Starting phenix.real_space_refine on Sun Sep 29 22:48:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/09_2024/7uj0_26559_trim.cif" } resolution = 3.26 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 31 5.49 5 Mg 9 5.21 5 S 169 5.16 5 C 23836 2.51 5 N 6725 2.21 5 O 7236 1.98 5 H 38308 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76314 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9101 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9140 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9152 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9142 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9143 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9130 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} Chain: "S" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 179 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "H" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "N" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.09, per 1000 atoms: 0.37 Number of scatterers: 76314 At special positions: 0 Unit cell: (151.38, 151.38, 164.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 169 16.00 P 31 15.00 Mg 9 11.99 O 7236 8.00 N 6725 7.00 C 23836 6.00 H 38308 1.00 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: 15.00 Conformation dependent library (CDL) restraints added in 4.8 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8908 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 47 sheets defined 56.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.844A pdb=" N VAL A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.763A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.850A pdb=" N ASP A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 261 through 275 Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.257A pdb=" N GLY A 292 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.568A pdb=" N ILE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.932A pdb=" N SER A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.689A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 350 through 370 removed outlier: 3.867A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix removed outlier: 4.119A pdb=" N HIS A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 389 removed outlier: 4.095A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 411 Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.649A pdb=" N ILE A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.893A pdb=" N THR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.517A pdb=" N GLU A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.878A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.918A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.540A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.292A pdb=" N PHE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.683A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.512A pdb=" N ARG A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 removed outlier: 4.024A pdb=" N ASP A 663 " --> pdb=" O HIS A 659 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 664 " --> pdb=" O GLN A 660 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 removed outlier: 3.519A pdb=" N TRP A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 4.106A pdb=" N ALA A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.658A pdb=" N LEU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.726A pdb=" N VAL B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 234 removed outlier: 3.555A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.046A pdb=" N ASP B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 4.496A pdb=" N GLY B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.698A pdb=" N GLY B 292 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Proline residue: B 309 - end of helix removed outlier: 3.632A pdb=" N SER B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 350 through 370 removed outlier: 3.662A pdb=" N GLN B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.529A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 411 Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.662A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 452 Processing helix chain 'B' and resid 463 through 480 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.903A pdb=" N ARG B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 565 through 570 removed outlier: 5.795A pdb=" N HIS B 570 " --> pdb=" O GLU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.793A pdb=" N ASN B 575 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 636 removed outlier: 3.524A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 654 through 675 removed outlier: 3.693A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.711A pdb=" N ALA B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.570A pdb=" N LEU B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 719 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.512A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 261 through 278 Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.639A pdb=" N GLY C 292 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.591A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 370 removed outlier: 3.594A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'C' and resid 393 through 411 removed outlier: 3.697A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 463 through 480 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.566A pdb=" N SER C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.606A pdb=" N SER C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 556 Processing helix chain 'C' and resid 566 through 570 removed outlier: 5.488A pdb=" N HIS C 570 " --> pdb=" O GLU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.617A pdb=" N ASN C 575 " --> pdb=" O PRO C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 583 Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.571A pdb=" N ALA C 628 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 Processing helix chain 'C' and resid 654 through 677 removed outlier: 3.713A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 695 Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.860A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.522A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 219 through 234 removed outlier: 3.889A pdb=" N ALA D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D 233 " --> pdb=" O TRP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 261 through 278 removed outlier: 3.505A pdb=" N GLN D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.911A pdb=" N ILE D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 Proline residue: D 309 - end of helix removed outlier: 3.574A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.593A pdb=" N ARG D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.708A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 393 through 412 removed outlier: 3.560A pdb=" N MET D 412 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 435 removed outlier: 3.725A pdb=" N ILE D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 451 removed outlier: 3.597A pdb=" N THR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 460 removed outlier: 3.560A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 479 removed outlier: 3.736A pdb=" N ILE D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.640A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.618A pdb=" N SER D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.961A pdb=" N ASN D 575 " --> pdb=" O PRO D 571 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 577 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 Processing helix chain 'D' and resid 626 through 636 removed outlier: 3.832A pdb=" N GLU D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 654 through 677 removed outlier: 3.550A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.877A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.975A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 727 removed outlier: 4.063A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.555A pdb=" N VAL E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 219 through 234 removed outlier: 3.678A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 261 through 277 Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.999A pdb=" N ILE E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 287 through 292' Processing helix chain 'E' and resid 302 through 314 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.598A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 370 removed outlier: 3.693A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.778A pdb=" N ARG E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 412 Processing helix chain 'E' and resid 422 through 435 Processing helix chain 'E' and resid 445 through 451 removed outlier: 3.818A pdb=" N LEU E 449 " --> pdb=" O ASP E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 460 Processing helix chain 'E' and resid 463 through 479 removed outlier: 3.644A pdb=" N ILE E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 513 removed outlier: 3.528A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 534 removed outlier: 3.844A pdb=" N SER E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG E 532 " --> pdb=" O HIS E 528 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE E 534 " --> pdb=" O VAL E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 556 removed outlier: 3.739A pdb=" N ILE E 554 " --> pdb=" O THR E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 584 removed outlier: 3.782A pdb=" N PHE E 574 " --> pdb=" O HIS E 570 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 4.383A pdb=" N ARG E 610 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 636 Processing helix chain 'E' and resid 637 through 644 Processing helix chain 'E' and resid 654 through 677 removed outlier: 3.677A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 662 " --> pdb=" O ILE E 658 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 672 " --> pdb=" O GLU E 668 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 695 Processing helix chain 'E' and resid 701 through 722 removed outlier: 3.768A pdb=" N ALA E 705 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 709 " --> pdb=" O ALA E 705 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 714 " --> pdb=" O ASP E 710 " (cutoff:3.500A) Proline residue: E 715 - end of helix removed outlier: 4.009A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 727 removed outlier: 3.810A pdb=" N ASP E 727 " --> pdb=" O SER E 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.744A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 219 through 234 removed outlier: 3.758A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 removed outlier: 4.092A pdb=" N ASP F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 3.641A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 277 removed outlier: 3.900A pdb=" N ASP F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 303 through 314 removed outlier: 3.610A pdb=" N ILE F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Proline residue: F 309 - end of helix Processing helix chain 'F' and resid 323 through 331 Processing helix chain 'F' and resid 334 through 340 removed outlier: 3.978A pdb=" N ARG F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 370 removed outlier: 3.618A pdb=" N GLN F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Proline residue: F 363 - end of helix removed outlier: 3.591A pdb=" N HIS F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 Processing helix chain 'F' and resid 393 through 412 removed outlier: 3.652A pdb=" N ILE F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.694A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 Processing helix chain 'F' and resid 444 through 460 removed outlier: 4.104A pdb=" N GLY F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 459 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 479 removed outlier: 3.994A pdb=" N ILE F 467 " --> pdb=" O GLN F 463 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 513 removed outlier: 4.255A pdb=" N GLU F 503 " --> pdb=" O VAL F 499 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 534 removed outlier: 4.015A pdb=" N SER F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU F 533 " --> pdb=" O THR F 529 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 534 " --> pdb=" O VAL F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 556 Processing helix chain 'F' and resid 570 through 583 removed outlier: 3.545A pdb=" N GLN F 579 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 removed outlier: 3.604A pdb=" N ARG F 610 " --> pdb=" O ASN F 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.019A pdb=" N GLU F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE F 632 " --> pdb=" O ALA F 628 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 644 removed outlier: 3.845A pdb=" N ARG F 641 " --> pdb=" O THR F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 677 removed outlier: 3.640A pdb=" N ILE F 658 " --> pdb=" O SER F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 703 through 721 removed outlier: 3.731A pdb=" N GLN F 709 " --> pdb=" O ALA F 705 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU F 712 " --> pdb=" O ILE F 708 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.974A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 721 " --> pdb=" O ALA F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 727 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.875A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.581A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.694A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 131 through 158 removed outlier: 3.610A pdb=" N ILE H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.706A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.568A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.699A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 131 through 158 Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 176 through 183 removed outlier: 3.555A pdb=" N VAL I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.698A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.600A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 104 Processing helix chain 'J' and resid 131 through 158 Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 175 through 183 Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.564A pdb=" N GLY K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 106 removed outlier: 3.519A pdb=" N GLY K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 158 Processing helix chain 'K' and resid 160 through 170 removed outlier: 4.379A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.610A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.691A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.690A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.576A pdb=" N GLY L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 158 Processing helix chain 'L' and resid 160 through 169 Processing helix chain 'L' and resid 176 through 183 removed outlier: 3.510A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU L 181 " --> pdb=" O PRO L 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.748A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 82 removed outlier: 3.856A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 104 Processing helix chain 'M' and resid 131 through 158 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.668A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.635A pdb=" N GLY N 73 " --> pdb=" O VAL N 69 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 106 removed outlier: 3.615A pdb=" N LEU N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 158 removed outlier: 3.517A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 170 removed outlier: 4.483A pdb=" N ARG N 170 " --> pdb=" O ARG N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 183 removed outlier: 3.758A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.557A pdb=" N THR A 174 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 247 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR A 246 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 515 through 520 removed outlier: 3.791A pdb=" N ASP A 564 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 600 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY A 489 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N MET A 603 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE A 491 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 605 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 493 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 648 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 492 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 681 removed outlier: 6.457A pdb=" N SER A 679 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL A 733 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU A 681 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 735 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.785A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG B 317 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 282 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 321 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 322 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN B 209 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE B 344 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 211 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.774A pdb=" N ARG B 372 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 516 through 520 removed outlier: 6.628A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 564 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE B 519 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.833A pdb=" N GLU B 681 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N LEU B 735 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.397A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG C 317 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 373 removed outlier: 6.473A pdb=" N ARG C 372 " --> pdb=" O VAL C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 490 through 494 removed outlier: 6.438A pdb=" N PHE C 491 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR C 605 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE C 493 " --> pdb=" O THR C 605 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 585 through 587 removed outlier: 3.591A pdb=" N LEU C 586 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 680 through 682 removed outlier: 3.624A pdb=" N ASP C 736 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.268A pdb=" N TYR D 246 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP D 285 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU D 248 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR D 322 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU D 212 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU D 211 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE D 346 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 213 " --> pdb=" O ILE D 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 372 through 373 removed outlier: 7.133A pdb=" N ARG D 372 " --> pdb=" O VAL D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 489 through 494 removed outlier: 4.129A pdb=" N GLY D 489 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AB8, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.561A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 174 through 175 removed outlier: 6.403A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 320 through 323 removed outlier: 3.666A pdb=" N THR E 322 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 372 through 373 removed outlier: 7.136A pdb=" N ARG E 372 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 515 through 520 removed outlier: 6.545A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 585 through 587 Processing sheet with id=AC5, first strand: chain 'E' and resid 733 through 736 removed outlier: 3.948A pdb=" N GLU E 741 " --> pdb=" O ASP E 736 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 174 through 175 removed outlier: 6.643A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG F 317 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 321 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU F 212 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU F 211 " --> pdb=" O ILE F 344 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 489 through 493 removed outlier: 5.387A pdb=" N GLY F 489 " --> pdb=" O LEU F 601 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N MET F 603 " --> pdb=" O GLY F 489 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE F 491 " --> pdb=" O MET F 603 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR F 604 " --> pdb=" O LEU F 563 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU F 517 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP F 564 " --> pdb=" O LEU F 517 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE F 519 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 678 through 682 removed outlier: 6.669A pdb=" N SER F 679 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL F 733 " --> pdb=" O SER F 679 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU F 681 " --> pdb=" O VAL F 733 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 734 " --> pdb=" O THR F 743 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AD1, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.661A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER H 187 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS H 113 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.120A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.404A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG I 111 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.242A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD7, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.841A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 94 through 95 removed outlier: 6.107A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE1, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.284A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 94 through 95 removed outlier: 6.307A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 9 removed outlier: 3.570A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.708A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS L 113 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 94 through 95 Processing sheet with id=AE6, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AE7, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.690A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 118 through 121 Processing sheet with id=AE9, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AF1, first strand: chain 'N' and resid 28 through 29 removed outlier: 6.926A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 119 through 121 1790 hydrogen bonds defined for protein. 5268 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: 30.30 Time building geometry restraints manager: 18.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38282 1.06 - 1.28: 6539 1.28 - 1.50: 15836 1.50 - 1.73: 15932 1.73 - 1.95: 305 Bond restraints: 76894 Sorted by residual: bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 802 " pdb=" C5 ADP E 802 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 802 " pdb=" C5 ADP A 802 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C4 ADP F 802 " pdb=" C5 ADP F 802 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 76889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 138094 2.48 - 4.96: 1098 4.96 - 7.44: 123 7.44 - 9.92: 33 9.92 - 12.39: 22 Bond angle restraints: 139370 Sorted by residual: angle pdb=" PA ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sigma weight residual 120.50 132.89 -12.39 3.00e+00 1.11e-01 1.71e+01 angle pdb=" PA ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sigma weight residual 120.50 132.72 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" PA ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PB ADP F 802 " ideal model delta sigma weight residual 120.50 132.44 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" PB AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 120.12 132.02 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PB AGS C 802 " pdb=" O3B AGS C 802 " pdb=" PG AGS C 802 " ideal model delta sigma weight residual 120.12 132.00 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 139365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 34113 28.42 - 56.85: 1342 56.85 - 85.27: 132 85.27 - 113.69: 12 113.69 - 142.12: 14 Dihedral angle restraints: 35613 sinusoidal: 20094 harmonic: 15519 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 74.16 -134.15 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual 300.00 166.98 133.02 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 62.98 -122.98 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 35610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4451 0.045 - 0.091: 1210 0.091 - 0.136: 288 0.136 - 0.182: 27 0.182 - 0.227: 5 Chirality restraints: 5981 Sorted by residual: chirality pdb=" C3' ADP E 801 " pdb=" C2' ADP E 801 " pdb=" C4' ADP E 801 " pdb=" O3' ADP E 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3' ADP F 802 " pdb=" C2' ADP F 802 " pdb=" C4' ADP F 802 " pdb=" O3' ADP F 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3' ADP A 802 " pdb=" C2' ADP A 802 " pdb=" C4' ADP A 802 " pdb=" O3' ADP A 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5978 not shown) Planarity restraints: 11378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 436 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO F 437 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 437 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 437 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 465 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.83e+00 pdb=" C LYS E 465 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS E 465 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA E 466 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 570 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 571 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " -0.033 5.00e-02 4.00e+02 ... (remaining 11375 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 8479 2.25 - 2.84: 176011 2.84 - 3.42: 199634 3.42 - 4.01: 275878 4.01 - 4.60: 427395 Nonbonded interactions: 1087397 Sorted by model distance: nonbonded pdb=" HG1 THR B 221 " pdb="MG MG B 803 " model vdw 1.659 1.700 nonbonded pdb=" O TYR F 246 " pdb=" H PHE F 283 " model vdw 1.689 2.450 nonbonded pdb=" HG1 THR M 89 " pdb=" O LEU M 103 " model vdw 1.693 2.450 nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.694 2.450 nonbonded pdb=" OE1 GLU E 192 " pdb=" H GLU E 192 " model vdw 1.695 2.450 ... (remaining 1087392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 501 or (resid 50 \ 2 and (name N or name CA or name C or name O or name CB or name OG1 or name CG2 \ or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resi \ d 503 through 748)) selection = (chain 'B' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 222 through 748)) selection = (chain 'C' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 748)) selection = (chain 'D' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 748)) selection = (chain 'E' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 501 or (resid 502 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 503 through 748)) selection = (chain 'F' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 222 through 501 or (resid 502 and \ (name N or name CA or name C or name O or name CB or name OG1 or name CG2 or na \ me H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 \ through 748)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = chain 'N' } 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: 0.380 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: 0.970 Extract box with map and model: 2.110 Check model and map are aligned: 0.430 Set scattering table: 0.530 Process input model: 126.660 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.005 0.109 38586 Z= 0.361 Angle : 0.830 12.394 52137 Z= 0.423 Chirality : 0.044 0.227 5981 Planarity : 0.004 0.073 6728 Dihedral : 14.411 142.116 14702 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -1.04 (0.11), residues: 4795 helix: -0.13 (0.09), residues: 2317 sheet: -1.25 (0.19), residues: 638 loop : -1.02 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 649 HIS 0.017 0.001 HIS D 528 PHE 0.021 0.002 PHE E 331 TYR 0.013 0.001 TYR F 540 ARG 0.010 0.001 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1515 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1515 time to evaluate : 4.375 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 240 MET cc_start: 0.8139 (mmp) cc_final: 0.7926 (mmp) REVERT: A 284 ILE cc_start: 0.7686 (mp) cc_final: 0.7142 (mt) REVERT: A 327 PHE cc_start: 0.7796 (t80) cc_final: 0.7526 (t80) REVERT: A 335 ARG cc_start: 0.6071 (ttt-90) cc_final: 0.5581 (ttt-90) REVERT: A 348 GLU cc_start: 0.8631 (pt0) cc_final: 0.8317 (tt0) REVERT: A 352 GLU cc_start: 0.8374 (tp30) cc_final: 0.8172 (tp30) REVERT: A 379 ARG cc_start: 0.8609 (ptm160) cc_final: 0.7925 (ptm-80) REVERT: A 404 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 501 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7808 (mtmt) REVERT: A 503 GLU cc_start: 0.8366 (mp0) cc_final: 0.7835 (tt0) REVERT: A 520 ASP cc_start: 0.7588 (t0) cc_final: 0.7256 (t70) REVERT: A 525 MET cc_start: 0.8427 (tmm) cc_final: 0.8000 (tmm) REVERT: A 744 TYR cc_start: 0.8627 (m-80) cc_final: 0.8345 (m-80) REVERT: B 286 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7585 (mt-10) REVERT: C 196 GLU cc_start: 0.7572 (tt0) cc_final: 0.7236 (tt0) REVERT: C 697 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7788 (mtm180) REVERT: C 699 MET cc_start: 0.7276 (mmm) cc_final: 0.6980 (mmp) REVERT: D 265 LYS cc_start: 0.8620 (tttm) cc_final: 0.8407 (ttpp) REVERT: D 332 GLU cc_start: 0.8203 (tt0) cc_final: 0.7951 (tt0) REVERT: D 503 GLU cc_start: 0.7158 (tp30) cc_final: 0.6764 (tp30) REVERT: E 194 GLU cc_start: 0.8638 (mp0) cc_final: 0.8237 (mp0) REVERT: E 258 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8373 (tptt) REVERT: E 432 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7754 (ptm-80) REVERT: E 527 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7408 (ttm-80) REVERT: E 551 ASP cc_start: 0.6186 (m-30) cc_final: 0.5955 (m-30) REVERT: F 233 GLN cc_start: 0.7351 (mm110) cc_final: 0.6821 (tp40) REVERT: F 271 LEU cc_start: 0.8779 (mt) cc_final: 0.8578 (mt) REVERT: F 343 LYS cc_start: 0.7943 (tttt) cc_final: 0.7644 (ttmm) REVERT: F 390 ASN cc_start: 0.7225 (p0) cc_final: 0.6700 (t0) REVERT: F 503 GLU cc_start: 0.8910 (tp30) cc_final: 0.8523 (tp30) REVERT: F 564 ASP cc_start: 0.8532 (t0) cc_final: 0.8124 (t0) REVERT: F 668 GLU cc_start: 0.8610 (mp0) cc_final: 0.8240 (mp0) REVERT: F 706 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8842 (ttp80) REVERT: H 9 GLN cc_start: 0.8592 (mm110) cc_final: 0.8351 (mm110) REVERT: H 110 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8413 (mmmm) REVERT: H 140 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7785 (mtp85) REVERT: H 149 MET cc_start: 0.8385 (mmp) cc_final: 0.8013 (mmp) REVERT: I 108 LYS cc_start: 0.7593 (ptmm) cc_final: 0.7390 (ptmm) REVERT: I 144 LYS cc_start: 0.8493 (mttp) cc_final: 0.8243 (mttp) REVERT: I 167 ASP cc_start: 0.8037 (m-30) cc_final: 0.7799 (m-30) REVERT: J 15 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6810 (mmm160) REVERT: J 150 ASN cc_start: 0.9041 (m110) cc_final: 0.8654 (m-40) REVERT: K 26 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7769 (mm-30) REVERT: K 169 GLU cc_start: 0.7893 (tp30) cc_final: 0.7579 (tp30) REVERT: L 77 TYR cc_start: 0.8529 (t80) cc_final: 0.8217 (t80) REVERT: L 117 SER cc_start: 0.9177 (m) cc_final: 0.8920 (m) REVERT: L 166 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.7103 (ptt-90) REVERT: L 169 GLU cc_start: 0.7681 (pt0) cc_final: 0.7309 (pt0) REVERT: M 123 GLN cc_start: 0.8397 (pt0) cc_final: 0.8065 (pt0) REVERT: M 138 HIS cc_start: 0.8423 (m90) cc_final: 0.8042 (m-70) REVERT: M 151 GLU cc_start: 0.7864 (tt0) cc_final: 0.7542 (tt0) REVERT: N 58 ASP cc_start: 0.7844 (p0) cc_final: 0.7421 (p0) REVERT: N 136 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7796 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1515 average time/residue: 1.1282 time to fit residues: 2680.4640 Evaluate side-chains 1288 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1288 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 711 ASN B 642 ASN C 356 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN D 325 GLN D 709 GLN D 730 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 GLN F 305 ASN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN H 41 ASN I 41 ASN I 116 ASN I 131 GLN L 41 ASN N 41 ASN N 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 38586 Z= 0.330 Angle : 0.637 8.074 52137 Z= 0.340 Chirality : 0.042 0.218 5981 Planarity : 0.005 0.075 6728 Dihedral : 9.150 145.647 5411 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.23 % Allowed : 9.66 % Favored : 89.11 % 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: -0.28 (0.11), residues: 4795 helix: 0.69 (0.10), residues: 2459 sheet: -1.21 (0.20), residues: 609 loop : -0.95 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 229 HIS 0.010 0.001 HIS A 556 PHE 0.031 0.001 PHE C 746 TYR 0.015 0.001 TYR C 259 ARG 0.008 0.001 ARG M 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1434 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1384 time to evaluate : 4.433 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8379 (ttt90) cc_final: 0.8030 (ptm160) REVERT: A 240 MET cc_start: 0.8200 (mmp) cc_final: 0.7878 (mmp) REVERT: A 334 ASP cc_start: 0.7376 (t0) cc_final: 0.7130 (t0) REVERT: A 335 ARG cc_start: 0.5902 (ttt-90) cc_final: 0.5632 (ttt-90) REVERT: A 343 LYS cc_start: 0.8804 (tmmt) cc_final: 0.8219 (tmmt) REVERT: A 379 ARG cc_start: 0.8607 (ptm160) cc_final: 0.7878 (tpt90) REVERT: A 404 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 503 GLU cc_start: 0.8617 (mp0) cc_final: 0.7986 (tt0) REVERT: A 525 MET cc_start: 0.8511 (tmm) cc_final: 0.8151 (tmm) REVERT: A 711 ASN cc_start: 0.7939 (m110) cc_final: 0.7600 (m-40) REVERT: A 744 TYR cc_start: 0.8714 (m-80) cc_final: 0.8132 (m-80) REVERT: B 279 ASN cc_start: 0.7446 (t0) cc_final: 0.6699 (t0) REVERT: B 408 ARG cc_start: 0.7747 (ttm170) cc_final: 0.7087 (ttm170) REVERT: B 593 LYS cc_start: 0.8703 (tppp) cc_final: 0.8386 (tptp) REVERT: B 727 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: C 196 GLU cc_start: 0.7831 (tt0) cc_final: 0.7456 (tt0) REVERT: C 332 GLU cc_start: 0.7875 (tp30) cc_final: 0.7613 (tp30) REVERT: C 697 ARG cc_start: 0.8271 (mtp180) cc_final: 0.8053 (mtm180) REVERT: C 699 MET cc_start: 0.7718 (mmm) cc_final: 0.7484 (mmm) REVERT: C 704 MET cc_start: 0.8067 (tpp) cc_final: 0.7822 (mmm) REVERT: D 366 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8328 (mt-10) REVERT: D 503 GLU cc_start: 0.7332 (tp30) cc_final: 0.6893 (tp30) REVERT: D 675 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7917 (tp40) REVERT: E 258 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8442 (tptt) REVERT: E 366 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7075 (mt-10) REVERT: E 432 ARG cc_start: 0.8364 (ptm-80) cc_final: 0.7860 (tmm160) REVERT: E 527 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7294 (ttm-80) REVERT: E 551 ASP cc_start: 0.6515 (m-30) cc_final: 0.6210 (m-30) REVERT: E 597 ARG cc_start: 0.7812 (ptp-170) cc_final: 0.7429 (mtm-85) REVERT: E 699 MET cc_start: 0.7811 (mmp) cc_final: 0.7610 (mmp) REVERT: F 195 LEU cc_start: 0.8985 (tp) cc_final: 0.8731 (mp) REVERT: F 209 ASN cc_start: 0.8742 (m-40) cc_final: 0.8499 (m-40) REVERT: F 215 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7476 (mm-30) REVERT: F 305 ASN cc_start: 0.7533 (m-40) cc_final: 0.7296 (m-40) REVERT: F 352 GLU cc_start: 0.7710 (mp0) cc_final: 0.7299 (mp0) REVERT: F 390 ASN cc_start: 0.7320 (p0) cc_final: 0.6938 (t0) REVERT: F 412 MET cc_start: 0.6952 (mtp) cc_final: 0.6674 (mtp) REVERT: F 706 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8662 (tpt-90) REVERT: F 710 ASP cc_start: 0.8662 (t0) cc_final: 0.8245 (t0) REVERT: H 140 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7913 (mmm-85) REVERT: H 149 MET cc_start: 0.8574 (mmp) cc_final: 0.8100 (mmp) REVERT: H 161 LEU cc_start: 0.8267 (pt) cc_final: 0.7411 (pt) REVERT: I 10 THR cc_start: 0.7382 (p) cc_final: 0.7139 (p) REVERT: I 136 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8005 (tm-30) REVERT: I 165 GLU cc_start: 0.8148 (pt0) cc_final: 0.7797 (pt0) REVERT: I 166 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7686 (mtp-110) REVERT: J 60 TYR cc_start: 0.8586 (m-80) cc_final: 0.8356 (m-10) REVERT: J 74 MET cc_start: 0.8294 (mmm) cc_final: 0.7995 (mmt) REVERT: J 123 GLN cc_start: 0.8453 (pt0) cc_final: 0.8083 (pt0) REVERT: K 144 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8305 (mttp) REVERT: K 151 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7116 (mt-10) REVERT: L 17 PHE cc_start: 0.8113 (m-80) cc_final: 0.7772 (m-80) REVERT: L 34 GLN cc_start: 0.8488 (tp40) cc_final: 0.8247 (tp40) REVERT: L 117 SER cc_start: 0.9102 (m) cc_final: 0.8856 (m) REVERT: L 141 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7229 (tm-30) REVERT: L 168 THR cc_start: 0.8515 (m) cc_final: 0.8298 (p) REVERT: M 14 GLU cc_start: 0.6692 (mp0) cc_final: 0.6425 (mp0) REVERT: M 151 GLU cc_start: 0.8026 (tt0) cc_final: 0.7639 (tt0) REVERT: N 58 ASP cc_start: 0.7927 (p0) cc_final: 0.7586 (p0) REVERT: N 136 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8349 (tm-30) outliers start: 50 outliers final: 36 residues processed: 1394 average time/residue: 1.1728 time to fit residues: 2552.7744 Evaluate side-chains 1329 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1292 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 191 HIS Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 161 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 120 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS B 200 GLN C 177 ASN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 747 GLN H 41 ASN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 41 ASN I 163 GLN K 122 HIS K 159 GLN L 9 GLN L 41 ASN N 41 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 38586 Z= 0.376 Angle : 0.608 7.902 52137 Z= 0.322 Chirality : 0.042 0.215 5981 Planarity : 0.005 0.082 6728 Dihedral : 9.002 162.203 5411 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.97 % Allowed : 12.29 % Favored : 85.74 % 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: -0.27 (0.11), residues: 4795 helix: 0.67 (0.10), residues: 2495 sheet: -1.22 (0.20), residues: 603 loop : -0.92 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.019 0.001 HIS E 558 PHE 0.019 0.002 PHE M 17 TYR 0.017 0.001 TYR J 60 ARG 0.013 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1430 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1350 time to evaluate : 4.492 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8202 (mmp) cc_final: 0.7885 (mmp) REVERT: A 335 ARG cc_start: 0.5777 (ttt-90) cc_final: 0.5472 (ttt-90) REVERT: A 343 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8285 (ttpp) REVERT: A 345 ASP cc_start: 0.7177 (p0) cc_final: 0.6956 (p0) REVERT: A 348 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: A 379 ARG cc_start: 0.8671 (ptm160) cc_final: 0.7914 (tpt90) REVERT: A 404 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 455 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8440 (tpp-160) REVERT: A 503 GLU cc_start: 0.8630 (mp0) cc_final: 0.8011 (tt0) REVERT: A 525 MET cc_start: 0.8591 (tmm) cc_final: 0.8165 (tmm) REVERT: B 279 ASN cc_start: 0.7694 (t0) cc_final: 0.7350 (t0) REVERT: B 727 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: C 332 GLU cc_start: 0.7914 (tp30) cc_final: 0.7623 (tp30) REVERT: C 410 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8228 (ttm170) REVERT: D 396 ASP cc_start: 0.7839 (t0) cc_final: 0.7630 (t0) REVERT: D 476 MET cc_start: 0.8682 (mtt) cc_final: 0.8453 (mtt) REVERT: E 258 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8475 (tptt) REVERT: E 366 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7093 (mt-10) REVERT: E 527 ARG cc_start: 0.7684 (mtp-110) cc_final: 0.7289 (ttm-80) REVERT: E 633 LYS cc_start: 0.8536 (mttt) cc_final: 0.8156 (mttm) REVERT: F 195 LEU cc_start: 0.8986 (tp) cc_final: 0.8764 (mp) REVERT: F 215 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7431 (mm-30) REVERT: F 233 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: F 288 HIS cc_start: 0.7978 (p90) cc_final: 0.7751 (p90) REVERT: F 352 GLU cc_start: 0.7717 (mp0) cc_final: 0.7358 (mp0) REVERT: F 390 ASN cc_start: 0.7210 (p0) cc_final: 0.6900 (t0) REVERT: F 706 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8837 (tpt-90) REVERT: H 9 GLN cc_start: 0.8664 (mm110) cc_final: 0.8439 (mm110) REVERT: H 78 ASP cc_start: 0.7928 (m-30) cc_final: 0.7652 (m-30) REVERT: H 86 ASP cc_start: 0.8243 (m-30) cc_final: 0.7988 (t0) REVERT: H 101 PHE cc_start: 0.8668 (t80) cc_final: 0.8129 (t80) REVERT: H 144 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8737 (mtmm) REVERT: H 149 MET cc_start: 0.8703 (mmp) cc_final: 0.8226 (mmp) REVERT: H 175 SER cc_start: 0.8791 (t) cc_final: 0.8548 (p) REVERT: I 136 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7967 (tm-30) REVERT: I 144 LYS cc_start: 0.8668 (mttp) cc_final: 0.8364 (mttp) REVERT: I 165 GLU cc_start: 0.8243 (pt0) cc_final: 0.7886 (pt0) REVERT: I 166 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7789 (mtp-110) REVERT: J 53 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8069 (mm-30) REVERT: J 120 MET cc_start: 0.7387 (ttt) cc_final: 0.7160 (ttt) REVERT: J 123 GLN cc_start: 0.8501 (pt0) cc_final: 0.7920 (pt0) REVERT: J 140 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8059 (ttm-80) REVERT: K 144 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8318 (mttp) REVERT: K 151 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7168 (mt-10) REVERT: K 169 GLU cc_start: 0.8185 (tp30) cc_final: 0.7719 (tp30) REVERT: L 34 GLN cc_start: 0.8552 (tp40) cc_final: 0.8322 (tp40) REVERT: L 117 SER cc_start: 0.9058 (m) cc_final: 0.8855 (m) REVERT: L 141 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7185 (tm-30) REVERT: L 148 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7731 (mmm-85) REVERT: L 172 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7248 (ttm-80) REVERT: M 54 ASN cc_start: 0.8433 (t0) cc_final: 0.7967 (t0) REVERT: M 151 GLU cc_start: 0.8146 (tt0) cc_final: 0.7761 (tt0) REVERT: N 58 ASP cc_start: 0.8051 (p0) cc_final: 0.7834 (p0) REVERT: N 136 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8278 (tm-30) REVERT: N 140 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7663 (mtp85) REVERT: N 169 GLU cc_start: 0.7878 (pp20) cc_final: 0.7639 (pp20) outliers start: 80 outliers final: 56 residues processed: 1377 average time/residue: 1.1659 time to fit residues: 2502.5032 Evaluate side-chains 1336 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1274 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 191 HIS Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 6.9990 chunk 328 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 415 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 369 HIS C 575 ASN D 325 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 GLN E 747 GLN F 178 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN I 41 ASN I 131 GLN K 122 HIS M 41 ASN M 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 38586 Z= 0.352 Angle : 0.587 8.261 52137 Z= 0.310 Chirality : 0.042 0.198 5981 Planarity : 0.004 0.069 6728 Dihedral : 8.901 164.330 5411 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % Favored : 84.11 % 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: -0.24 (0.12), residues: 4795 helix: 0.71 (0.10), residues: 2506 sheet: -1.25 (0.20), residues: 579 loop : -0.93 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 649 HIS 0.007 0.001 HIS H 138 PHE 0.020 0.001 PHE E 596 TYR 0.014 0.001 TYR C 259 ARG 0.007 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1422 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1339 time to evaluate : 4.466 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: 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: 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: 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: 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: 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: 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: 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: 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: A 240 MET cc_start: 0.8172 (mmp) cc_final: 0.7863 (mmp) REVERT: A 284 ILE cc_start: 0.8115 (mt) cc_final: 0.7898 (mt) REVERT: A 335 ARG cc_start: 0.5885 (ttt-90) cc_final: 0.5554 (ttt-90) REVERT: A 343 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8260 (ttpp) REVERT: A 379 ARG cc_start: 0.8733 (ptm160) cc_final: 0.7919 (tpt90) REVERT: A 404 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 455 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8478 (tpp-160) REVERT: A 503 GLU cc_start: 0.8614 (mp0) cc_final: 0.8038 (tt0) REVERT: B 279 ASN cc_start: 0.7766 (t0) cc_final: 0.7370 (t0) REVERT: B 447 ASP cc_start: 0.7422 (t0) cc_final: 0.7216 (t0) REVERT: B 722 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.7488 (p90) REVERT: B 727 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: C 410 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8303 (ttm170) REVERT: C 747 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6953 (tm-30) REVERT: D 476 MET cc_start: 0.8669 (mtt) cc_final: 0.8463 (mtt) REVERT: E 215 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: E 225 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8247 (mt-10) REVERT: E 258 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8378 (tptt) REVERT: E 366 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7092 (mt-10) REVERT: E 527 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7491 (ttm-80) REVERT: E 551 ASP cc_start: 0.6925 (m-30) cc_final: 0.6492 (m-30) REVERT: E 558 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.6042 (m170) REVERT: E 633 LYS cc_start: 0.8557 (mttt) cc_final: 0.8172 (mttp) REVERT: F 195 LEU cc_start: 0.8987 (tp) cc_final: 0.8740 (mp) REVERT: F 215 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7487 (mm-30) REVERT: F 352 GLU cc_start: 0.7733 (mp0) cc_final: 0.7392 (mp0) REVERT: F 390 ASN cc_start: 0.7297 (p0) cc_final: 0.6923 (t0) REVERT: F 558 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6370 (t-90) REVERT: F 706 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8694 (tpt-90) REVERT: F 710 ASP cc_start: 0.8722 (t0) cc_final: 0.8335 (t0) REVERT: H 9 GLN cc_start: 0.8647 (mm110) cc_final: 0.8407 (mm110) REVERT: H 101 PHE cc_start: 0.8723 (t80) cc_final: 0.8193 (t80) REVERT: H 149 MET cc_start: 0.8717 (mmp) cc_final: 0.8293 (mmp) REVERT: I 136 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8007 (tm-30) REVERT: I 144 LYS cc_start: 0.8660 (mttp) cc_final: 0.8357 (mttp) REVERT: I 165 GLU cc_start: 0.8244 (pt0) cc_final: 0.7920 (pt0) REVERT: I 166 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.7844 (mtp-110) REVERT: J 60 TYR cc_start: 0.8452 (m-10) cc_final: 0.8230 (m-10) REVERT: J 123 GLN cc_start: 0.8533 (pt0) cc_final: 0.8015 (pt0) REVERT: J 169 GLU cc_start: 0.6639 (tp30) cc_final: 0.6022 (tp30) REVERT: K 140 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: K 144 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8315 (mttp) REVERT: L 34 GLN cc_start: 0.8545 (tp40) cc_final: 0.8315 (tp40) REVERT: L 86 ASP cc_start: 0.7767 (m-30) cc_final: 0.7468 (t0) REVERT: L 141 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7175 (tm-30) REVERT: L 172 ARG cc_start: 0.7584 (ttt90) cc_final: 0.7275 (ttm-80) REVERT: L 181 GLU cc_start: 0.7818 (mp0) cc_final: 0.7573 (mp0) REVERT: M 15 ARG cc_start: 0.6838 (mmp80) cc_final: 0.6638 (mmp80) REVERT: M 54 ASN cc_start: 0.8482 (t0) cc_final: 0.8025 (t0) REVERT: M 151 GLU cc_start: 0.8170 (tt0) cc_final: 0.7781 (tt0) REVERT: N 26 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8518 (mm-30) REVERT: N 34 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8087 (mm-40) REVERT: N 58 ASP cc_start: 0.8085 (p0) cc_final: 0.7885 (p0) REVERT: N 136 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8367 (tm-30) REVERT: N 169 GLU cc_start: 0.7849 (pp20) cc_final: 0.7581 (pp20) REVERT: N 178 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7960 (mp0) outliers start: 83 outliers final: 57 residues processed: 1372 average time/residue: 1.1747 time to fit residues: 2519.1122 Evaluate side-chains 1355 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1292 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 558 HIS Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 345 optimal weight: 40.0000 chunk 191 optimal weight: 1.9990 chunk 395 optimal weight: 8.9990 chunk 320 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 chunk 416 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN D 325 GLN ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN K 122 HIS M 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 38586 Z= 0.260 Angle : 0.559 11.426 52137 Z= 0.292 Chirality : 0.040 0.182 5981 Planarity : 0.004 0.064 6728 Dihedral : 8.752 163.449 5411 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.97 % Allowed : 14.95 % Favored : 83.07 % 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: -0.14 (0.12), residues: 4795 helix: 0.82 (0.10), residues: 2509 sheet: -1.27 (0.20), residues: 588 loop : -0.89 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.008 0.001 HIS F 652 PHE 0.021 0.001 PHE M 82 TYR 0.013 0.001 TYR F 695 ARG 0.008 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1397 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1317 time to evaluate : 4.432 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8626 (mt0) cc_final: 0.8422 (tt0) REVERT: A 240 MET cc_start: 0.8155 (mmp) cc_final: 0.7842 (mmp) REVERT: A 335 ARG cc_start: 0.5819 (ttt-90) cc_final: 0.5502 (ttt-90) REVERT: A 343 LYS cc_start: 0.8732 (tmmt) cc_final: 0.8263 (ttpp) REVERT: A 348 GLU cc_start: 0.8772 (pt0) cc_final: 0.8432 (tt0) REVERT: A 379 ARG cc_start: 0.8724 (ptm160) cc_final: 0.7891 (tpt90) REVERT: A 404 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 503 GLU cc_start: 0.8641 (mp0) cc_final: 0.8099 (tt0) REVERT: B 204 ARG cc_start: 0.8391 (ptm160) cc_final: 0.8165 (ptm160) REVERT: B 279 ASN cc_start: 0.7878 (t0) cc_final: 0.7422 (t0) REVERT: B 593 LYS cc_start: 0.8721 (tppp) cc_final: 0.8254 (tptm) REVERT: B 722 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7442 (p90) REVERT: B 727 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: C 275 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 410 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8269 (ttm170) REVERT: C 699 MET cc_start: 0.8151 (mmm) cc_final: 0.7596 (mmm) REVERT: D 277 ASP cc_start: 0.8190 (t70) cc_final: 0.7973 (t0) REVERT: E 215 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: E 258 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8376 (tptt) REVERT: E 366 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7082 (mt-10) REVERT: E 527 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7475 (ttm-80) REVERT: E 551 ASP cc_start: 0.6994 (m-30) cc_final: 0.6548 (m-30) REVERT: F 172 PHE cc_start: 0.7988 (m-80) cc_final: 0.7647 (m-80) REVERT: F 200 GLN cc_start: 0.8665 (tt0) cc_final: 0.8346 (tt0) REVERT: F 288 HIS cc_start: 0.8052 (p90) cc_final: 0.7745 (p90) REVERT: F 343 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8115 (ttmm) REVERT: F 352 GLU cc_start: 0.7715 (mp0) cc_final: 0.7371 (mp0) REVERT: F 390 ASN cc_start: 0.7240 (p0) cc_final: 0.6891 (t0) REVERT: F 706 ARG cc_start: 0.9109 (ttp80) cc_final: 0.8685 (tpt-90) REVERT: F 710 ASP cc_start: 0.8701 (t0) cc_final: 0.8359 (t0) REVERT: H 9 GLN cc_start: 0.8606 (mm110) cc_final: 0.8401 (mm110) REVERT: H 101 PHE cc_start: 0.8724 (t80) cc_final: 0.8191 (t80) REVERT: H 140 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7785 (mtp85) REVERT: H 149 MET cc_start: 0.8703 (mmp) cc_final: 0.8330 (mmp) REVERT: I 136 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8024 (tm-30) REVERT: I 144 LYS cc_start: 0.8669 (mttp) cc_final: 0.8358 (mttp) REVERT: I 165 GLU cc_start: 0.8244 (pt0) cc_final: 0.7963 (pt0) REVERT: I 166 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7875 (mtp-110) REVERT: J 60 TYR cc_start: 0.8457 (m-10) cc_final: 0.8254 (m-10) REVERT: J 118 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.8035 (mmm-85) REVERT: J 123 GLN cc_start: 0.8588 (pt0) cc_final: 0.8053 (pt0) REVERT: K 140 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7410 (ttm-80) REVERT: K 144 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8350 (mttp) REVERT: K 151 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7184 (mt-10) REVERT: L 34 GLN cc_start: 0.8547 (tp40) cc_final: 0.8315 (tp40) REVERT: L 172 ARG cc_start: 0.7599 (ttt90) cc_final: 0.7300 (ttm-80) REVERT: M 54 ASN cc_start: 0.8484 (t0) cc_final: 0.8017 (t0) REVERT: M 120 MET cc_start: 0.8272 (tmm) cc_final: 0.7966 (tmm) REVERT: M 151 GLU cc_start: 0.8152 (tt0) cc_final: 0.7754 (tt0) REVERT: N 34 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8122 (mm-40) REVERT: N 58 ASP cc_start: 0.8075 (p0) cc_final: 0.7868 (p0) REVERT: N 136 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8351 (tm-30) outliers start: 80 outliers final: 62 residues processed: 1349 average time/residue: 1.1465 time to fit residues: 2409.6694 Evaluate side-chains 1347 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1281 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN D 325 GLN E 558 HIS E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN K 122 HIS L 116 ASN M 123 GLN N 41 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38586 Z= 0.190 Angle : 0.535 6.997 52137 Z= 0.277 Chirality : 0.040 0.170 5981 Planarity : 0.004 0.058 6728 Dihedral : 8.544 159.559 5411 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.63 % Allowed : 16.21 % Favored : 82.16 % 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: 0.04 (0.12), residues: 4795 helix: 0.98 (0.10), residues: 2505 sheet: -1.25 (0.20), residues: 588 loop : -0.80 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.006 0.001 HIS F 652 PHE 0.020 0.001 PHE M 82 TYR 0.017 0.001 TYR L 77 ARG 0.008 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1374 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1308 time to evaluate : 4.412 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8640 (mt0) cc_final: 0.8410 (tt0) REVERT: A 240 MET cc_start: 0.8125 (mmp) cc_final: 0.7788 (mmp) REVERT: A 335 ARG cc_start: 0.5758 (ttt-90) cc_final: 0.5491 (ttt-90) REVERT: A 343 LYS cc_start: 0.8735 (tmmt) cc_final: 0.8266 (ttpp) REVERT: A 348 GLU cc_start: 0.8786 (pt0) cc_final: 0.8437 (tt0) REVERT: A 379 ARG cc_start: 0.8723 (ptm160) cc_final: 0.7868 (tpt90) REVERT: A 503 GLU cc_start: 0.8601 (mp0) cc_final: 0.8129 (tt0) REVERT: B 279 ASN cc_start: 0.7916 (t0) cc_final: 0.7465 (t0) REVERT: B 408 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7746 (ttm170) REVERT: B 722 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.7416 (p90) REVERT: B 727 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: C 273 GLN cc_start: 0.8281 (mt0) cc_final: 0.8079 (mt0) REVERT: C 403 ASP cc_start: 0.8785 (t0) cc_final: 0.8490 (m-30) REVERT: C 410 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8220 (ttm170) REVERT: C 699 MET cc_start: 0.8106 (mmm) cc_final: 0.7548 (mmm) REVERT: D 366 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 503 GLU cc_start: 0.7323 (tp30) cc_final: 0.6848 (tp30) REVERT: E 215 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: E 258 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8360 (tptt) REVERT: E 366 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 432 ARG cc_start: 0.8455 (ptm-80) cc_final: 0.7989 (tmm160) REVERT: E 527 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7460 (ttm-80) REVERT: E 551 ASP cc_start: 0.7051 (m-30) cc_final: 0.6595 (m-30) REVERT: F 200 GLN cc_start: 0.8658 (tt0) cc_final: 0.8326 (tt0) REVERT: F 215 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7525 (mm-30) REVERT: F 288 HIS cc_start: 0.8018 (p90) cc_final: 0.7656 (p90) REVERT: F 352 GLU cc_start: 0.7819 (mp0) cc_final: 0.7413 (mp0) REVERT: F 390 ASN cc_start: 0.7286 (p0) cc_final: 0.6933 (t0) REVERT: F 468 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8004 (mt-10) REVERT: F 631 GLU cc_start: 0.8432 (mp0) cc_final: 0.7583 (pt0) REVERT: H 101 PHE cc_start: 0.8733 (t80) cc_final: 0.8037 (t80) REVERT: H 140 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7781 (mtp85) REVERT: H 143 LEU cc_start: 0.8723 (mt) cc_final: 0.8511 (mt) REVERT: H 149 MET cc_start: 0.8704 (mmp) cc_final: 0.8211 (mmp) REVERT: I 136 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8034 (tm-30) REVERT: I 144 LYS cc_start: 0.8649 (mttp) cc_final: 0.8336 (mttp) REVERT: I 165 GLU cc_start: 0.8224 (pt0) cc_final: 0.7917 (pt0) REVERT: I 166 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7862 (mtp-110) REVERT: J 60 TYR cc_start: 0.8425 (m-10) cc_final: 0.8221 (m-10) REVERT: J 118 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.8035 (mmm-85) REVERT: J 123 GLN cc_start: 0.8569 (pt0) cc_final: 0.8112 (pt0) REVERT: J 169 GLU cc_start: 0.6536 (tp30) cc_final: 0.5991 (tp30) REVERT: K 144 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8382 (mttp) REVERT: L 9 GLN cc_start: 0.7929 (tp40) cc_final: 0.7582 (mm110) REVERT: L 34 GLN cc_start: 0.8510 (tp40) cc_final: 0.8261 (tp40) REVERT: L 86 ASP cc_start: 0.7767 (m-30) cc_final: 0.7507 (t0) REVERT: L 172 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7254 (ttm-80) REVERT: M 54 ASN cc_start: 0.8440 (t0) cc_final: 0.7981 (t0) REVERT: M 151 GLU cc_start: 0.8153 (tt0) cc_final: 0.7761 (tt0) REVERT: N 169 GLU cc_start: 0.7854 (pp20) cc_final: 0.7625 (pp20) outliers start: 66 outliers final: 52 residues processed: 1336 average time/residue: 1.1537 time to fit residues: 2400.4875 Evaluate side-chains 1341 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1285 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 339 optimal weight: 40.0000 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN D 325 GLN E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 159 GLN K 122 HIS K 150 ASN L 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 38586 Z= 0.328 Angle : 0.574 7.856 52137 Z= 0.300 Chirality : 0.041 0.182 5981 Planarity : 0.004 0.070 6728 Dihedral : 8.648 168.544 5411 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.90 % Allowed : 16.26 % Favored : 81.84 % 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: -0.02 (0.12), residues: 4795 helix: 0.94 (0.10), residues: 2519 sheet: -1.32 (0.20), residues: 593 loop : -0.83 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 649 HIS 0.019 0.001 HIS F 483 PHE 0.023 0.001 PHE F 665 TYR 0.027 0.001 TYR M 77 ARG 0.009 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1399 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1322 time to evaluate : 4.454 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: 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: 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: 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: 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: 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: 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: 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: A 200 GLN cc_start: 0.8644 (mt0) cc_final: 0.8437 (tt0) REVERT: A 240 MET cc_start: 0.8171 (mmp) cc_final: 0.7845 (mmp) REVERT: A 335 ARG cc_start: 0.5871 (ttt-90) cc_final: 0.5576 (ttt-90) REVERT: A 343 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8271 (ttpp) REVERT: A 348 GLU cc_start: 0.8815 (pt0) cc_final: 0.8456 (tt0) REVERT: A 379 ARG cc_start: 0.8733 (ptm160) cc_final: 0.7893 (tpt90) REVERT: A 475 LYS cc_start: 0.8504 (mttt) cc_final: 0.7947 (mmtt) REVERT: A 503 GLU cc_start: 0.8634 (mp0) cc_final: 0.8149 (tt0) REVERT: B 279 ASN cc_start: 0.8001 (t0) cc_final: 0.7522 (t0) REVERT: B 408 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7813 (ttm170) REVERT: B 722 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.7421 (p90) REVERT: B 727 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: C 273 GLN cc_start: 0.8366 (mt0) cc_final: 0.8121 (mt0) REVERT: C 410 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8314 (ttm170) REVERT: C 699 MET cc_start: 0.8195 (mmm) cc_final: 0.7670 (mmm) REVERT: D 503 GLU cc_start: 0.7372 (tp30) cc_final: 0.6918 (tp30) REVERT: D 697 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.7999 (mmm160) REVERT: E 215 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: E 258 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8346 (tptt) REVERT: E 366 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7112 (mt-10) REVERT: E 432 ARG cc_start: 0.8480 (ptm-80) cc_final: 0.7997 (tmm160) REVERT: E 527 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7510 (ttm-80) REVERT: E 551 ASP cc_start: 0.7215 (m-30) cc_final: 0.6672 (m-30) REVERT: E 633 LYS cc_start: 0.8540 (mttt) cc_final: 0.8138 (mttp) REVERT: F 200 GLN cc_start: 0.8721 (tt0) cc_final: 0.8405 (tt0) REVERT: F 215 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7699 (mm-30) REVERT: F 288 HIS cc_start: 0.8111 (p90) cc_final: 0.7858 (p90) REVERT: F 352 GLU cc_start: 0.7862 (mp0) cc_final: 0.7451 (mp0) REVERT: F 390 ASN cc_start: 0.7266 (p0) cc_final: 0.6922 (t0) REVERT: F 412 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6808 (ttp) REVERT: F 468 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8055 (mt-10) REVERT: F 631 GLU cc_start: 0.8410 (mp0) cc_final: 0.7665 (pt0) REVERT: H 101 PHE cc_start: 0.8775 (t80) cc_final: 0.8290 (t80) REVERT: H 149 MET cc_start: 0.8685 (mmp) cc_final: 0.8333 (mmp) REVERT: I 136 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8032 (tm-30) REVERT: I 149 MET cc_start: 0.8628 (mmp) cc_final: 0.8276 (mmp) REVERT: I 165 GLU cc_start: 0.8248 (pt0) cc_final: 0.7929 (pt0) REVERT: I 166 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7901 (mtp-110) REVERT: J 60 TYR cc_start: 0.8525 (m-10) cc_final: 0.8298 (m-10) REVERT: J 118 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.8035 (mmm-85) REVERT: J 123 GLN cc_start: 0.8671 (pt0) cc_final: 0.8082 (pt0) REVERT: K 140 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7399 (ttm-80) REVERT: K 144 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8411 (mttp) REVERT: L 34 GLN cc_start: 0.8569 (tp40) cc_final: 0.8330 (tp40) REVERT: L 86 ASP cc_start: 0.7822 (m-30) cc_final: 0.7551 (t0) REVERT: L 172 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7381 (ttm-80) REVERT: M 54 ASN cc_start: 0.8502 (t0) cc_final: 0.7979 (t0) REVERT: M 151 GLU cc_start: 0.8174 (tt0) cc_final: 0.7791 (tt0) REVERT: N 34 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8009 (mm-40) REVERT: N 140 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7838 (mtp85) REVERT: N 169 GLU cc_start: 0.7835 (pp20) cc_final: 0.7597 (pp20) outliers start: 77 outliers final: 63 residues processed: 1354 average time/residue: 1.1515 time to fit residues: 2428.8179 Evaluate side-chains 1368 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1300 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain F residue 743 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 123 GLN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 20.0000 chunk 184 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 363 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN B 642 ASN D 325 GLN E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN J 150 ASN K 122 HIS K 150 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN M 163 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38586 Z= 0.230 Angle : 0.549 7.075 52137 Z= 0.285 Chirality : 0.040 0.168 5981 Planarity : 0.004 0.062 6728 Dihedral : 8.508 166.536 5411 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.87 % Allowed : 16.93 % Favored : 81.20 % 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: 0.10 (0.12), residues: 4795 helix: 1.06 (0.10), residues: 2504 sheet: -1.34 (0.20), residues: 598 loop : -0.78 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 649 HIS 0.008 0.001 HIS F 652 PHE 0.018 0.001 PHE A 746 TYR 0.021 0.001 TYR F 695 ARG 0.009 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1413 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1337 time to evaluate : 4.371 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 240 MET cc_start: 0.8149 (mmp) cc_final: 0.7843 (mmp) REVERT: A 335 ARG cc_start: 0.5892 (ttt-90) cc_final: 0.5627 (ttt-90) REVERT: A 343 LYS cc_start: 0.8713 (tmmt) cc_final: 0.8266 (ttpp) REVERT: A 348 GLU cc_start: 0.8822 (pt0) cc_final: 0.8456 (tt0) REVERT: A 379 ARG cc_start: 0.8738 (ptm160) cc_final: 0.7895 (tpt90) REVERT: A 410 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.7135 (ptm160) REVERT: A 475 LYS cc_start: 0.8499 (mttt) cc_final: 0.7995 (mmtt) REVERT: A 503 GLU cc_start: 0.8630 (mp0) cc_final: 0.8156 (tt0) REVERT: B 204 ARG cc_start: 0.8567 (ptm160) cc_final: 0.8035 (ptm160) REVERT: B 279 ASN cc_start: 0.8045 (t0) cc_final: 0.7564 (t0) REVERT: B 408 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7774 (ttm170) REVERT: B 582 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: B 722 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7394 (p90) REVERT: B 727 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: C 273 GLN cc_start: 0.8332 (mt0) cc_final: 0.8089 (mt0) REVERT: C 592 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7542 (ttt180) REVERT: C 699 MET cc_start: 0.8147 (mmm) cc_final: 0.7607 (mmm) REVERT: D 366 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 631 GLU cc_start: 0.7881 (tp30) cc_final: 0.7613 (tp30) REVERT: D 697 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8001 (mmm160) REVERT: E 215 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: E 258 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8327 (tptt) REVERT: E 366 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7111 (mt-10) REVERT: E 432 ARG cc_start: 0.8455 (ptm-80) cc_final: 0.7943 (tmm160) REVERT: E 527 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7520 (ttm-80) REVERT: E 551 ASP cc_start: 0.7215 (m-30) cc_final: 0.6659 (m-30) REVERT: F 200 GLN cc_start: 0.8692 (tt0) cc_final: 0.8359 (tt0) REVERT: F 212 LEU cc_start: 0.8743 (mt) cc_final: 0.8368 (mp) REVERT: F 279 ASN cc_start: 0.6390 (m-40) cc_final: 0.6176 (m110) REVERT: F 288 HIS cc_start: 0.8065 (p90) cc_final: 0.7745 (p90) REVERT: F 352 GLU cc_start: 0.7840 (mp0) cc_final: 0.7418 (mp0) REVERT: F 390 ASN cc_start: 0.7296 (p0) cc_final: 0.6953 (t0) REVERT: F 468 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8062 (mt-10) REVERT: F 516 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8199 (tp) REVERT: F 629 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7696 (pmm) REVERT: F 631 GLU cc_start: 0.8462 (mp0) cc_final: 0.7728 (pt0) REVERT: H 101 PHE cc_start: 0.8806 (t80) cc_final: 0.8135 (t80) REVERT: H 149 MET cc_start: 0.8702 (mmp) cc_final: 0.8217 (mmp) REVERT: I 136 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8039 (tm-30) REVERT: I 165 GLU cc_start: 0.8193 (pt0) cc_final: 0.7924 (pt0) REVERT: I 166 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7906 (mtp-110) REVERT: J 53 GLU cc_start: 0.8350 (tp30) cc_final: 0.8147 (mm-30) REVERT: J 60 TYR cc_start: 0.8486 (m-10) cc_final: 0.8272 (m-10) REVERT: J 123 GLN cc_start: 0.8669 (pt0) cc_final: 0.8152 (pt0) REVERT: J 169 GLU cc_start: 0.6634 (tp30) cc_final: 0.6182 (tp30) REVERT: K 140 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7402 (ttm-80) REVERT: K 144 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8416 (mttp) REVERT: L 9 GLN cc_start: 0.7910 (tp40) cc_final: 0.7584 (mm110) REVERT: L 34 GLN cc_start: 0.8535 (tp40) cc_final: 0.8282 (tp40) REVERT: L 86 ASP cc_start: 0.7783 (m-30) cc_final: 0.7528 (t0) REVERT: L 172 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7321 (ttm-80) REVERT: M 54 ASN cc_start: 0.8474 (t0) cc_final: 0.7998 (t0) REVERT: M 149 MET cc_start: 0.8498 (mmm) cc_final: 0.8295 (mmm) REVERT: M 151 GLU cc_start: 0.8171 (tt0) cc_final: 0.7792 (tt0) REVERT: N 34 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7933 (mm-40) REVERT: N 162 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7289 (tm-30) REVERT: N 169 GLU cc_start: 0.7845 (pp20) cc_final: 0.7586 (pp20) REVERT: N 178 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8022 (mt-10) outliers start: 76 outliers final: 57 residues processed: 1367 average time/residue: 1.1447 time to fit residues: 2446.4453 Evaluate side-chains 1362 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1299 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.0470 chunk 443 optimal weight: 4.9990 chunk 404 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 389 optimal weight: 3.9990 chunk 407 optimal weight: 7.9990 chunk 429 optimal weight: 8.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN D 325 GLN E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN J 131 GLN K 122 HIS ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38586 Z= 0.280 Angle : 0.567 9.633 52137 Z= 0.294 Chirality : 0.040 0.165 5981 Planarity : 0.004 0.067 6728 Dihedral : 8.506 169.371 5411 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.75 % Allowed : 17.34 % Favored : 80.91 % 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: 0.06 (0.12), residues: 4795 helix: 1.01 (0.10), residues: 2518 sheet: -1.31 (0.20), residues: 593 loop : -0.80 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 689 HIS 0.005 0.001 HIS C 393 PHE 0.017 0.001 PHE I 173 TYR 0.023 0.001 TYR C 259 ARG 0.010 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1379 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1308 time to evaluate : 4.396 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: 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: 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: 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: 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: 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: 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: 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: A 240 MET cc_start: 0.8160 (mmp) cc_final: 0.7854 (mmp) REVERT: A 335 ARG cc_start: 0.5897 (ttt-90) cc_final: 0.5627 (ttt-90) REVERT: A 343 LYS cc_start: 0.8710 (tmmt) cc_final: 0.8264 (ttpp) REVERT: A 348 GLU cc_start: 0.8835 (pt0) cc_final: 0.8455 (tt0) REVERT: A 379 ARG cc_start: 0.8742 (ptm160) cc_final: 0.7886 (tpt90) REVERT: A 410 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.7103 (ptm160) REVERT: A 427 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 503 GLU cc_start: 0.8685 (mp0) cc_final: 0.8192 (tt0) REVERT: A 577 LEU cc_start: 0.8529 (mt) cc_final: 0.8212 (mp) REVERT: B 279 ASN cc_start: 0.8088 (t0) cc_final: 0.7586 (t0) REVERT: B 408 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7471 (ttm170) REVERT: B 722 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.7419 (p90) REVERT: B 727 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: C 273 GLN cc_start: 0.8347 (mt0) cc_final: 0.8103 (mt0) REVERT: C 699 MET cc_start: 0.8169 (mmm) cc_final: 0.7638 (mmm) REVERT: D 503 GLU cc_start: 0.7341 (tp30) cc_final: 0.6897 (tp30) REVERT: D 631 GLU cc_start: 0.7885 (tp30) cc_final: 0.7630 (tp30) REVERT: D 697 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.7998 (mmm160) REVERT: E 215 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: E 258 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8354 (tptt) REVERT: E 366 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7136 (mt-10) REVERT: E 432 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.7950 (tmm160) REVERT: E 472 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7917 (mt-10) REVERT: E 527 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7514 (ttm-80) REVERT: E 551 ASP cc_start: 0.7300 (m-30) cc_final: 0.6762 (m-30) REVERT: E 633 LYS cc_start: 0.8502 (mttt) cc_final: 0.8106 (mttp) REVERT: F 200 GLN cc_start: 0.8706 (tt0) cc_final: 0.8419 (tt0) REVERT: F 279 ASN cc_start: 0.6405 (m-40) cc_final: 0.6194 (m110) REVERT: F 343 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8409 (ttpp) REVERT: F 352 GLU cc_start: 0.7810 (mp0) cc_final: 0.7405 (mp0) REVERT: F 390 ASN cc_start: 0.7331 (p0) cc_final: 0.6981 (t0) REVERT: F 468 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8066 (mt-10) REVERT: F 629 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7720 (pmm) REVERT: F 631 GLU cc_start: 0.8439 (mp0) cc_final: 0.7751 (pt0) REVERT: H 101 PHE cc_start: 0.8821 (t80) cc_final: 0.8160 (t80) REVERT: H 149 MET cc_start: 0.8702 (mmp) cc_final: 0.8224 (mmp) REVERT: I 136 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8047 (tm-30) REVERT: I 165 GLU cc_start: 0.8159 (pt0) cc_final: 0.7918 (pt0) REVERT: I 166 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7916 (mtp-110) REVERT: J 53 GLU cc_start: 0.8406 (tp30) cc_final: 0.8194 (mm-30) REVERT: J 60 TYR cc_start: 0.8471 (m-10) cc_final: 0.8255 (m-10) REVERT: J 123 GLN cc_start: 0.8693 (pt0) cc_final: 0.8131 (pt0) REVERT: J 169 GLU cc_start: 0.6631 (tp30) cc_final: 0.6180 (tp30) REVERT: K 144 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8416 (mttp) REVERT: L 9 GLN cc_start: 0.7905 (tp40) cc_final: 0.7574 (mm110) REVERT: L 34 GLN cc_start: 0.8554 (tp40) cc_final: 0.8302 (tp40) REVERT: L 54 ASN cc_start: 0.8499 (t0) cc_final: 0.8080 (t0) REVERT: L 86 ASP cc_start: 0.7808 (m-30) cc_final: 0.7534 (t0) REVERT: L 172 ARG cc_start: 0.7623 (ttt90) cc_final: 0.7343 (ttm-80) REVERT: M 54 ASN cc_start: 0.8497 (t0) cc_final: 0.8003 (t0) REVERT: M 151 GLU cc_start: 0.8172 (tt0) cc_final: 0.7793 (tt0) REVERT: N 34 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8000 (mm-40) REVERT: N 162 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7259 (tm-30) REVERT: N 169 GLU cc_start: 0.7837 (pp20) cc_final: 0.7575 (pp20) REVERT: N 178 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8039 (mt-10) outliers start: 71 outliers final: 61 residues processed: 1336 average time/residue: 1.1554 time to fit residues: 2406.6165 Evaluate side-chains 1360 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1295 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 476 MET Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 30.0000 chunk 455 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 709 GLN E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN I 156 HIS K 122 HIS ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38586 Z= 0.324 Angle : 0.585 9.324 52137 Z= 0.305 Chirality : 0.041 0.181 5981 Planarity : 0.004 0.096 6728 Dihedral : 8.563 171.953 5411 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.87 % Allowed : 17.39 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4795 helix: 0.94 (0.10), residues: 2527 sheet: -1.30 (0.20), residues: 595 loop : -0.88 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 649 HIS 0.006 0.001 HIS H 138 PHE 0.024 0.001 PHE B 263 TYR 0.024 0.001 TYR C 259 ARG 0.011 0.000 ARG B 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1389 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1313 time to evaluate : 4.461 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8190 (mmp) cc_final: 0.7891 (mmp) REVERT: A 335 ARG cc_start: 0.6050 (ttt-90) cc_final: 0.5774 (ttt-90) REVERT: A 343 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8269 (ttpp) REVERT: A 348 GLU cc_start: 0.8827 (pt0) cc_final: 0.8445 (tt0) REVERT: A 379 ARG cc_start: 0.8757 (ptm160) cc_final: 0.7919 (tpt90) REVERT: A 410 ARG cc_start: 0.7428 (ptm-80) cc_final: 0.7140 (ptm160) REVERT: A 503 GLU cc_start: 0.8671 (mp0) cc_final: 0.8203 (tt0) REVERT: A 577 LEU cc_start: 0.8582 (mt) cc_final: 0.8270 (mp) REVERT: B 279 ASN cc_start: 0.8160 (t0) cc_final: 0.7673 (t0) REVERT: B 408 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7737 (ttm170) REVERT: B 582 ASP cc_start: 0.7475 (m-30) cc_final: 0.7197 (m-30) REVERT: B 722 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.7310 (p90) REVERT: B 727 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: C 273 GLN cc_start: 0.8369 (mt0) cc_final: 0.8124 (mt0) REVERT: D 631 GLU cc_start: 0.7894 (tp30) cc_final: 0.7675 (tp30) REVERT: D 697 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8049 (mmm160) REVERT: E 215 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: E 258 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8329 (tptt) REVERT: E 366 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7145 (mt-10) REVERT: E 432 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.7949 (tmm160) REVERT: E 472 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7926 (mt-10) REVERT: E 527 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7557 (ttm-80) REVERT: E 551 ASP cc_start: 0.7337 (m-30) cc_final: 0.6767 (m-30) REVERT: E 633 LYS cc_start: 0.8611 (mttt) cc_final: 0.8197 (mttp) REVERT: F 200 GLN cc_start: 0.8747 (tt0) cc_final: 0.8476 (tt0) REVERT: F 279 ASN cc_start: 0.6460 (m-40) cc_final: 0.6246 (m110) REVERT: F 288 HIS cc_start: 0.8165 (p90) cc_final: 0.7909 (p90) REVERT: F 352 GLU cc_start: 0.7782 (mp0) cc_final: 0.7383 (mp0) REVERT: F 390 ASN cc_start: 0.7364 (p0) cc_final: 0.6993 (t0) REVERT: F 468 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8020 (mt-10) REVERT: F 629 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7787 (pmm) REVERT: S 23 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6723 (mtpp) REVERT: H 86 ASP cc_start: 0.8355 (m-30) cc_final: 0.8135 (t0) REVERT: H 101 PHE cc_start: 0.8837 (t80) cc_final: 0.8323 (t80) REVERT: H 149 MET cc_start: 0.8708 (mmp) cc_final: 0.8355 (mmp) REVERT: I 136 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8052 (tm-30) REVERT: I 144 LYS cc_start: 0.8705 (mttp) cc_final: 0.8469 (mttp) REVERT: I 165 GLU cc_start: 0.8188 (pt0) cc_final: 0.7917 (pt0) REVERT: I 166 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7929 (mtp-110) REVERT: J 53 GLU cc_start: 0.8413 (tp30) cc_final: 0.8186 (mm-30) REVERT: J 60 TYR cc_start: 0.8518 (m-10) cc_final: 0.8292 (m-10) REVERT: J 123 GLN cc_start: 0.8746 (pt0) cc_final: 0.8208 (pt0) REVERT: J 169 GLU cc_start: 0.6620 (tp30) cc_final: 0.6176 (tp30) REVERT: K 140 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: K 144 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8412 (mttp) REVERT: L 9 GLN cc_start: 0.7865 (tp40) cc_final: 0.7526 (mm110) REVERT: L 34 GLN cc_start: 0.8553 (tp40) cc_final: 0.8304 (tp40) REVERT: L 54 ASN cc_start: 0.8543 (t0) cc_final: 0.8030 (t0) REVERT: L 86 ASP cc_start: 0.7826 (m-30) cc_final: 0.7549 (t0) REVERT: L 172 ARG cc_start: 0.7640 (ttt90) cc_final: 0.7375 (ttm-80) REVERT: L 175 SER cc_start: 0.8910 (t) cc_final: 0.8689 (p) REVERT: M 54 ASN cc_start: 0.8535 (t0) cc_final: 0.8034 (t0) REVERT: M 151 GLU cc_start: 0.8213 (tt0) cc_final: 0.7792 (tt0) REVERT: N 140 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7703 (mtp85) REVERT: N 162 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7279 (tm-30) REVERT: N 169 GLU cc_start: 0.7827 (pp20) cc_final: 0.7560 (pp20) REVERT: N 178 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8024 (mt-10) outliers start: 76 outliers final: 66 residues processed: 1341 average time/residue: 1.1538 time to fit residues: 2417.1057 Evaluate side-chains 1369 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1298 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 443 GLN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 476 MET Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain F residue 743 THR Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 20.0000 chunk 405 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 381 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN E 747 GLN ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN K 122 HIS K 150 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109563 restraints weight = 156873.379| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.81 r_work: 0.3046 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 38586 Z= 0.305 Angle : 0.581 10.719 52137 Z= 0.303 Chirality : 0.041 0.174 5981 Planarity : 0.004 0.067 6728 Dihedral : 8.527 170.586 5411 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 17.81 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4795 helix: 0.97 (0.10), residues: 2516 sheet: -1.34 (0.20), residues: 616 loop : -0.91 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 649 HIS 0.010 0.001 HIS F 483 PHE 0.027 0.001 PHE F 665 TYR 0.014 0.001 TYR F 388 ARG 0.010 0.000 ARG E 592 =============================================================================== Job complete usr+sys time: 32001.24 seconds wall clock time: 540 minutes 2.82 seconds (32402.82 seconds total)