (t70) cc_final: 0.7664 (t0) REVERT: G 165 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: H 60 GLU cc_start: 0.7987 (mp0) cc_final: 0.7680 (mp0) REVERT: H 76 ASP cc_start: 0.8021 (m-30) cc_final: 0.7619 (m-30) REVERT: H 161 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 171 GLU cc_start: 0.7684 (tt0) cc_final: 0.7438 (tt0) REVERT: H 175 ASN cc_start: 0.8286 (m-40) cc_final: 0.7908 (m-40) REVERT: I 76 ASP cc_start: 0.7869 (m-30) cc_final: 0.7644 (m-30) REVERT: I 176 GLU cc_start: 0.8113 (tp30) cc_final: 0.7674 (tm-30) REVERT: K 161 GLU cc_start: 0.8045 (pt0) cc_final: 0.7815 (pt0) REVERT: K 164 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7625 (ttm110) REVERT: K 176 GLU cc_start: 0.8166 (tp30) cc_final: 0.7943 (tm-30) REVERT: K 185 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: L 76 ASP cc_start: 0.7599 (m-30) cc_final: 0.7260 (m-30) REVERT: L 87 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6118 (mpp) REVERT: L 115 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: L 146 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8335 (ptp) REVERT: M 85 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7991 (tt0) REVERT: M 99 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8890 (t) REVERT: M 160 SER cc_start: 0.8496 (t) cc_final: 0.8243 (t) REVERT: M 212 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: N 91 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7184 (mmm-85) REVERT: N 166 GLN cc_start: 0.8099 (mt0) cc_final: 0.7853 (mt0) REVERT: N 180 MET cc_start: 0.7692 (mtt) cc_final: 0.7383 (mmm) REVERT: N 190 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8048 (tttp) outliers start: 155 outliers final: 74 residues processed: 1045 average time/residue: 1.7396 time to fit residues: 2158.5429 Evaluate side-chains 1056 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 952 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 256 ARG Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 669 ILE Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 369 SER Chi-restraints excluded: chain R residue 531 THR Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 666 THR Chi-restraints excluded: chain R residue 729 ASP Chi-restraints excluded: chain R residue 746 ILE 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 582 SER Chi-restraints excluded: chain Q residue 584 LYS Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 223 GLU 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 389 ARG Chi-restraints excluded: chain P residue 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN 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 P residue 799 VAL Chi-restraints excluded: chain O residue 278 ILE 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 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 673 PHE 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 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 B residue 182 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 80 ASN 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 163 LYS 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 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 165 MET Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 160 SER 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 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 K residue 64 PHE Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 185 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 87 MET Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 117 VAL 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 190 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 555 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 420 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 484 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 573 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 O 795 HIS ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 132 ASN B 58 ASN C 80 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS E 38 ASN E 154 HIS E 179 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** N 222 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 48088 Z= 0.428 Angle : 0.672 14.372 64975 Z= 0.343 Chirality : 0.047 0.287 7482 Planarity : 0.005 0.088 8435 Dihedral : 8.492 141.615 6908 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.78 % Rotamer: Outliers : 3.27 % Allowed : 17.81 % Favored : 78.92 % 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: 0.82 (0.11), residues: 5991 helix: 1.55 (0.09), residues: 3170 sheet: 0.36 (0.18), residues: 731 loop : -0.94 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 189 HIS 0.012 0.001 HIS A 138 PHE 0.033 0.002 PHE O 565 TYR 0.021 0.002 TYR L 159 ARG 0.020 0.001 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 1136 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 971 time to evaluate : 4.289 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: 0.7257 (p0) cc_final: 0.6775 (p0) REVERT: S 239 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7324 (mttt) REVERT: S 270 LYS cc_start: 0.8052 (tmmt) cc_final: 0.7491 (tppt) REVERT: S 273 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7538 (tmm-80) REVERT: S 286 HIS cc_start: 0.7613 (p-80) cc_final: 0.7266 (p-80) REVERT: S 367 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6916 (mtm-85) REVERT: S 373 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7206 (pp20) REVERT: S 397 ASP cc_start: 0.7168 (m-30) cc_final: 0.6595 (m-30) REVERT: S 407 ARG cc_start: 0.7874 (ttt90) cc_final: 0.7443 (tmm-80) REVERT: S 514 VAL cc_start: 0.8253 (t) cc_final: 0.8007 (p) REVERT: S 539 LYS cc_start: 0.8407 (mppt) cc_final: 0.8085 (mtpp) REVERT: S 540 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7650 (mtm110) REVERT: S 571 ASP cc_start: 0.7853 (m-30) cc_final: 0.7403 (m-30) REVERT: S 584 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8320 (ptpp) REVERT: S 612 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7024 (mpt180) REVERT: S 636 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7400 (mp10) REVERT: S 668 ASP cc_start: 0.8315 (t70) cc_final: 0.7905 (p0) REVERT: S 669 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7872 (mp) REVERT: S 693 LYS cc_start: 0.8159 (tppt) cc_final: 0.7803 (tppp) REVERT: S 696 ASP cc_start: 0.7853 (t0) cc_final: 0.7371 (m-30) REVERT: S 712 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: S 743 ASP cc_start: 0.7926 (t0) cc_final: 0.7138 (t0) REVERT: S 754 GLU cc_start: 0.7814 (tp30) cc_final: 0.7522 (mp0) REVERT: S 758 LYS cc_start: 0.8368 (tttm) cc_final: 0.8139 (mttp) REVERT: S 784 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7031 (mm-30) REVERT: S 806 GLU cc_start: 0.7890 (mp0) cc_final: 0.7628 (tm-30) REVERT: S 815 GLU cc_start: 0.6462 (mm-30) cc_final: 0.6160 (mm-30) REVERT: R 194 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6995 (tm-30) REVERT: R 263 GLU cc_start: 0.7203 (tt0) cc_final: 0.6664 (tp30) REVERT: R 267 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6614 (mmtt) REVERT: R 273 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7195 (ttm110) REVERT: R 406 MET cc_start: 0.8192 (tpt) cc_final: 0.7976 (tpt) REVERT: R 499 GLU cc_start: 0.7677 (pt0) cc_final: 0.7385 (pp20) REVERT: R 584 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8183 (mtpm) REVERT: R 645 ASP cc_start: 0.7807 (t0) cc_final: 0.7470 (t0) REVERT: R 703 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7489 (mmm-85) REVERT: R 712 ASP cc_start: 0.7952 (m-30) cc_final: 0.7710 (m-30) REVERT: R 736 ASP cc_start: 0.8585 (t70) cc_final: 0.8270 (t70) REVERT: R 775 GLN cc_start: 0.8189 (tt0) cc_final: 0.7897 (tt0) REVERT: R 790 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7632 (tm-30) REVERT: R 804 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7252 (mm-30) REVERT: Q 191 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7424 (mtpp) REVERT: Q 236 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8053 (mp0) REVERT: Q 256 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7187 (tpp80) REVERT: Q 312 GLU cc_start: 0.7620 (mp0) cc_final: 0.7243 (mp0) REVERT: Q 322 ASP cc_start: 0.7959 (m-30) cc_final: 0.7724 (m-30) REVERT: Q 325 ARG cc_start: 0.8180 (tmm160) cc_final: 0.7930 (ttp80) REVERT: Q 326 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8022 (ttmm) REVERT: Q 478 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: Q 482 GLU cc_start: 0.7451 (tp30) cc_final: 0.7162 (tm-30) REVERT: Q 499 GLU cc_start: 0.7630 (mp0) cc_final: 0.7333 (mp0) REVERT: Q 509 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7693 (mp0) REVERT: Q 564 GLU cc_start: 0.7855 (tt0) cc_final: 0.7579 (tt0) REVERT: Q 734 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7760 (mmtt) REVERT: Q 743 ASP cc_start: 0.7207 (t0) cc_final: 0.6469 (t70) REVERT: Q 747 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7647 (tm-30) REVERT: P 182 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8220 (mptt) REVERT: P 223 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: P 240 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: P 273 ARG cc_start: 0.8451 (ttt90) cc_final: 0.8221 (tpm170) REVERT: P 307 MET cc_start: 0.8650 (ptp) cc_final: 0.8232 (ptp) REVERT: P 310 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7756 (mmm160) REVERT: P 326 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8186 (ttpp) REVERT: P 329 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7235 (mm-30) REVERT: P 401 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7957 (mm-30) REVERT: P 478 GLU cc_start: 0.7725 (tt0) cc_final: 0.7495 (pp20) REVERT: P 492 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (m) REVERT: P 505 ARG cc_start: 0.7463 (ptt90) cc_final: 0.7068 (ptt-90) REVERT: P 509 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7595 (mm-30) REVERT: P 560 LYS cc_start: 0.7703 (mttm) cc_final: 0.7449 (mtpp) REVERT: P 601 GLU cc_start: 0.7911 (mp0) cc_final: 0.7595 (mp0) REVERT: P 605 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: P 608 GLU cc_start: 0.7067 (mp0) cc_final: 0.6421 (mp0) REVERT: P 703 ARG cc_start: 0.7460 (mmt180) cc_final: 0.7220 (mmt180) REVERT: P 712 ASP cc_start: 0.7831 (m-30) cc_final: 0.7603 (t0) REVERT: P 733 ASP cc_start: 0.8078 (m-30) cc_final: 0.7711 (m-30) REVERT: P 744 MET cc_start: 0.7503 (mtt) cc_final: 0.6977 (mmm) REVERT: P 771 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7535 (tpm-80) REVERT: P 779 GLU cc_start: 0.7195 (pt0) cc_final: 0.6828 (pm20) REVERT: O 205 LYS cc_start: 0.8349 (mmpt) cc_final: 0.7801 (ttmm) REVERT: O 270 LYS cc_start: 0.8500 (pttt) cc_final: 0.8215 (pptt) REVERT: O 342 GLN cc_start: 0.8297 (mp10) cc_final: 0.8021 (mp10) REVERT: O 406 MET cc_start: 0.8211 (mmm) cc_final: 0.7439 (pp-130) REVERT: O 578 MET cc_start: 0.7439 (mpp) cc_final: 0.7096 (mpp) REVERT: O 584 LYS cc_start: 0.8227 (tppt) cc_final: 0.7766 (tmmt) REVERT: O 587 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7629 (t) REVERT: O 660 MET cc_start: 0.7694 (mtm) cc_final: 0.7104 (ttm) REVERT: O 690 MET cc_start: 0.7769 (ptp) cc_final: 0.7480 (pmm) REVERT: O 713 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8074 (t) REVERT: O 727 ILE cc_start: 0.8817 (mp) cc_final: 0.8579 (pp) REVERT: O 734 LYS cc_start: 0.8901 (mmtm) cc_final: 0.8577 (mmpt) REVERT: O 788 PHE cc_start: 0.8002 (t80) cc_final: 0.7354 (t80) REVERT: T 223 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: T 319 THR cc_start: 0.5171 (OUTLIER) cc_final: 0.4821 (p) REVERT: T 348 LEU cc_start: 0.8189 (pp) cc_final: 0.7851 (tt) REVERT: T 564 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7797 (tm-30) REVERT: T 569 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7111 (t70) REVERT: T 636 GLN cc_start: 0.7539 (mt0) cc_final: 0.7332 (mp10) REVERT: T 660 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7175 (mmp) REVERT: T 693 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8094 (mtmt) REVERT: T 806 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7919 (tm-30) REVERT: A 54 ASP cc_start: 0.7518 (m-30) cc_final: 0.7199 (m-30) REVERT: B 35 GLN cc_start: 0.7769 (mp10) cc_final: 0.7220 (mp10) REVERT: B 38 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7723 (m-40) REVERT: B 182 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7659 (ttm110) REVERT: B 187 ASP cc_start: 0.8066 (m-30) cc_final: 0.7670 (m-30) REVERT: C 42 ASN cc_start: 0.8533 (m-40) cc_final: 0.8182 (m-40) REVERT: C 54 ASP cc_start: 0.7378 (m-30) cc_final: 0.7163 (m-30) REVERT: C 59 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7863 (ttmm) REVERT: C 97 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6819 (mp10) REVERT: C 134 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 164 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7104 (mmp-170) REVERT: C 167 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7089 (tp30) REVERT: D 136 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8115 (tp) REVERT: D 156 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 163 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: D 188 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6260 (ttt-90) REVERT: E 72 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7826 (mp0) REVERT: E 102 ASP cc_start: 0.8190 (m-30) cc_final: 0.7857 (m-30) REVERT: E 157 ARG cc_start: 0.7297 (tpp-160) cc_final: 0.6713 (tpt170) REVERT: E 178 GLU cc_start: 0.8077 (mp0) cc_final: 0.7724 (mp0) REVERT: E 205 MET cc_start: 0.7883 (ttm) cc_final: 0.7484 (ttp) REVERT: F 163 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7958 (tmtp) REVERT: F 186 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6490 (mpt90) REVERT: H 60 GLU cc_start: 0.8011 (mp0) cc_final: 0.7761 (mp0) REVERT: H 76 ASP cc_start: 0.8022 (m-30) cc_final: 0.7595 (m-30) REVERT: H 161 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7511 (tm-30) REVERT: H 171 GLU cc_start: 0.7785 (tt0) cc_final: 0.7554 (tt0) REVERT: H 175 ASN cc_start: 0.8271 (m-40) cc_final: 0.7888 (m-40) REVERT: I 76 ASP cc_start: 0.7916 (m-30) cc_final: 0.7649 (m-30) REVERT: I 176 GLU cc_start: 0.8152 (tp30) cc_final: 0.7711 (tm-30) REVERT: K 115 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: K 161 GLU cc_start: 0.8050 (pt0) cc_final: 0.7844 (pm20) REVERT: K 164 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7644 (ttm110) REVERT: K 176 GLU cc_start: 0.8186 (tp30) cc_final: 0.7966 (tm-30) REVERT: K 185 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: L 76 ASP cc_start: 0.7633 (m-30) cc_final: 0.7285 (m-30) REVERT: L 87 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6305 (mpp) REVERT: L 146 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8222 (mtp) REVERT: M 85 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7987 (tt0) REVERT: M 99 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8937 (t) REVERT: M 160 SER cc_start: 0.8533 (t) cc_final: 0.8271 (t) REVERT: M 186 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: M 198 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7571 (tppt) REVERT: M 212 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: M 225 SER cc_start: 0.8546 (p) cc_final: 0.8316 (p) REVERT: N 91 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7254 (mmm-85) REVERT: N 180 MET cc_start: 0.7699 (mtt) cc_final: 0.7479 (mmm) outliers start: 165 outliers final: 78 residues processed: 1052 average time/residue: 1.6891 time to fit residues: 2108.4483 Evaluate side-chains 1059 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 947 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 367 ARG Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 634 LEU Chi-restraints excluded: chain S residue 669 ILE Chi-restraints excluded: chain S residue 712 ASP Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 369 SER Chi-restraints excluded: chain R residue 474 GLU Chi-restraints excluded: chain R residue 503 LEU Chi-restraints excluded: chain R residue 531 THR Chi-restraints excluded: chain R residue 575 SER Chi-restraints excluded: chain R residue 623 VAL Chi-restraints excluded: chain R residue 666 THR Chi-restraints excluded: chain R residue 729 ASP Chi-restraints excluded: chain R residue 746 ILE Chi-restraints excluded: chain Q residue 191 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 582 SER Chi-restraints excluded: chain Q residue 584 LYS Chi-restraints excluded: chain Q residue 671 LYS Chi-restraints excluded: chain Q residue 729 ASP Chi-restraints excluded: chain P residue 197 MET Chi-restraints excluded: chain P residue 223 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 240 ASP 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 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN Chi-restraints excluded: chain P residue 623 VAL Chi-restraints excluded: chain P residue 634 LEU Chi-restraints excluded: chain P residue 746 ILE Chi-restraints excluded: chain P residue 797 VAL Chi-restraints excluded: chain P residue 799 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 319 THR 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 A residue 35 GLN Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 97 GLN 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 163 LYS 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 163 LYS 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 160 SER Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 126 MET 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 171 GLU 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 185 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 87 MET Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 204 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 354 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 364 optimal weight: 0.9980 chunk 390 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 450 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 686 ASN R 692 ASN P 339 GLN P 692 ASN ** T 647 GLN ** 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 38 ASN E 97 GLN E 154 HIS E 171 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN I 231 ASN K 222 GLN L 75 ASN N 222 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 48088 Z= 0.203 Angle : 0.604 14.136 64975 Z= 0.306 Chirality : 0.042 0.239 7482 Planarity : 0.004 0.057 8435 Dihedral : 8.242 133.761 6908 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 2.30 % Allowed : 19.36 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.07 (0.11), residues: 5991 helix: 1.77 (0.09), residues: 3168 sheet: 0.45 (0.18), residues: 730 loop : -0.84 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 189 HIS 0.005 0.001 HIS A 138 PHE 0.030 0.001 PHE O 565 TYR 0.021 0.001 TYR L 159 ARG 0.013 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 1088 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 972 time to evaluate : 4.034 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: symmetry clash revert: symmetry clash REVERT: S 179 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7811 (mtm110) REVERT: S 239 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7389 (ttmt) REVERT: S 270 LYS cc_start: 0.8052 (tmmt) cc_final: 0.7492 (tppt) REVERT: S 273 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7510 (tmm-80) REVERT: S 303 ILE cc_start: 0.8236 (mt) cc_final: 0.8010 (mp) REVERT: S 305 LYS cc_start: 0.8748 (mmtp) cc_final: 0.8466 (tppt) REVERT: S 308 LEU cc_start: 0.8349 (mp) cc_final: 0.8131 (mp) REVERT: S 338 PHE cc_start: 0.7559 (m-10) cc_final: 0.7201 (m-80) REVERT: S 407 ARG cc_start: 0.7814 (ttt90) cc_final: 0.7470 (tmm-80) REVERT: S 514 VAL cc_start: 0.8211 (t) cc_final: 0.7981 (p) REVERT: S 539 LYS cc_start: 0.8410 (mppt) cc_final: 0.8103 (mtpp) REVERT: S 571 ASP cc_start: 0.7771 (m-30) cc_final: 0.7317 (m-30) REVERT: S 584 LYS cc_start: 0.8665 (ptpt) cc_final: 0.8308 (ptpp) REVERT: S 612 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7020 (mpt180) REVERT: S 668 ASP cc_start: 0.8286 (t70) cc_final: 0.7937 (p0) REVERT: S 669 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7965 (mp) REVERT: S 693 LYS cc_start: 0.8144 (tppt) cc_final: 0.7852 (tppp) REVERT: S 696 ASP cc_start: 0.7833 (t0) cc_final: 0.7378 (m-30) REVERT: S 743 ASP cc_start: 0.7928 (t0) cc_final: 0.7173 (t0) REVERT: S 754 GLU cc_start: 0.7772 (tp30) cc_final: 0.7500 (mp0) REVERT: S 758 LYS cc_start: 0.8337 (tttm) cc_final: 0.8112 (mttp) REVERT: S 779 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7185 (mt-10) REVERT: S 784 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6992 (mm-30) REVERT: S 806 GLU cc_start: 0.7927 (mp0) cc_final: 0.7620 (tm-30) REVERT: S 813 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7470 (ttp-170) REVERT: S 815 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6138 (mm-30) REVERT: R 194 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6980 (tm-30) REVERT: R 273 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.7188 (ttm110) REVERT: R 406 MET cc_start: 0.8217 (tpt) cc_final: 0.7959 (tpt) REVERT: R 407 ARG cc_start: 0.7553 (tpm170) cc_final: 0.7323 (tpm170) REVERT: R 499 GLU cc_start: 0.7676 (pt0) cc_final: 0.7470 (pp20) REVERT: R 584 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8184 (mtpm) REVERT: R 645 ASP cc_start: 0.7769 (t0) cc_final: 0.7421 (t0) REVERT: R 736 ASP cc_start: 0.8567 (t70) cc_final: 0.8291 (t70) REVERT: R 775 GLN cc_start: 0.8149 (tt0) cc_final: 0.7928 (tt0) REVERT: R 790 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7613 (tm-30) REVERT: R 804 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7221 (mm-30) REVERT: Q 236 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8043 (mp0) REVERT: Q 312 GLU cc_start: 0.7622 (mp0) cc_final: 0.7377 (mp0) REVERT: Q 322 ASP cc_start: 0.7948 (m-30) cc_final: 0.7721 (m-30) REVERT: Q 325 ARG cc_start: 0.8165 (tmm160) cc_final: 0.7918 (ttp80) REVERT: Q 326 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8052 (ttmm) REVERT: Q 478 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: Q 482 GLU cc_start: 0.7439 (tp30) cc_final: 0.7172 (tm-30) REVERT: Q 499 GLU cc_start: 0.7608 (mp0) cc_final: 0.7206 (mp0) REVERT: Q 509 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7657 (mp0) REVERT: Q 564 GLU cc_start: 0.7841 (tt0) cc_final: 0.7566 (tt0) REVERT: Q 734 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7818 (mttm) REVERT: Q 743 ASP cc_start: 0.7250 (t0) cc_final: 0.6501 (t70) REVERT: Q 747 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7608 (tm-30) REVERT: P 182 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8208 (mptt) REVERT: P 223 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: P 273 ARG cc_start: 0.8433 (ttt90) cc_final: 0.8196 (tpm170) REVERT: P 307 MET cc_start: 0.8627 (ptp) cc_final: 0.8254 (ptp) REVERT: P 310 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7744 (mmm160) REVERT: P 326 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8157 (ttpp) REVERT: P 329 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7264 (mm-30) REVERT: P 389 ARG cc_start: 0.8208 (ptp90) cc_final: 0.7448 (mtm-85) REVERT: P 401 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7978 (mm-30) REVERT: P 478 GLU cc_start: 0.7723 (tt0) cc_final: 0.7484 (pp20) REVERT: P 492 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7857 (m) REVERT: P 505 ARG cc_start: 0.7441 (ptt90) cc_final: 0.6781 (ptt-90) REVERT: P 509 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7633 (mm-30) REVERT: P 557 GLU cc_start: 0.7717 (tp30) cc_final: 0.7298 (tp30) REVERT: P 560 LYS cc_start: 0.7704 (mttm) cc_final: 0.7436 (mtpp) REVERT: P 601 GLU cc_start: 0.7910 (mp0) cc_final: 0.7586 (mp0) REVERT: P 605 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: P 608 GLU cc_start: 0.7128 (mp0) cc_final: 0.6457 (mp0) REVERT: P 625 LYS cc_start: 0.8692 (mttm) cc_final: 0.8404 (mtmt) REVERT: P 703 ARG cc_start: 0.7400 (mmt180) cc_final: 0.7115 (mmm-85) REVERT: P 712 ASP cc_start: 0.7785 (m-30) cc_final: 0.7585 (t0) REVERT: P 715 VAL cc_start: 0.8665 (t) cc_final: 0.8188 (p) REVERT: P 744 MET cc_start: 0.7495 (mtt) cc_final: 0.6977 (mmm) REVERT: P 771 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7524 (tpm-80) REVERT: P 779 GLU cc_start: 0.7251 (pt0) cc_final: 0.6926 (pm20) REVERT: O 270 LYS cc_start: 0.8472 (pttt) cc_final: 0.8160 (pptt) REVERT: O 342 GLN cc_start: 0.8290 (mp10) cc_final: 0.7965 (mp10) REVERT: O 401 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7502 (tm-30) REVERT: O 406 MET cc_start: 0.8175 (mmm) cc_final: 0.7381 (pp-130) REVERT: O 578 MET cc_start: 0.7453 (mpp) cc_final: 0.7150 (mpp) REVERT: O 584 LYS cc_start: 0.8235 (tppt) cc_final: 0.7634 (pttp) REVERT: O 587 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7756 (t) REVERT: O 660 MET cc_start: 0.7658 (mtm) cc_final: 0.7091 (ttm) REVERT: O 664 LEU cc_start: 0.6590 (tp) cc_final: 0.6375 (pp) REVERT: O 690 MET cc_start: 0.7714 (ptp) cc_final: 0.7467 (pmm) REVERT: O 713 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8059 (t) REVERT: O 727 ILE cc_start: 0.8818 (mp) cc_final: 0.8584 (pp) REVERT: O 734 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8562 (mmpt) REVERT: O 788 PHE cc_start: 0.7993 (t80) cc_final: 0.7367 (t80) REVERT: T 223 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: T 348 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7830 (tt) REVERT: T 564 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7671 (pp20) REVERT: T 569 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7120 (t70) REVERT: T 636 GLN cc_start: 0.7640 (mt0) cc_final: 0.7385 (mp10) REVERT: T 660 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7173 (mmp) REVERT: T 693 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8073 (mtmt) REVERT: T 765 LEU cc_start: 0.8047 (mm) cc_final: 0.7553 (mt) REVERT: T 806 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7878 (tm-30) REVERT: A 54 ASP cc_start: 0.7513 (m-30) cc_final: 0.7156 (m-30) REVERT: A 73 LYS cc_start: 0.8469 (mtpp) cc_final: 0.7985 (mttp) REVERT: B 35 GLN cc_start: 0.7755 (mp10) cc_final: 0.7300 (mp10) REVERT: B 38 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: B 182 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7646 (ttm110) REVERT: B 187 ASP cc_start: 0.8066 (m-30) cc_final: 0.7647 (m-30) REVERT: C 38 ASN cc_start: 0.7883 (t0) cc_final: 0.7670 (m-40) REVERT: C 42 ASN cc_start: 0.8478 (m-40) cc_final: 0.8103 (m-40) REVERT: C 59 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7838 (ttmm) REVERT: C 69 SER cc_start: 0.8280 (m) cc_final: 0.8026 (t) REVERT: C 80 ASN cc_start: 0.8522 (p0) cc_final: 0.8281 (p0) REVERT: C 134 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7301 (mm-30) REVERT: C 167 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7149 (tp30) REVERT: D 136 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8090 (tp) REVERT: D 188 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6218 (ttt-90) REVERT: E 72 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7811 (mp0) REVERT: E 102 ASP cc_start: 0.8129 (m-30) cc_final: 0.7805 (m-30) REVERT: E 157 ARG cc_start: 0.7215 (tpp-160) cc_final: 0.6686 (tpt170) REVERT: E 167 GLU cc_start: 0.7293 (tp30) cc_final: 0.7037 (tp30) REVERT: E 178 GLU cc_start: 0.8058 (mp0) cc_final: 0.7719 (mp0) REVERT: E 205 MET cc_start: 0.7875 (ttm) cc_final: 0.7474 (ttp) REVERT: F 163 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (tmtp) REVERT: F 186 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.6427 (mpt90) REVERT: H 60 GLU cc_start: 0.7949 (mp0) cc_final: 0.7634 (mp0) REVERT: H 76 ASP cc_start: 0.8016 (m-30) cc_final: 0.7627 (m-30) REVERT: H 161 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7539 (tm-30) REVERT: H 171 GLU cc_start: 0.7634 (tt0) cc_final: 0.7399 (tt0) REVERT: H 175 ASN cc_start: 0.8263 (m-40) cc_final: 0.7906 (m-40) REVERT: I 76 ASP cc_start: 0.7866 (m-30) cc_final: 0.7603 (m-30) REVERT: J 85 GLU cc_start: 0.8653 (tt0) cc_final: 0.8226 (tt0) REVERT: K 115 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: K 161 GLU cc_start: 0.8033 (pt0) cc_final: 0.7808 (pt0) REVERT: K 164 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7598 (ttm110) REVERT: K 176 GLU cc_start: 0.8120 (tp30) cc_final: 0.7897 (tm-30) REVERT: K 185 GLU cc_start: 0.7037 (tp30) cc_final: 0.6686 (mp0) REVERT: L 76 ASP cc_start: 0.7585 (m-30) cc_final: 0.7255 (m-30) REVERT: L 87 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6079 (mpp) REVERT: L 146 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8263 (ptp) REVERT: M 85 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7999 (tt0) REVERT: M 99 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8859 (t) REVERT: M 160 SER cc_start: 0.8479 (t) cc_final: 0.8223 (t) REVERT: M 198 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7567 (tppt) REVERT: N 91 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7179 (mmm-85) REVERT: N 166 GLN cc_start: 0.8147 (mt0) cc_final: 0.7859 (mt0) REVERT: N 180 MET cc_start: 0.7741 (mtt) cc_final: 0.7430 (mmm) outliers start: 116 outliers final: 55 residues processed: 1032 average time/residue: 1.7678 time to fit residues: 2185.8982 Evaluate side-chains 1027 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 951 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 669 ILE 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 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 582 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain P residue 223 GLU Chi-restraints excluded: chain P residue 238 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN 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 278 ILE 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 319 THR Chi-restraints excluded: chain T residue 348 LEU 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 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B 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 170 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 188 ARG 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 163 LYS 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 160 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 I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE 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 222 GLN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 521 optimal weight: 6.9990 chunk 549 optimal weight: 3.9990 chunk 501 optimal weight: 0.0270 chunk 534 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 419 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 482 optimal weight: 6.9990 chunk 505 optimal weight: 2.9990 chunk 532 optimal weight: 4.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 P 692 ASN O 511 HIS ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 58 ASN B 139 GLN C 80 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 154 HIS E 171 GLN E 179 GLN F 38 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN I 231 ASN K 222 GLN L 75 ASN N 222 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 48088 Z= 0.256 Angle : 0.635 14.928 64975 Z= 0.319 Chirality : 0.043 0.258 7482 Planarity : 0.004 0.072 8435 Dihedral : 8.177 125.050 6908 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.08 % Rotamer: Outliers : 2.28 % Allowed : 19.71 % Favored : 78.00 % 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: 1.04 (0.11), residues: 5991 helix: 1.76 (0.09), residues: 3159 sheet: 0.38 (0.18), residues: 740 loop : -0.83 (0.14), residues: 2092 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 0.030 0.001 PHE O 565 TYR 0.024 0.001 TYR S 600 ARG 0.016 0.000 ARG T 361 *********************** 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 1068 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 953 time to evaluate : 4.020 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 179 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7752 (mtm110) REVERT: S 239 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7427 (mttt) REVERT: S 270 LYS cc_start: 0.8040 (tmmt) cc_final: 0.7470 (tppt) REVERT: S 273 ARG cc_start: 0.8073 (tmm-80) cc_final: 0.7574 (tmm-80) REVERT: S 286 HIS cc_start: 0.7590 (p-80) cc_final: 0.7245 (p-80) REVERT: S 303 ILE cc_start: 0.8236 (mt) cc_final: 0.8017 (mp) REVERT: S 338 PHE cc_start: 0.7532 (m-10) cc_final: 0.7167 (m-80) REVERT: S 407 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7546 (tmm-80) REVERT: S 514 VAL cc_start: 0.8230 (t) cc_final: 0.8009 (p) REVERT: S 539 LYS cc_start: 0.8419 (mppt) cc_final: 0.8112 (mtpp) REVERT: S 540 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7612 (mtm180) REVERT: S 571 ASP cc_start: 0.7824 (m-30) cc_final: 0.7415 (m-30) REVERT: S 584 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8312 (ptpp) REVERT: S 612 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7039 (mpt180) REVERT: S 668 ASP cc_start: 0.8299 (t70) cc_final: 0.7811 (p0) REVERT: S 669 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7957 (mp) REVERT: S 673 PHE cc_start: 0.8380 (p90) cc_final: 0.8058 (p90) REVERT: S 693 LYS cc_start: 0.8148 (tppt) cc_final: 0.7823 (tppp) REVERT: S 696 ASP cc_start: 0.7855 (t0) cc_final: 0.7380 (m-30) REVERT: S 712 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: S 743 ASP cc_start: 0.7931 (t0) cc_final: 0.7163 (t0) REVERT: S 754 GLU cc_start: 0.7790 (tp30) cc_final: 0.7509 (mp0) REVERT: S 758 LYS cc_start: 0.8341 (tttm) cc_final: 0.8117 (mttp) REVERT: S 784 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7004 (mm-30) REVERT: S 806 GLU cc_start: 0.7920 (mp0) cc_final: 0.7616 (tm-30) REVERT: S 813 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7493 (ttp-170) REVERT: S 815 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6219 (mm-30) REVERT: R 194 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6984 (tm-30) REVERT: R 236 GLU cc_start: 0.8361 (pp20) cc_final: 0.8019 (pp20) REVERT: R 263 GLU cc_start: 0.7290 (tt0) cc_final: 0.6752 (tp30) REVERT: R 267 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6660 (mmtt) REVERT: R 273 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7203 (ttm110) REVERT: R 406 MET cc_start: 0.8196 (tpt) cc_final: 0.7943 (tpt) REVERT: R 499 GLU cc_start: 0.7678 (pt0) cc_final: 0.7468 (pp20) REVERT: R 584 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8189 (mtpm) REVERT: R 645 ASP cc_start: 0.7792 (t0) cc_final: 0.7432 (t0) REVERT: R 712 ASP cc_start: 0.7910 (m-30) cc_final: 0.7676 (m-30) REVERT: R 736 ASP cc_start: 0.8581 (t70) cc_final: 0.8312 (t70) REVERT: R 737 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7414 (pp20) REVERT: R 775 GLN cc_start: 0.8145 (tt0) cc_final: 0.7931 (tt0) REVERT: R 790 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7602 (tm-30) REVERT: R 804 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7220 (mm-30) REVERT: Q 236 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8043 (mp0) REVERT: Q 256 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7163 (tpp80) REVERT: Q 312 GLU cc_start: 0.7715 (mp0) cc_final: 0.7483 (mp0) REVERT: Q 322 ASP cc_start: 0.7939 (m-30) cc_final: 0.7722 (m-30) REVERT: Q 325 ARG cc_start: 0.8163 (tmm160) cc_final: 0.7909 (ttp80) REVERT: Q 326 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8047 (ttmm) REVERT: Q 478 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: Q 482 GLU cc_start: 0.7442 (tp30) cc_final: 0.7182 (tm-30) REVERT: Q 499 GLU cc_start: 0.7649 (mp0) cc_final: 0.7200 (mp0) REVERT: Q 509 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7658 (mp0) REVERT: Q 564 GLU cc_start: 0.7846 (tt0) cc_final: 0.7559 (tt0) REVERT: Q 691 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7901 (mtpt) REVERT: Q 697 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: Q 734 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7807 (mmtt) REVERT: Q 743 ASP cc_start: 0.7238 (t0) cc_final: 0.6464 (t70) REVERT: Q 747 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7613 (tm-30) REVERT: Q 790 GLU cc_start: 0.7557 (tt0) cc_final: 0.7132 (tm-30) REVERT: P 182 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8214 (mptt) REVERT: P 223 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: P 240 ASP cc_start: 0.8520 (m-30) cc_final: 0.8048 (m-30) REVERT: P 273 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8194 (tpm170) REVERT: P 307 MET cc_start: 0.8608 (ptp) cc_final: 0.8241 (ptp) REVERT: P 310 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7751 (mmm160) REVERT: P 326 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8142 (ttpp) REVERT: P 329 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7237 (mm-30) REVERT: P 389 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7420 (mtm-85) REVERT: P 401 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7979 (mm-30) REVERT: P 478 GLU cc_start: 0.7730 (tt0) cc_final: 0.7488 (pp20) REVERT: P 492 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (m) REVERT: P 505 ARG cc_start: 0.7449 (ptt90) cc_final: 0.6349 (ptt-90) REVERT: P 509 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7684 (mp0) REVERT: P 557 GLU cc_start: 0.7715 (tp30) cc_final: 0.7287 (tp30) REVERT: P 560 LYS cc_start: 0.7701 (mttm) cc_final: 0.7432 (mtpp) REVERT: P 601 GLU cc_start: 0.7915 (mp0) cc_final: 0.7564 (mp0) REVERT: P 605 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: P 608 GLU cc_start: 0.7073 (mp0) cc_final: 0.6383 (mp0) REVERT: P 625 LYS cc_start: 0.8700 (mttm) cc_final: 0.8444 (mtmt) REVERT: P 703 ARG cc_start: 0.7404 (mmt180) cc_final: 0.7137 (mmm-85) REVERT: P 715 VAL cc_start: 0.8667 (t) cc_final: 0.8184 (p) REVERT: P 744 MET cc_start: 0.7528 (mtt) cc_final: 0.7026 (mmm) REVERT: P 771 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7525 (tpm-80) REVERT: P 779 GLU cc_start: 0.7195 (pt0) cc_final: 0.6843 (pm20) REVERT: O 270 LYS cc_start: 0.8481 (pttt) cc_final: 0.8160 (pptt) REVERT: O 342 GLN cc_start: 0.8290 (mp10) cc_final: 0.7958 (mp10) REVERT: O 401 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7504 (tm-30) REVERT: O 406 MET cc_start: 0.8169 (mmm) cc_final: 0.7818 (mmp) REVERT: O 578 MET cc_start: 0.7388 (mpp) cc_final: 0.7071 (mpp) REVERT: O 584 LYS cc_start: 0.8246 (tppt) cc_final: 0.7778 (tmmt) REVERT: O 587 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7748 (t) REVERT: O 660 MET cc_start: 0.7665 (mtm) cc_final: 0.7087 (ttm) REVERT: O 664 LEU cc_start: 0.6614 (tp) cc_final: 0.6390 (pp) REVERT: O 690 MET cc_start: 0.7729 (ptp) cc_final: 0.7475 (pmm) REVERT: O 713 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8069 (t) REVERT: O 727 ILE cc_start: 0.8803 (mp) cc_final: 0.8577 (pp) REVERT: O 734 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8562 (mmpt) REVERT: O 788 PHE cc_start: 0.7996 (t80) cc_final: 0.7372 (t80) REVERT: T 223 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: T 348 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7824 (tt) REVERT: T 564 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7658 (pp20) REVERT: T 569 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7102 (t70) REVERT: T 660 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7196 (mmp) REVERT: T 693 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8072 (mtmt) REVERT: T 765 LEU cc_start: 0.8035 (mm) cc_final: 0.7563 (mt) REVERT: T 806 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7887 (tm-30) REVERT: A 54 ASP cc_start: 0.7453 (m-30) cc_final: 0.7156 (m-30) REVERT: A 73 LYS cc_start: 0.8481 (mtpp) cc_final: 0.7972 (mttp) REVERT: A 97 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: B 35 GLN cc_start: 0.7771 (mp10) cc_final: 0.7303 (mp10) REVERT: B 38 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7758 (m-40) REVERT: B 73 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7598 (mmpt) REVERT: B 182 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7647 (ttm110) REVERT: B 187 ASP cc_start: 0.8039 (m-30) cc_final: 0.7621 (m-30) REVERT: C 38 ASN cc_start: 0.7876 (t0) cc_final: 0.7647 (m-40) REVERT: C 42 ASN cc_start: 0.8498 (m-40) cc_final: 0.8127 (m-40) REVERT: C 59 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7856 (ttmm) REVERT: C 69 SER cc_start: 0.8294 (m) cc_final: 0.8041 (t) REVERT: C 134 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7287 (mm-30) REVERT: C 167 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7141 (tp30) REVERT: D 136 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 188 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6252 (ttt-90) REVERT: E 72 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7830 (mp0) REVERT: E 102 ASP cc_start: 0.8140 (m-30) cc_final: 0.7801 (m-30) REVERT: E 157 ARG cc_start: 0.7252 (tpp-160) cc_final: 0.6690 (tpt170) REVERT: E 178 GLU cc_start: 0.8065 (mp0) cc_final: 0.7695 (mp0) REVERT: E 205 MET cc_start: 0.7896 (ttm) cc_final: 0.7501 (ttp) REVERT: F 163 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7984 (tmtp) REVERT: F 186 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6438 (mpt90) REVERT: G 50 GLN cc_start: 0.8723 (pt0) cc_final: 0.8501 (pm20) REVERT: H 60 GLU cc_start: 0.7956 (mp0) cc_final: 0.7659 (mp0) REVERT: H 76 ASP cc_start: 0.8025 (m-30) cc_final: 0.7605 (m-30) REVERT: H 161 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7544 (tm-30) REVERT: H 171 GLU cc_start: 0.7662 (tt0) cc_final: 0.7433 (tt0) REVERT: H 175 ASN cc_start: 0.8278 (m-40) cc_final: 0.7922 (m-40) REVERT: I 76 ASP cc_start: 0.7878 (m-30) cc_final: 0.7610 (m-30) REVERT: J 85 GLU cc_start: 0.8654 (tt0) cc_final: 0.8248 (tt0) REVERT: K 115 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: K 161 GLU cc_start: 0.8043 (pt0) cc_final: 0.7830 (pt0) REVERT: K 164 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7606 (ttm110) REVERT: K 176 GLU cc_start: 0.8153 (tp30) cc_final: 0.7931 (tm-30) REVERT: K 185 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: L 76 ASP cc_start: 0.7603 (m-30) cc_final: 0.7248 (m-30) REVERT: L 115 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: L 146 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8308 (ptp) REVERT: M 85 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8010 (tt0) REVERT: M 99 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8855 (t) REVERT: M 154 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8460 (mm) REVERT: M 160 SER cc_start: 0.8487 (t) cc_final: 0.8228 (t) REVERT: M 198 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7584 (tppt) REVERT: N 91 ARG cc_start: 0.7618 (mtp85) cc_final: 0.7202 (mmm-85) REVERT: N 166 GLN cc_start: 0.8150 (mt0) cc_final: 0.7879 (mt0) REVERT: N 180 MET cc_start: 0.7747 (mtt) cc_final: 0.7477 (mmm) outliers start: 115 outliers final: 61 residues processed: 1018 average time/residue: 1.6662 time to fit residues: 2005.5052 Evaluate side-chains 1025 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 937 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 669 ILE 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 575 SER Chi-restraints excluded: chain R residue 623 VAL 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 582 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 223 GLU 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 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN 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 278 ILE 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 348 LEU 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 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B 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 170 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 44 ARG 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 163 LYS 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 160 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 I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE 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 185 GLU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 350 optimal weight: 6.9990 chunk 565 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 392 optimal weight: 0.8980 chunk 592 optimal weight: 2.9990 chunk 545 optimal weight: 1.9990 chunk 472 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 364 optimal weight: 0.3980 chunk 289 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 P 692 ASN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 132 ASN B 58 ASN C 179 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 97 GLN E 154 HIS E 171 GLN E 179 GLN F 38 ASN F 58 ASN F 171 GLN I 231 ASN K 222 GLN N 222 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3612 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= 0.203 Angle : 0.623 14.600 64975 Z= 0.312 Chirality : 0.043 0.510 7482 Planarity : 0.004 0.066 8435 Dihedral : 8.039 117.894 6908 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer: Outliers : 1.73 % Allowed : 20.37 % Favored : 77.91 % 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: 1.15 (0.11), residues: 5991 helix: 1.84 (0.09), residues: 3172 sheet: 0.44 (0.18), residues: 732 loop : -0.79 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 189 HIS 0.004 0.001 HIS A 138 PHE 0.029 0.001 PHE O 565 TYR 0.022 0.001 TYR L 159 ARG 0.015 0.000 ARG T 359 ********************** 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 1044 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 957 time to evaluate : 4.794 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 179 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7789 (mtm110) REVERT: S 239 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7459 (mttt) REVERT: S 270 LYS cc_start: 0.8028 (tmmt) cc_final: 0.7483 (tppt) REVERT: S 273 ARG cc_start: 0.8024 (tmm-80) cc_final: 0.7556 (tmm-80) REVERT: S 303 ILE cc_start: 0.8169 (mt) cc_final: 0.7956 (mp) REVERT: S 338 PHE cc_start: 0.7519 (m-10) cc_final: 0.7187 (m-80) REVERT: S 367 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7097 (mtm-85) REVERT: S 407 ARG cc_start: 0.7739 (ttt90) cc_final: 0.7506 (tmm-80) REVERT: S 514 VAL cc_start: 0.8188 (t) cc_final: 0.7971 (p) REVERT: S 539 LYS cc_start: 0.8433 (mppt) cc_final: 0.8132 (mtpp) REVERT: S 571 ASP cc_start: 0.7770 (m-30) cc_final: 0.7343 (m-30) REVERT: S 584 LYS cc_start: 0.8663 (ptpt) cc_final: 0.8266 (ptpp) REVERT: S 612 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7063 (mpt180) REVERT: S 668 ASP cc_start: 0.8279 (t70) cc_final: 0.7800 (p0) REVERT: S 669 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7957 (mp) REVERT: S 673 PHE cc_start: 0.8331 (p90) cc_final: 0.8121 (p90) REVERT: S 693 LYS cc_start: 0.8143 (tppt) cc_final: 0.7822 (tppp) REVERT: S 696 ASP cc_start: 0.7869 (t0) cc_final: 0.7395 (m-30) REVERT: S 712 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: S 743 ASP cc_start: 0.7935 (t0) cc_final: 0.7170 (t0) REVERT: S 754 GLU cc_start: 0.7768 (tp30) cc_final: 0.7504 (mp0) REVERT: S 758 LYS cc_start: 0.8341 (tttm) cc_final: 0.8125 (mttp) REVERT: S 779 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7198 (mt-10) REVERT: S 813 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7471 (ttp-170) REVERT: S 815 GLU cc_start: 0.6457 (mm-30) cc_final: 0.6199 (mm-30) REVERT: R 194 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6972 (tm-30) REVERT: R 258 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7310 (tmm-80) REVERT: R 263 GLU cc_start: 0.7257 (tt0) cc_final: 0.6677 (tp30) REVERT: R 267 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6582 (mmtt) REVERT: R 273 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7192 (ttm110) REVERT: R 307 MET cc_start: 0.8168 (mtm) cc_final: 0.7911 (mtm) REVERT: R 406 MET cc_start: 0.8211 (tpt) cc_final: 0.7976 (tpt) REVERT: R 584 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8169 (mtpm) REVERT: R 645 ASP cc_start: 0.7764 (t0) cc_final: 0.7416 (t0) REVERT: R 736 ASP cc_start: 0.8581 (t70) cc_final: 0.8334 (t70) REVERT: R 737 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7413 (pp20) REVERT: R 742 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7884 (ptp-110) REVERT: R 790 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7604 (tm-30) REVERT: R 804 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7203 (mm-30) REVERT: Q 236 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8075 (mp0) REVERT: Q 256 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7272 (tpp80) REVERT: Q 264 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7359 (mtt90) REVERT: Q 312 GLU cc_start: 0.7738 (mp0) cc_final: 0.7481 (mp0) REVERT: Q 322 ASP cc_start: 0.7933 (m-30) cc_final: 0.7694 (m-30) REVERT: Q 325 ARG cc_start: 0.8156 (tmm160) cc_final: 0.7904 (ttp80) REVERT: Q 326 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8110 (ttmm) REVERT: Q 476 ASP cc_start: 0.7369 (p0) cc_final: 0.7133 (p0) REVERT: Q 478 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: Q 482 GLU cc_start: 0.7395 (tp30) cc_final: 0.7081 (tm-30) REVERT: Q 499 GLU cc_start: 0.7648 (mp0) cc_final: 0.7183 (mp0) REVERT: Q 509 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7619 (mp0) REVERT: Q 532 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7955 (mmm160) REVERT: Q 564 GLU cc_start: 0.7839 (tt0) cc_final: 0.7558 (tt0) REVERT: Q 691 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7895 (mtpt) REVERT: Q 697 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: Q 734 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7806 (mmtt) REVERT: Q 743 ASP cc_start: 0.7269 (t0) cc_final: 0.6494 (t70) REVERT: Q 747 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7589 (tm-30) REVERT: P 182 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8208 (mptt) REVERT: P 223 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: P 273 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8194 (tpm170) REVERT: P 307 MET cc_start: 0.8596 (ptp) cc_final: 0.8229 (ptp) REVERT: P 310 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7742 (mmm160) REVERT: P 326 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8109 (ttpp) REVERT: P 329 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7276 (mm-30) REVERT: P 401 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7991 (mm-30) REVERT: P 478 GLU cc_start: 0.7731 (tt0) cc_final: 0.7495 (pp20) REVERT: P 492 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7826 (m) REVERT: P 505 ARG cc_start: 0.7458 (ptt90) cc_final: 0.6356 (ptt-90) REVERT: P 509 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7722 (mp0) REVERT: P 557 GLU cc_start: 0.7724 (tp30) cc_final: 0.7328 (tp30) REVERT: P 560 LYS cc_start: 0.7705 (mttm) cc_final: 0.7403 (mtpp) REVERT: P 601 GLU cc_start: 0.7885 (mp0) cc_final: 0.7544 (mp0) REVERT: P 605 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: P 608 GLU cc_start: 0.7093 (mp0) cc_final: 0.6440 (mp0) REVERT: P 625 LYS cc_start: 0.8676 (mttm) cc_final: 0.8384 (mtmt) REVERT: P 703 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7052 (mmm-85) REVERT: P 715 VAL cc_start: 0.8681 (t) cc_final: 0.8209 (p) REVERT: P 744 MET cc_start: 0.7550 (mtt) cc_final: 0.7045 (mmm) REVERT: P 771 ARG cc_start: 0.8095 (ttt90) cc_final: 0.7535 (tpm-80) REVERT: P 779 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: O 270 LYS cc_start: 0.8388 (pttt) cc_final: 0.8012 (pptt) REVERT: O 342 GLN cc_start: 0.8300 (mp10) cc_final: 0.7961 (mp10) REVERT: O 401 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7509 (tm-30) REVERT: O 406 MET cc_start: 0.8134 (mmm) cc_final: 0.7783 (mmp) REVERT: O 578 MET cc_start: 0.7393 (mpp) cc_final: 0.7091 (mpp) REVERT: O 584 LYS cc_start: 0.8268 (tppt) cc_final: 0.7599 (pttp) REVERT: O 660 MET cc_start: 0.7619 (mtm) cc_final: 0.7048 (ttm) REVERT: O 664 LEU cc_start: 0.6642 (tp) cc_final: 0.6430 (pp) REVERT: O 690 MET cc_start: 0.7685 (ptp) cc_final: 0.7428 (pmm) REVERT: O 713 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8093 (t) REVERT: O 727 ILE cc_start: 0.8780 (mp) cc_final: 0.8558 (pp) REVERT: O 734 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8549 (mmpt) REVERT: O 788 PHE cc_start: 0.8000 (t80) cc_final: 0.7377 (t80) REVERT: T 223 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8295 (mm-30) REVERT: T 348 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7833 (tt) REVERT: T 564 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7638 (pp20) REVERT: T 569 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7083 (t70) REVERT: T 660 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7255 (mmp) REVERT: T 693 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8063 (mtmt) REVERT: T 765 LEU cc_start: 0.8001 (mm) cc_final: 0.7556 (mt) REVERT: T 806 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7856 (tm-30) REVERT: A 54 ASP cc_start: 0.7436 (m-30) cc_final: 0.6993 (m-30) REVERT: A 58 ASN cc_start: 0.8417 (m110) cc_final: 0.8190 (m110) REVERT: A 73 LYS cc_start: 0.8473 (mtpp) cc_final: 0.7983 (mttp) REVERT: B 35 GLN cc_start: 0.7758 (mp10) cc_final: 0.7294 (mp10) REVERT: B 38 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7768 (m-40) REVERT: B 73 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7610 (mmpt) REVERT: B 182 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7629 (ttm110) REVERT: B 187 ASP cc_start: 0.8068 (m-30) cc_final: 0.7645 (m-30) REVERT: C 59 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7795 (ttmm) REVERT: C 69 SER cc_start: 0.8289 (m) cc_final: 0.8044 (t) REVERT: C 134 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7311 (mm-30) REVERT: C 167 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7120 (tp30) REVERT: D 136 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8129 (tp) REVERT: D 188 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6294 (ttt-90) REVERT: D 198 TYR cc_start: 0.8507 (t80) cc_final: 0.8212 (t80) REVERT: E 72 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7827 (mp0) REVERT: E 102 ASP cc_start: 0.8117 (m-30) cc_final: 0.7785 (m-30) REVERT: E 157 ARG cc_start: 0.7200 (tpp-160) cc_final: 0.6647 (tpt170) REVERT: E 167 GLU cc_start: 0.7260 (tp30) cc_final: 0.7009 (tp30) REVERT: E 178 GLU cc_start: 0.8099 (mp0) cc_final: 0.7701 (mp0) REVERT: E 205 MET cc_start: 0.7899 (ttm) cc_final: 0.7500 (ttp) REVERT: F 163 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7884 (tmtp) REVERT: F 186 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.6410 (mpt90) REVERT: H 60 GLU cc_start: 0.7932 (mp0) cc_final: 0.7592 (mp0) REVERT: H 76 ASP cc_start: 0.8013 (m-30) cc_final: 0.7637 (m-30) REVERT: H 85 GLU cc_start: 0.8881 (tt0) cc_final: 0.8470 (tt0) REVERT: H 161 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7544 (tm-30) REVERT: H 171 GLU cc_start: 0.7572 (tt0) cc_final: 0.7332 (tt0) REVERT: H 175 ASN cc_start: 0.8264 (m-40) cc_final: 0.7909 (m-40) REVERT: I 76 ASP cc_start: 0.7872 (m-30) cc_final: 0.7612 (m-30) REVERT: K 115 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: K 161 GLU cc_start: 0.8038 (pt0) cc_final: 0.7833 (pt0) REVERT: K 164 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7589 (ttm110) REVERT: K 176 GLU cc_start: 0.8142 (tp30) cc_final: 0.7916 (tm-30) REVERT: K 185 GLU cc_start: 0.6998 (tp30) cc_final: 0.6638 (mp0) REVERT: L 76 ASP cc_start: 0.7590 (m-30) cc_final: 0.7245 (m-30) REVERT: L 146 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8275 (ptp) REVERT: L 212 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7351 (mp0) REVERT: M 85 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8020 (tt0) REVERT: M 99 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8871 (t) REVERT: M 154 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8451 (mm) REVERT: M 157 GLN cc_start: 0.8779 (pt0) cc_final: 0.8572 (pt0) REVERT: M 198 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7579 (tppt) REVERT: N 91 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7185 (mmm-85) REVERT: N 166 GLN cc_start: 0.8153 (mt0) cc_final: 0.7867 (mt0) REVERT: N 180 MET cc_start: 0.7735 (mtt) cc_final: 0.7446 (mmm) outliers start: 87 outliers final: 55 residues processed: 1005 average time/residue: 1.7026 time to fit residues: 2018.5682 Evaluate side-chains 1030 residues out of total 5043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 951 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain S residue 612 ARG Chi-restraints excluded: chain S residue 669 ILE 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 746 ILE 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 582 SER Chi-restraints excluded: chain Q residue 669 ILE Chi-restraints excluded: chain Q residue 697 GLU Chi-restraints excluded: chain P residue 223 GLU 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 492 VAL Chi-restraints excluded: chain P residue 493 PHE Chi-restraints excluded: chain P residue 501 SER Chi-restraints excluded: chain P residue 605 GLN 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 779 GLU Chi-restraints excluded: chain P residue 797 VAL 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 348 LEU 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 634 LEU Chi-restraints excluded: chain T residue 657 VAL Chi-restraints excluded: chain T residue 660 MET Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B 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 170 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 44 ARG 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 163 LYS 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 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 I residue 199 ILE Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain J residue 64 PHE 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 222 GLN Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 146 MET Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 374 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 chunk 144 optimal weight: 0.0270 chunk 435 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 472 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 227 GLN S 342 GLN S 686 ASN R 692 ASN R 775 GLN Q 700 GLN P 173 ASN T 636 GLN ** T 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 58 ASN E 154 HIS E 171 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 58 ASN F 171 GLN ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN K 222 GLN 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 = 0.123129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.094295 restraints weight = 78678.058| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.86 r_work: 0.3519 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 48088 Z= 0.255 Angle : 0.685 59.175 64975 Z= 0.361 Chirality : 0.044 0.922 7482 Planarity : 0.004 0.064 8435 Dihedral : 8.036 117.837 6908 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 1.88 % Allowed : 20.67 % Favored : 77.45 % Cbeta Deviations : 0.02 % 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: 1.15 (0.11), residues: 5991 helix: 1.85 (0.09), residues: 3172 sheet: 0.44 (0.18), residues: 732 loop : -0.79 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.004 0.001 HIS A 138 PHE 0.027 0.001 PHE O 565 TYR 0.021 0.001 TYR L 159 ARG 0.015 0.000 ARG P 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28559.26 seconds wall clock time: 491 minutes 28.03 seconds (29488.03 seconds total)