Starting phenix.real_space_refine on Sun Sep 29 22:41:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/09_2024/7uiy_26557_trim.cif" } resolution = 3.22 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 5 5.21 5 S 169 5.16 5 C 23824 2.51 5 N 6720 2.21 5 O 7230 1.98 5 H 38283 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 254 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76262 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: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9138 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9154 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9137 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 9087 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 18, 'TRANS': 556} Chain breaks: 1 Chain: "S" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 178 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.14, per 1000 atoms: 0.36 Number of scatterers: 76262 At special positions: 0 Unit cell: (150.51, 155.73, 166.17, 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 5 11.99 O 7230 8.00 N 6720 7.00 C 23824 6.00 H 38283 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: 14.23 Conformation dependent library (CDL) restraints added in 4.6 seconds 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 48 sheets defined 56.2% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 176 through 183 removed outlier: 3.831A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.874A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.543A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 275 removed outlier: 3.990A pdb=" N LYS A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.911A pdb=" N ILE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.760A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 350 through 370 removed outlier: 3.717A pdb=" N GLY A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.626A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.612A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 removed outlier: 4.329A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.506A pdb=" N ASN A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.688A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.591A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.728A pdb=" N SER A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.715A pdb=" N ASP A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.195A pdb=" N PHE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 580 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 removed outlier: 4.203A pdb=" N ARG A 610 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.816A pdb=" N LYS A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.041A 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 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 676 removed outlier: 3.959A pdb=" N HIS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.696A pdb=" N ARG A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.997A pdb=" N ALA A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 724 through 727 removed outlier: 3.960A pdb=" N ASP A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.713A 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: 3.747A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.597A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.528A pdb=" N ALA B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.842A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 370 removed outlier: 3.524A 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: 3.514A pdb=" N VAL B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.727A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.568A pdb=" N LYS B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) 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: 3.539A pdb=" N VAL B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 3.982A 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 571 through 584 removed outlier: 3.626A pdb=" N ASN B 575 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 3.865A 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 Processing helix chain 'B' and resid 637 through 643 Processing helix chain 'B' and resid 654 through 675 removed outlier: 3.532A pdb=" N ASP B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.747A pdb=" N ALA B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.511A pdb=" N VAL C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.628A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.501A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 278 Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.771A pdb=" N ILE C 291 " --> pdb=" O HIS C 288 " (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 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.552A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 370 removed outlier: 3.721A 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 removed outlier: 3.507A pdb=" N VAL C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 412 removed outlier: 3.920A pdb=" N ILE C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 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 500 through 513 removed outlier: 3.926A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 527 through 531 Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 566 through 570 removed outlier: 5.601A pdb=" N HIS C 570 " --> pdb=" O GLU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.605A 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 Processing helix chain 'C' and resid 637 through 644 removed outlier: 3.687A pdb=" N LEU C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 677 removed outlier: 3.593A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.575A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.548A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 219 through 234 removed outlier: 3.539A pdb=" N ALA D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 233 " --> pdb=" O TRP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 278 Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.839A pdb=" N ILE D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY D 292 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 313 Proline residue: D 309 - end of helix removed outlier: 3.546A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.526A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.655A 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: 3.658A pdb=" N ILE D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 435 removed outlier: 3.696A pdb=" N ILE D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 451 through 460 Processing helix chain 'D' and resid 463 through 479 removed outlier: 3.518A pdb=" N ILE D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.849A pdb=" N VAL D 506 " --> pdb=" O THR D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.636A pdb=" N VAL D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 531' Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 571 through 584 removed outlier: 3.891A pdb=" N ASN D 575 " --> pdb=" O PRO D 571 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 577 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 4.031A 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 Processing helix chain 'D' and resid 637 through 644 Processing helix chain 'D' and resid 654 through 676 removed outlier: 3.795A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.040A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.606A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.655A 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 233 removed outlier: 3.941A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 261 through 277 Processing helix chain 'E' and resid 287 through 292 removed outlier: 4.333A pdb=" N ILE E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.866A 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 313 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.751A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 370 removed outlier: 3.765A 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: 3.504A pdb=" N LYS E 387 " --> pdb=" O GLU E 383 " (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: 4.022A pdb=" N ASN E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 460 Processing helix chain 'E' and resid 463 through 478 removed outlier: 3.835A pdb=" N ILE E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 513 removed outlier: 3.867A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 529 through 534 removed outlier: 4.478A pdb=" N LEU E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 534 " --> pdb=" O VAL E 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 529 through 534' Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.865A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 569 Processing helix chain 'E' and resid 570 through 584 removed outlier: 3.880A pdb=" N PHE E 574 " --> pdb=" O HIS E 570 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 614 removed outlier: 4.025A pdb=" N ARG E 610 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.283A 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 removed outlier: 3.591A pdb=" N LEU E 644 " --> pdb=" O PHE E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 677 removed outlier: 3.873A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 695 removed outlier: 3.536A pdb=" N ARG E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN E 688 " --> pdb=" O GLN E 684 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP E 689 " --> pdb=" O GLU E 685 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 693 " --> pdb=" O TRP E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 712 removed outlier: 3.576A pdb=" N VAL E 707 " --> pdb=" O PRO E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.660A pdb=" N LEU E 716 " --> pdb=" O LEU E 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 removed outlier: 3.547A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 219 through 234 removed outlier: 3.786A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 242 removed outlier: 4.222A pdb=" N ASP F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 261 through 277 removed outlier: 4.065A pdb=" N ASP F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.124A pdb=" N ILE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 314 removed outlier: 3.773A pdb=" N LEU F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.629A pdb=" N ALA F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 370 Proline residue: F 363 - end of helix removed outlier: 3.650A pdb=" N HIS F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.596A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 412 Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.678A pdb=" N ILE F 426 " --> pdb=" O ASN F 422 " (cutoff:3.500A) removed outlier: 3.502A 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 451 Processing helix chain 'F' and resid 451 through 460 removed outlier: 3.824A pdb=" N LEU F 459 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 480 removed outlier: 3.517A pdb=" N ALA F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 483 No H-bonds generated for 'chain 'F' and resid 481 through 483' Processing helix chain 'F' and resid 500 through 513 removed outlier: 3.534A pdb=" N VAL F 504 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 534 removed outlier: 3.524A pdb=" N ILE F 534 " --> pdb=" O VAL F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 556 Processing helix chain 'F' and resid 570 through 583 removed outlier: 3.733A pdb=" N PHE F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN F 575 " --> pdb=" O PRO F 571 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 579 " --> pdb=" O ASN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 614 removed outlier: 3.699A pdb=" N THR F 612 " --> pdb=" O GLY F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.547A pdb=" N ILE F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 677 removed outlier: 3.735A pdb=" N ASP F 663 " --> pdb=" O HIS F 659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 667 " --> pdb=" O ASP F 663 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 668 " --> pdb=" O LYS F 664 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 669 " --> pdb=" O PHE F 665 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 removed outlier: 3.681A pdb=" N GLU F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 693 " --> pdb=" O TRP F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 722 removed outlier: 3.952A pdb=" N ALA F 705 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix Processing helix chain 'F' and resid 723 through 727 removed outlier: 4.227A pdb=" N ASP F 727 " --> pdb=" O SER F 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.747A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.522A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.571A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.791A 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 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.565A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.757A 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: 3.586A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 131 through 158 removed outlier: 3.574A pdb=" N GLU I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 183 removed outlier: 3.666A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.504A 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: 3.773A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.921A 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 170 removed outlier: 4.501A pdb=" N ARG J 170 " --> pdb=" O ARG J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 183 removed outlier: 3.643A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) 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: 3.649A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 105 Processing helix chain 'K' and resid 131 through 158 Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.642A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.702A 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: 3.551A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 131 through 158 Processing helix chain 'L' and resid 160 through 170 removed outlier: 4.294A pdb=" N ARG L 170 " --> pdb=" O ARG L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.591A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 Processing helix chain 'M' and resid 96 through 104 Processing helix chain 'M' and resid 131 through 158 removed outlier: 3.529A pdb=" N GLU M 141 " --> pdb=" O ILE M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 170 removed outlier: 4.420A pdb=" N ARG M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 183 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.543A 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: 3.552A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 106 Processing helix chain 'N' and resid 131 through 158 removed outlier: 3.574A pdb=" N ILE N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 175 through 183 removed outlier: 3.602A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 5.680A pdb=" N ASP A 285 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR A 322 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 212 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.872A pdb=" N ARG A 372 " --> pdb=" O VAL A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 493 removed outlier: 5.995A pdb=" N GLY A 489 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N MET A 603 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 491 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 559 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 602 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU A 561 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 604 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 563 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AA5, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.784A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.024A pdb=" N TYR B 246 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP B 285 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 248 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 282 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N SER B 321 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE B 284 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 211 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 346 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 213 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.514A pdb=" N ARG B 372 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 515 through 520 removed outlier: 7.397A pdb=" N GLU B 515 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 562 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 564 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 519 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.584A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 594 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.656A pdb=" N GLU B 681 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N LEU B 735 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN B 730 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN B 747 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.327A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER C 280 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE C 319 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 282 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 321 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE C 284 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C 209 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE C 344 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU C 211 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 372 through 373 removed outlier: 6.286A pdb=" N ARG C 372 " --> pdb=" O VAL C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 515 through 520 removed outlier: 3.858A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 585 through 587 removed outlier: 3.624A pdb=" N LEU C 586 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 679 through 682 removed outlier: 6.150A pdb=" N SER C 679 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 733 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU C 681 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU C 735 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.383A pdb=" N THR D 244 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE D 283 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR D 246 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP D 285 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU D 248 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER D 280 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE D 319 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR D 322 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 212 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN D 209 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE D 344 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU D 211 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 372 through 373 removed outlier: 6.964A pdb=" N ARG D 372 " --> pdb=" O VAL D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 516 through 520 removed outlier: 3.581A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 492 " --> pdb=" O ASN D 646 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AC2, first strand: chain 'D' and resid 680 through 682 removed outlier: 7.014A pdb=" N GLU D 681 " --> pdb=" O VAL D 733 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU D 735 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP D 736 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 173 through 175 removed outlier: 3.556A pdb=" N THR E 174 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP E 285 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU E 248 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU E 282 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER E 321 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 284 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY E 214 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN E 209 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE E 344 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 211 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 346 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL E 213 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 515 through 520 removed outlier: 6.936A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA E 559 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER E 490 " --> pdb=" O ASN E 646 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 648 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU E 492 " --> pdb=" O ILE E 648 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 585 through 587 Processing sheet with id=AC6, first strand: chain 'F' and resid 174 through 175 removed outlier: 3.511A pdb=" N THR F 174 " --> pdb=" O SER F 247 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG F 317 " --> pdb=" O SER F 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 492 through 494 removed outlier: 6.384A pdb=" N LEU F 492 " --> pdb=" O ILE F 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 517 through 520 removed outlier: 6.698A pdb=" N LEU F 517 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP F 564 " --> pdb=" O LEU F 517 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE F 519 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 731 through 736 removed outlier: 3.565A pdb=" N ASP F 736 " --> pdb=" O GLU F 741 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD2, first strand: chain 'H' and resid 28 through 32 removed outlier: 7.996A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.339A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 6 through 9 Processing sheet with id=AD5, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.402A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.402A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG I 111 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 5 through 8 Processing sheet with id=AD8, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.738A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.738A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER J 65 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLN J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS J 113 " --> pdb=" O SER J 187 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AE2, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.099A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG K 111 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 94 through 95 removed outlier: 6.253A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 5 through 9 Processing sheet with id=AE5, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.587A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG L 118 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY L 93 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N MET L 120 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.587A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG L 111 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AE8, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.994A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AF1, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AF2, first strand: chain 'N' and resid 28 through 32 removed outlier: 7.132A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.716A pdb=" N VAL N 119 " --> pdb=" O LEU N 174 " (cutoff:3.500A) 1808 hydrogen bonds defined for protein. 5328 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: 29.78 Time building geometry restraints manager: 17.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 38257 1.06 - 1.28: 6534 1.28 - 1.50: 15829 1.50 - 1.73: 15920 1.73 - 1.95: 305 Bond restraints: 76845 Sorted by residual: bond pdb=" C4 ADP D 802 " pdb=" C5 ADP D 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP E 802 " pdb=" C5 ADP E 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 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 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+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 2.94e+01 ... (remaining 76840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 138647 3.28 - 6.55: 537 6.55 - 9.83: 73 9.83 - 13.10: 21 13.10 - 16.38: 1 Bond angle restraints: 139279 Sorted by residual: angle pdb=" PA AGS C 801 " pdb=" O3A AGS C 801 " pdb=" PB AGS C 801 " ideal model delta sigma weight residual 119.76 136.14 -16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 132.85 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N LEU C 394 " pdb=" CA LEU C 394 " pdb=" C LEU C 394 " ideal model delta sigma weight residual 113.16 119.17 -6.01 1.42e+00 4.96e-01 1.79e+01 angle pdb=" PA AGS D 801 " pdb=" O3A AGS D 801 " pdb=" PB AGS D 801 " ideal model delta sigma weight residual 119.76 132.13 -12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" PB AGS C 802 " pdb=" O3B AGS C 802 " pdb=" PG AGS C 802 " ideal model delta sigma weight residual 120.12 132.32 -12.20 3.00e+00 1.11e-01 1.65e+01 ... (remaining 139274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 34130 28.99 - 57.98: 1325 57.98 - 86.97: 100 86.97 - 115.96: 15 115.96 - 144.95: 18 Dihedral angle restraints: 35588 sinusoidal: 20083 harmonic: 15505 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 84.96 -144.95 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" C5' ADP D 802 " pdb=" O5' ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 82.83 -142.83 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP F 802 " pdb=" O5' ADP F 802 " pdb=" PA ADP F 802 " pdb=" O2A ADP F 802 " ideal model delta sinusoidal sigma weight residual 300.00 160.87 139.14 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 35585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4619 0.050 - 0.101: 1110 0.101 - 0.151: 231 0.151 - 0.201: 15 0.201 - 0.252: 4 Chirality restraints: 5979 Sorted by residual: chirality pdb=" CA PHE M 82 " pdb=" N PHE M 82 " pdb=" C PHE M 82 " pdb=" CB PHE M 82 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 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 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE F 436 " pdb=" N ILE F 436 " pdb=" C ILE F 436 " pdb=" CB ILE F 436 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 5976 not shown) Planarity restraints: 11367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 545 " -0.128 2.00e-02 2.50e+03 4.32e-01 2.80e+03 pdb=" CD GLN E 545 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN E 545 " 0.123 2.00e-02 2.50e+03 pdb=" NE2 GLN E 545 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN E 545 " -0.743 2.00e-02 2.50e+03 pdb="HE22 GLN E 545 " 0.734 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 544 " -0.017 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" N GLN E 545 " 0.054 2.00e-02 2.50e+03 pdb=" CA GLN E 545 " -0.014 2.00e-02 2.50e+03 pdb=" H GLN E 545 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 362 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 363 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.042 5.00e-02 4.00e+02 ... (remaining 11364 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 10039 2.26 - 2.84: 176791 2.84 - 3.43: 199097 3.43 - 4.01: 277508 4.01 - 4.60: 427316 Nonbonded interactions: 1090751 Sorted by model distance: nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.674 2.450 nonbonded pdb=" O TYR F 246 " pdb=" H PHE F 283 " model vdw 1.677 2.450 nonbonded pdb="HH22 ARG D 339 " pdb=" O2B AGS C 801 " model vdw 1.686 2.450 nonbonded pdb=" O TYR E 246 " pdb=" H PHE E 283 " model vdw 1.691 2.450 nonbonded pdb=" OD2 ASP C 396 " pdb=" HZ3 LYS D 207 " model vdw 1.694 2.450 ... (remaining 1090746 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 296 or (resid 30 \ 1 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or nam \ e HG22 or name HG23)) or resid 302 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 542 or \ (resid 543 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) o \ r resid 544 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 296 or (resid 301 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 302 \ through 542 or (resid 543 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 \ or name HA )) or resid 544 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 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 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 503 through 542 or (resi \ d 543 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or res \ id 544 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 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 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 503 through 542 or (resi \ d 543 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or res \ id 544 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 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 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me 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 542 or (resid 543 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 \ or name HA )) or resid 544 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.150 Check model and map are aligned: 0.430 Set scattering table: 0.530 Process input model: 123.780 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.190 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.006 0.110 38562 Z= 0.382 Angle : 0.855 16.376 52104 Z= 0.440 Chirality : 0.045 0.252 5979 Planarity : 0.005 0.076 6722 Dihedral : 14.468 144.954 14693 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.25 (0.11), residues: 4789 helix: 0.45 (0.10), residues: 2331 sheet: -0.34 (0.19), residues: 666 loop : -0.78 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 229 HIS 0.010 0.001 HIS D 393 PHE 0.038 0.002 PHE M 82 TYR 0.014 0.001 TYR F 540 ARG 0.006 0.000 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1263 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1263 time to evaluate : 4.346 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: A 200 GLN cc_start: 0.8008 (mt0) cc_final: 0.7795 (mt0) REVERT: A 286 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6672 (mm-30) REVERT: A 432 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6691 (mtm180) REVERT: A 507 GLN cc_start: 0.7865 (mm110) cc_final: 0.7614 (mp10) REVERT: A 565 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6873 (mt-10) REVERT: A 624 ASN cc_start: 0.6468 (p0) cc_final: 0.6248 (p0) REVERT: A 658 ILE cc_start: 0.7478 (mm) cc_final: 0.7230 (mm) REVERT: A 692 GLU cc_start: 0.6287 (tm-30) cc_final: 0.5988 (tp30) REVERT: B 370 ASP cc_start: 0.7244 (t0) cc_final: 0.6877 (t0) REVERT: B 425 ASP cc_start: 0.7208 (t70) cc_final: 0.6985 (t0) REVERT: C 207 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8537 (mtpt) REVERT: C 229 TRP cc_start: 0.8196 (t60) cc_final: 0.7716 (t60) REVERT: C 674 ASP cc_start: 0.8034 (t70) cc_final: 0.7829 (t70) REVERT: D 178 GLN cc_start: 0.6844 (tp-100) cc_final: 0.6357 (tp40) REVERT: D 370 ASP cc_start: 0.7285 (t0) cc_final: 0.6944 (t0) REVERT: D 451 ASN cc_start: 0.8169 (m110) cc_final: 0.7886 (m110) REVERT: D 646 ASN cc_start: 0.9019 (t0) cc_final: 0.8811 (t0) REVERT: D 647 ILE cc_start: 0.8828 (mt) cc_final: 0.8625 (mp) REVERT: E 258 LYS cc_start: 0.8138 (pttp) cc_final: 0.7814 (ptmm) REVERT: E 383 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 422 ASN cc_start: 0.7353 (t0) cc_final: 0.7041 (t0) REVERT: E 532 ARG cc_start: 0.7089 (mmm160) cc_final: 0.6835 (mmm160) REVERT: E 582 ASP cc_start: 0.7465 (t0) cc_final: 0.6920 (t70) REVERT: E 613 GLU cc_start: 0.8091 (pp20) cc_final: 0.7783 (pp20) REVERT: E 697 ARG cc_start: 0.7815 (tpt-90) cc_final: 0.7559 (ttm-80) REVERT: F 191 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.6950 (mmt90) REVERT: F 197 ARG cc_start: 0.6975 (tpt-90) cc_final: 0.6765 (tpt90) REVERT: F 272 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7763 (mmtm) REVERT: F 366 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6961 (mt-10) REVERT: F 422 ASN cc_start: 0.6821 (m-40) cc_final: 0.6602 (m-40) REVERT: F 507 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7818 (mm-40) REVERT: F 523 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8601 (tm-30) REVERT: F 551 ASP cc_start: 0.6734 (m-30) cc_final: 0.6417 (m-30) REVERT: F 620 ILE cc_start: 0.5110 (tp) cc_final: 0.4867 (tp) REVERT: F 711 ASN cc_start: 0.7800 (t0) cc_final: 0.7489 (t0) REVERT: F 719 GLU cc_start: 0.7632 (tp30) cc_final: 0.6934 (tp30) REVERT: H 162 GLU cc_start: 0.6264 (tm-30) cc_final: 0.6044 (tm-30) REVERT: I 15 ARG cc_start: 0.6575 (ttm-80) cc_final: 0.6288 (mtp-110) REVERT: I 69 VAL cc_start: 0.8641 (t) cc_final: 0.8407 (p) REVERT: I 118 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.7180 (ttm-80) REVERT: I 151 GLU cc_start: 0.7177 (tt0) cc_final: 0.6955 (tt0) REVERT: J 35 VAL cc_start: 0.8736 (t) cc_final: 0.8402 (t) REVERT: J 53 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6862 (mm-30) REVERT: J 161 LEU cc_start: 0.7590 (pp) cc_final: 0.6872 (pp) REVERT: K 36 GLU cc_start: 0.7402 (tp30) cc_final: 0.7119 (tt0) REVERT: L 34 GLN cc_start: 0.7691 (tp-100) cc_final: 0.7467 (tp-100) REVERT: L 57 LYS cc_start: 0.7894 (mttm) cc_final: 0.7684 (mttm) REVERT: L 74 MET cc_start: 0.8084 (mmp) cc_final: 0.7769 (mmm) REVERT: L 78 ASP cc_start: 0.8052 (m-30) cc_final: 0.7793 (m-30) REVERT: L 149 MET cc_start: 0.7600 (mmt) cc_final: 0.7341 (mmt) REVERT: L 172 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7290 (ttt180) REVERT: L 173 PHE cc_start: 0.8741 (m-80) cc_final: 0.8205 (m-80) REVERT: M 169 GLU cc_start: 0.7323 (tp30) cc_final: 0.7082 (tp30) REVERT: M 170 ARG cc_start: 0.7150 (mmt-90) cc_final: 0.5967 (mmt180) REVERT: N 42 LEU cc_start: 0.8869 (tp) cc_final: 0.8647 (tp) outliers start: 0 outliers final: 0 residues processed: 1263 average time/residue: 1.1651 time to fit residues: 2318.8837 Evaluate side-chains 1050 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1050 time to evaluate : 4.448 ------------------------------------------------------------------------------- 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: 20.0000 chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 376 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS B 209 ASN B 528 HIS B 642 ASN C 622 GLN D 178 GLN D 356 GLN D 598 ASN D 659 HIS E 273 GLN E 507 GLN E 740 ASN F 688 ASN F 709 GLN I 41 ASN J 41 ASN K 41 ASN K 191 HIS L 116 ASN M 41 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 38562 Z= 0.324 Angle : 0.621 7.257 52104 Z= 0.332 Chirality : 0.042 0.171 5979 Planarity : 0.005 0.051 6722 Dihedral : 9.934 161.587 5406 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 9.47 % Favored : 89.35 % 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: 0.26 (0.11), residues: 4789 helix: 0.94 (0.10), residues: 2424 sheet: -0.28 (0.19), residues: 691 loop : -0.64 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 229 HIS 0.008 0.001 HIS D 393 PHE 0.024 0.001 PHE M 82 TYR 0.013 0.001 TYR E 540 ARG 0.007 0.001 ARG C 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1196 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1148 time to evaluate : 4.369 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: A 306 LEU cc_start: 0.8479 (mt) cc_final: 0.8146 (mt) REVERT: A 307 ILE cc_start: 0.8535 (pt) cc_final: 0.8092 (mt) REVERT: A 362 LYS cc_start: 0.7086 (tttt) cc_final: 0.6799 (tttm) REVERT: A 387 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8637 (ttmm) REVERT: A 507 GLN cc_start: 0.7862 (mm110) cc_final: 0.7610 (mp10) REVERT: A 624 ASN cc_start: 0.6482 (p0) cc_final: 0.6275 (p0) REVERT: A 692 GLU cc_start: 0.6553 (tm-30) cc_final: 0.6292 (tp30) REVERT: B 215 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 362 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8691 (mtpt) REVERT: B 370 ASP cc_start: 0.7270 (t0) cc_final: 0.6884 (t0) REVERT: B 613 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: C 207 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8718 (mtpt) REVERT: C 229 TRP cc_start: 0.8660 (t60) cc_final: 0.7522 (t60) REVERT: C 233 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7913 (mm110) REVERT: C 573 VAL cc_start: 0.9005 (t) cc_final: 0.8767 (m) REVERT: D 370 ASP cc_start: 0.7290 (t0) cc_final: 0.6923 (t0) REVERT: D 451 ASN cc_start: 0.8177 (m110) cc_final: 0.7846 (m110) REVERT: E 225 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 235 ASP cc_start: 0.6593 (t0) cc_final: 0.6327 (t0) REVERT: E 252 SER cc_start: 0.8658 (m) cc_final: 0.8224 (m) REVERT: E 258 LYS cc_start: 0.8289 (pttp) cc_final: 0.7915 (ptmm) REVERT: E 348 GLU cc_start: 0.6874 (pt0) cc_final: 0.6367 (pt0) REVERT: E 387 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8487 (mtpp) REVERT: E 520 ASP cc_start: 0.7285 (t0) cc_final: 0.6874 (t0) REVERT: E 532 ARG cc_start: 0.7076 (mmm160) cc_final: 0.6820 (mmm160) REVERT: E 582 ASP cc_start: 0.7655 (t0) cc_final: 0.7045 (t70) REVERT: E 611 GLU cc_start: 0.7833 (mp0) cc_final: 0.7608 (mp0) REVERT: E 704 MET cc_start: 0.6997 (ttt) cc_final: 0.6568 (ttt) REVERT: F 268 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7381 (ttmt) REVERT: F 272 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7814 (mmmm) REVERT: F 523 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8587 (tm-30) REVERT: F 551 ASP cc_start: 0.7134 (m-30) cc_final: 0.6742 (m-30) REVERT: F 719 GLU cc_start: 0.7705 (tp30) cc_final: 0.6932 (tp30) REVERT: H 22 ARG cc_start: 0.8933 (tpt90) cc_final: 0.8317 (tpt90) REVERT: H 141 GLU cc_start: 0.8186 (tp30) cc_final: 0.7861 (tp30) REVERT: H 162 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5141 (tm-30) REVERT: I 25 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8467 (mtpp) REVERT: I 118 ARG cc_start: 0.7464 (mmt-90) cc_final: 0.7128 (mpt180) REVERT: I 151 GLU cc_start: 0.7236 (tt0) cc_final: 0.7034 (tt0) REVERT: J 123 GLN cc_start: 0.8173 (pt0) cc_final: 0.7929 (pt0) REVERT: J 146 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8449 (ttpp) REVERT: J 166 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.7112 (ttp-110) REVERT: K 18 ASP cc_start: 0.8209 (p0) cc_final: 0.7905 (p0) REVERT: K 26 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8048 (mm-30) REVERT: L 34 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7576 (mm-40) REVERT: L 140 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7392 (ttm110) REVERT: L 149 MET cc_start: 0.7943 (mmt) cc_final: 0.7698 (mmt) REVERT: L 172 ARG cc_start: 0.7463 (ttt90) cc_final: 0.7094 (ttt180) REVERT: L 173 PHE cc_start: 0.8706 (m-80) cc_final: 0.8203 (m-80) REVERT: M 22 ARG cc_start: 0.8636 (tpt90) cc_final: 0.7615 (tpt90) REVERT: M 101 PHE cc_start: 0.8263 (t80) cc_final: 0.7843 (t80) REVERT: M 170 ARG cc_start: 0.7251 (mmt-90) cc_final: 0.6150 (mmt180) REVERT: N 41 ASN cc_start: 0.8268 (m110) cc_final: 0.7838 (m110) REVERT: N 140 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7899 (mmm-85) outliers start: 48 outliers final: 36 residues processed: 1166 average time/residue: 1.1295 time to fit residues: 2056.7672 Evaluate side-chains 1135 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1097 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 436 optimal weight: 6.9990 chunk 471 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 359 ASN A 483 HIS A 507 GLN A 528 HIS ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS C 711 ASN E 273 GLN F 688 ASN H 41 ASN I 41 ASN J 150 ASN K 191 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 38562 Z= 0.316 Angle : 0.580 10.383 52104 Z= 0.305 Chirality : 0.041 0.159 5979 Planarity : 0.004 0.095 6722 Dihedral : 9.910 163.850 5406 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.21 % Allowed : 11.71 % Favored : 87.08 % 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: 0.20 (0.12), residues: 4789 helix: 0.94 (0.10), residues: 2436 sheet: -0.44 (0.19), residues: 676 loop : -0.71 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.008 0.001 HIS J 122 PHE 0.023 0.001 PHE A 640 TYR 0.013 0.001 TYR D 324 ARG 0.009 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1216 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1167 time to evaluate : 4.490 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: A 240 MET cc_start: 0.7939 (mmt) cc_final: 0.7726 (mmt) REVERT: A 285 ASP cc_start: 0.7966 (t0) cc_final: 0.7736 (t0) REVERT: A 306 LEU cc_start: 0.8490 (mt) cc_final: 0.8153 (mt) REVERT: A 307 ILE cc_start: 0.8487 (pt) cc_final: 0.8054 (mt) REVERT: A 387 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8636 (ttmm) REVERT: A 503 GLU cc_start: 0.7204 (tp30) cc_final: 0.6282 (tp30) REVERT: A 505 THR cc_start: 0.7661 (m) cc_final: 0.7418 (p) REVERT: A 507 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7642 (mp10) REVERT: A 624 ASN cc_start: 0.6447 (p0) cc_final: 0.6245 (p0) REVERT: A 699 MET cc_start: 0.5210 (mmp) cc_final: 0.4780 (mmt) REVERT: A 730 GLN cc_start: 0.5849 (mp10) cc_final: 0.5523 (mp10) REVERT: B 206 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6949 (mmt180) REVERT: B 215 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 370 ASP cc_start: 0.7306 (t0) cc_final: 0.6993 (t0) REVERT: B 419 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8148 (tttt) REVERT: B 674 ASP cc_start: 0.7488 (m-30) cc_final: 0.7244 (m-30) REVERT: C 207 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8727 (mtpt) REVERT: C 573 VAL cc_start: 0.9146 (t) cc_final: 0.8907 (m) REVERT: C 718 ASN cc_start: 0.7865 (m-40) cc_final: 0.7655 (m-40) REVERT: D 370 ASP cc_start: 0.7292 (t0) cc_final: 0.6998 (t0) REVERT: D 451 ASN cc_start: 0.8221 (m110) cc_final: 0.7948 (m-40) REVERT: D 532 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7353 (mmm-85) REVERT: D 688 ASN cc_start: 0.8186 (m-40) cc_final: 0.7948 (m-40) REVERT: E 225 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7966 (mt-10) REVERT: E 235 ASP cc_start: 0.6912 (t0) cc_final: 0.6434 (t0) REVERT: E 348 GLU cc_start: 0.7474 (pt0) cc_final: 0.6552 (pt0) REVERT: E 520 ASP cc_start: 0.7372 (t0) cc_final: 0.6978 (t0) REVERT: E 532 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6882 (mmm160) REVERT: E 582 ASP cc_start: 0.7866 (t0) cc_final: 0.7465 (t0) REVERT: E 611 GLU cc_start: 0.7907 (mp0) cc_final: 0.7691 (mp0) REVERT: E 704 MET cc_start: 0.7105 (ttt) cc_final: 0.6733 (ttt) REVERT: F 268 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7416 (ttmt) REVERT: F 272 LYS cc_start: 0.8427 (mtmt) cc_final: 0.7855 (mmmm) REVERT: F 523 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8617 (tm-30) REVERT: F 551 ASP cc_start: 0.7152 (m-30) cc_final: 0.6770 (m-30) REVERT: H 22 ARG cc_start: 0.8997 (tpt90) cc_final: 0.8377 (tpt90) REVERT: H 162 GLU cc_start: 0.6462 (tm-30) cc_final: 0.5581 (tm-30) REVERT: I 8 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7065 (tm-30) REVERT: I 25 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8651 (mtpp) REVERT: I 118 ARG cc_start: 0.7427 (mmt-90) cc_final: 0.7149 (mpt180) REVERT: I 151 GLU cc_start: 0.7289 (tt0) cc_final: 0.7050 (tt0) REVERT: J 123 GLN cc_start: 0.8313 (pt0) cc_final: 0.7973 (pt0) REVERT: K 18 ASP cc_start: 0.8263 (p0) cc_final: 0.8062 (p0) REVERT: K 172 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7870 (ttt90) REVERT: L 34 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7731 (mm-40) REVERT: L 144 LYS cc_start: 0.8126 (mttm) cc_final: 0.7802 (mtpp) REVERT: L 149 MET cc_start: 0.8096 (mmt) cc_final: 0.7800 (mmt) REVERT: L 172 ARG cc_start: 0.7576 (ttt90) cc_final: 0.7193 (ttt180) REVERT: M 101 PHE cc_start: 0.8316 (t80) cc_final: 0.7859 (t80) REVERT: M 170 ARG cc_start: 0.6998 (mmt-90) cc_final: 0.6767 (mmt180) REVERT: N 53 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7850 (mm-30) outliers start: 49 outliers final: 37 residues processed: 1187 average time/residue: 1.1428 time to fit residues: 2144.5965 Evaluate side-chains 1155 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1118 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 180 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 5.9990 chunk 328 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 chunk 438 optimal weight: 8.9990 chunk 463 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 415 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 GLN B 642 ASN C 178 GLN C 342 GLN C 356 GLN C 483 HIS C 575 ASN C 622 GLN D 606 ASN E 273 GLN F 177 ASN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 659 HIS H 41 ASN I 41 ASN J 150 ASN K 191 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 38562 Z= 0.451 Angle : 0.640 7.873 52104 Z= 0.337 Chirality : 0.043 0.265 5979 Planarity : 0.005 0.083 6722 Dihedral : 10.247 177.140 5406 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 13.24 % Favored : 84.77 % 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: -0.13 (0.11), residues: 4789 helix: 0.73 (0.10), residues: 2483 sheet: -0.68 (0.18), residues: 670 loop : -0.96 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.014 0.002 HIS I 191 PHE 0.028 0.002 PHE J 101 TYR 0.018 0.002 TYR D 324 ARG 0.009 0.001 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1238 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1157 time to evaluate : 4.489 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: A 306 LEU cc_start: 0.8509 (mt) cc_final: 0.8148 (mt) REVERT: A 307 ILE cc_start: 0.8527 (pt) cc_final: 0.8094 (mt) REVERT: A 321 SER cc_start: 0.8786 (m) cc_final: 0.8541 (p) REVERT: A 387 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8660 (ttmm) REVERT: A 408 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7628 (ttm-80) REVERT: A 427 GLU cc_start: 0.7294 (pt0) cc_final: 0.6776 (pt0) REVERT: A 503 GLU cc_start: 0.7381 (tp30) cc_final: 0.6540 (tp30) REVERT: A 507 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7550 (mp10) REVERT: B 206 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6981 (mmt180) REVERT: B 247 SER cc_start: 0.8504 (t) cc_final: 0.8181 (p) REVERT: B 425 ASP cc_start: 0.8001 (t70) cc_final: 0.7485 (t0) REVERT: B 674 ASP cc_start: 0.7470 (m-30) cc_final: 0.7158 (m-30) REVERT: C 207 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8770 (mtpt) REVERT: C 259 TYR cc_start: 0.8700 (m-80) cc_final: 0.7862 (m-80) REVERT: C 280 SER cc_start: 0.7530 (m) cc_final: 0.7230 (m) REVERT: C 573 VAL cc_start: 0.9294 (t) cc_final: 0.9019 (m) REVERT: C 697 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7780 (ttp-110) REVERT: D 370 ASP cc_start: 0.7381 (t0) cc_final: 0.7109 (t0) REVERT: D 396 ASP cc_start: 0.8201 (t70) cc_final: 0.7718 (t0) REVERT: D 451 ASN cc_start: 0.8256 (m110) cc_final: 0.7856 (m110) REVERT: D 454 ASP cc_start: 0.8279 (m-30) cc_final: 0.7996 (m-30) REVERT: D 532 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: D 688 ASN cc_start: 0.8216 (m-40) cc_final: 0.7971 (m110) REVERT: E 225 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 230 ARG cc_start: 0.7534 (mtp180) cc_final: 0.7307 (mtm180) REVERT: E 532 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6947 (mmm160) REVERT: E 617 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8833 (mt) REVERT: E 697 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7630 (ttm-80) REVERT: E 704 MET cc_start: 0.7196 (ttt) cc_final: 0.6903 (ttt) REVERT: F 268 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7504 (ttmt) REVERT: F 272 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7970 (mmtm) REVERT: F 353 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7489 (mt-10) REVERT: F 391 ASP cc_start: 0.7772 (t70) cc_final: 0.7406 (m-30) REVERT: F 523 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8635 (tm-30) REVERT: F 551 ASP cc_start: 0.7102 (m-30) cc_final: 0.6738 (m-30) REVERT: H 22 ARG cc_start: 0.9011 (tpt90) cc_final: 0.8328 (tpt90) REVERT: H 162 GLU cc_start: 0.6601 (tm-30) cc_final: 0.5756 (tm-30) REVERT: H 172 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6875 (ttm110) REVERT: I 25 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8656 (tttp) REVERT: I 136 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6601 (tm-30) REVERT: I 151 GLU cc_start: 0.7366 (tt0) cc_final: 0.7155 (tt0) REVERT: L 140 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.7524 (ttm110) REVERT: L 149 MET cc_start: 0.8215 (mmt) cc_final: 0.7892 (mmt) REVERT: L 167 ASP cc_start: 0.7753 (m-30) cc_final: 0.7481 (m-30) REVERT: L 172 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7181 (ttt180) REVERT: N 144 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8153 (mptt) REVERT: N 151 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7258 (mt-10) outliers start: 81 outliers final: 62 residues processed: 1190 average time/residue: 1.1644 time to fit residues: 2173.4566 Evaluate side-chains 1173 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1108 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 98 MET Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 chunk 395 optimal weight: 8.9990 chunk 320 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 416 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 528 HIS C 325 GLN C 622 GLN C 642 ASN D 329 ASN D 356 GLN D 579 GLN D 606 ASN F 369 HIS F 393 HIS F 422 ASN I 81 GLN I 156 HIS J 150 ASN K 191 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 38562 Z= 0.317 Angle : 0.574 7.233 52104 Z= 0.300 Chirality : 0.041 0.160 5979 Planarity : 0.004 0.053 6722 Dihedral : 10.227 176.152 5406 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 14.54 % Favored : 83.53 % 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: -0.04 (0.12), residues: 4789 helix: 0.84 (0.10), residues: 2488 sheet: -0.71 (0.18), residues: 668 loop : -0.94 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.011 0.001 HIS A 393 PHE 0.022 0.001 PHE A 640 TYR 0.017 0.001 TYR D 324 ARG 0.008 0.000 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1197 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1119 time to evaluate : 4.912 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: A 306 LEU cc_start: 0.8505 (mt) cc_final: 0.8147 (mt) REVERT: A 307 ILE cc_start: 0.8522 (pt) cc_final: 0.8089 (mt) REVERT: A 321 SER cc_start: 0.8775 (m) cc_final: 0.8556 (p) REVERT: A 359 ASN cc_start: 0.7964 (m-40) cc_final: 0.7686 (m-40) REVERT: A 387 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8655 (ttmm) REVERT: A 427 GLU cc_start: 0.7275 (pt0) cc_final: 0.6755 (pt0) REVERT: A 483 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6013 (m-70) REVERT: A 503 GLU cc_start: 0.7383 (tp30) cc_final: 0.6644 (tp30) REVERT: A 730 GLN cc_start: 0.6051 (mp10) cc_final: 0.4951 (mp10) REVERT: B 206 ARG cc_start: 0.7271 (tpt170) cc_final: 0.7021 (mmt180) REVERT: B 247 SER cc_start: 0.8476 (t) cc_final: 0.8158 (p) REVERT: B 419 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8189 (tttt) REVERT: B 425 ASP cc_start: 0.7945 (t70) cc_final: 0.7415 (t0) REVERT: B 674 ASP cc_start: 0.7459 (m-30) cc_final: 0.7138 (m-30) REVERT: B 735 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 207 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8731 (mtpt) REVERT: C 259 TYR cc_start: 0.8679 (m-80) cc_final: 0.7835 (m-80) REVERT: C 573 VAL cc_start: 0.9269 (t) cc_final: 0.8982 (m) REVERT: D 370 ASP cc_start: 0.7354 (t0) cc_final: 0.7098 (t0) REVERT: D 396 ASP cc_start: 0.8077 (t70) cc_final: 0.7645 (t0) REVERT: D 451 ASN cc_start: 0.8245 (m110) cc_final: 0.7906 (m-40) REVERT: D 454 ASP cc_start: 0.8236 (m-30) cc_final: 0.7935 (m-30) REVERT: D 532 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: D 688 ASN cc_start: 0.8217 (m-40) cc_final: 0.8010 (m110) REVERT: E 225 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 235 ASP cc_start: 0.7213 (t0) cc_final: 0.6874 (t70) REVERT: E 348 GLU cc_start: 0.8072 (pt0) cc_final: 0.7246 (pt0) REVERT: E 532 ARG cc_start: 0.7207 (mmm160) cc_final: 0.6959 (mmm160) REVERT: E 617 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8782 (mt) REVERT: E 704 MET cc_start: 0.7193 (ttt) cc_final: 0.6922 (ttt) REVERT: F 268 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7808 (tttm) REVERT: F 272 LYS cc_start: 0.8436 (mtmt) cc_final: 0.7952 (mmtm) REVERT: F 353 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7458 (mt-10) REVERT: F 369 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.7051 (p90) REVERT: F 391 ASP cc_start: 0.7848 (t70) cc_final: 0.7386 (m-30) REVERT: F 523 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8633 (tm-30) REVERT: F 551 ASP cc_start: 0.7074 (m-30) cc_final: 0.6711 (m-30) REVERT: H 22 ARG cc_start: 0.9011 (tpt90) cc_final: 0.8346 (tpt90) REVERT: H 162 GLU cc_start: 0.6380 (tm-30) cc_final: 0.5789 (tm-30) REVERT: H 172 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.6881 (tpp80) REVERT: I 136 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6622 (tm-30) REVERT: I 151 GLU cc_start: 0.7356 (tt0) cc_final: 0.7145 (tt0) REVERT: L 140 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7308 (mtp85) REVERT: L 149 MET cc_start: 0.8194 (mmt) cc_final: 0.7916 (mmt) REVERT: L 172 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7141 (ttt180) REVERT: M 170 ARG cc_start: 0.6673 (mpt180) cc_final: 0.6349 (mmt180) REVERT: N 70 ILE cc_start: 0.8501 (mm) cc_final: 0.8088 (mm) REVERT: N 144 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8162 (mptt) outliers start: 78 outliers final: 62 residues processed: 1150 average time/residue: 1.1417 time to fit residues: 2062.6930 Evaluate side-chains 1162 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1096 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 642 ASN Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 369 HIS Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.7980 chunk 417 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN C 325 GLN C 622 GLN D 579 GLN D 606 ASN E 579 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN K 191 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 38562 Z= 0.312 Angle : 0.567 7.227 52104 Z= 0.297 Chirality : 0.041 0.156 5979 Planarity : 0.004 0.050 6722 Dihedral : 10.089 172.139 5406 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 14.57 % Favored : 83.36 % 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: 4789 helix: 0.86 (0.10), residues: 2486 sheet: -0.80 (0.17), residues: 710 loop : -0.93 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.029 0.001 HIS F 369 PHE 0.021 0.001 PHE A 640 TYR 0.016 0.001 TYR K 60 ARG 0.006 0.000 ARG C 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1207 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1123 time to evaluate : 4.430 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: A 306 LEU cc_start: 0.8528 (mt) cc_final: 0.8166 (mt) REVERT: A 307 ILE cc_start: 0.8535 (pt) cc_final: 0.8100 (mt) REVERT: A 321 SER cc_start: 0.8794 (m) cc_final: 0.8554 (p) REVERT: A 359 ASN cc_start: 0.7948 (m-40) cc_final: 0.7670 (m-40) REVERT: A 376 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7653 (mtpp) REVERT: A 387 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8664 (ttmm) REVERT: A 408 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7351 (ptm-80) REVERT: A 427 GLU cc_start: 0.7343 (pt0) cc_final: 0.6790 (pt0) REVERT: A 483 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5857 (m-70) REVERT: A 503 GLU cc_start: 0.7221 (tp30) cc_final: 0.6778 (tp30) REVERT: B 206 ARG cc_start: 0.7268 (tpt170) cc_final: 0.7018 (mmt180) REVERT: B 247 SER cc_start: 0.8468 (t) cc_final: 0.8158 (p) REVERT: B 419 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8194 (tttt) REVERT: B 425 ASP cc_start: 0.7993 (t70) cc_final: 0.7445 (t0) REVERT: B 674 ASP cc_start: 0.7459 (m-30) cc_final: 0.7078 (m-30) REVERT: B 735 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8535 (tt) REVERT: C 207 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8772 (mtpt) REVERT: C 259 TYR cc_start: 0.8700 (m-80) cc_final: 0.7852 (m-80) REVERT: C 573 VAL cc_start: 0.9251 (t) cc_final: 0.8979 (m) REVERT: D 370 ASP cc_start: 0.7343 (t0) cc_final: 0.7090 (t0) REVERT: D 396 ASP cc_start: 0.8070 (t70) cc_final: 0.7647 (t0) REVERT: D 454 ASP cc_start: 0.8237 (m-30) cc_final: 0.7955 (m-30) REVERT: D 502 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8256 (p) REVERT: D 532 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: D 688 ASN cc_start: 0.8172 (m-40) cc_final: 0.7971 (m110) REVERT: E 225 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 235 ASP cc_start: 0.7296 (t0) cc_final: 0.6917 (t0) REVERT: E 348 GLU cc_start: 0.8154 (pt0) cc_final: 0.7421 (pt0) REVERT: E 532 ARG cc_start: 0.7221 (mmm160) cc_final: 0.6942 (mmm160) REVERT: E 617 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8770 (mt) REVERT: E 704 MET cc_start: 0.7240 (ttt) cc_final: 0.6971 (ttt) REVERT: F 268 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7821 (tttm) REVERT: F 272 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7964 (mmtm) REVERT: F 340 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7385 (mmt90) REVERT: F 523 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8640 (tm-30) REVERT: F 551 ASP cc_start: 0.7065 (m-30) cc_final: 0.6695 (m-30) REVERT: H 22 ARG cc_start: 0.9009 (tpt90) cc_final: 0.8352 (tpt90) REVERT: H 162 GLU cc_start: 0.6418 (tm-30) cc_final: 0.5883 (tm-30) REVERT: H 172 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.6806 (tpp80) REVERT: I 136 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6659 (tm-30) REVERT: I 151 GLU cc_start: 0.7366 (tt0) cc_final: 0.7147 (tt0) REVERT: K 15 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: L 144 LYS cc_start: 0.8232 (mttm) cc_final: 0.7913 (mtpp) REVERT: L 148 ARG cc_start: 0.6806 (mmm160) cc_final: 0.6590 (mmm160) REVERT: L 149 MET cc_start: 0.8210 (mmt) cc_final: 0.7862 (mmt) REVERT: L 172 ARG cc_start: 0.7599 (ttt90) cc_final: 0.7139 (ttt180) REVERT: M 89 THR cc_start: 0.8170 (p) cc_final: 0.7970 (p) REVERT: M 170 ARG cc_start: 0.6691 (mpt180) cc_final: 0.6446 (mmt180) REVERT: N 70 ILE cc_start: 0.8502 (mm) cc_final: 0.8109 (mm) REVERT: N 144 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8188 (mptt) outliers start: 84 outliers final: 67 residues processed: 1156 average time/residue: 1.1027 time to fit residues: 1991.4579 Evaluate side-chains 1168 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1096 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 264 optimal weight: 3.9990 chunk 339 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 462 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 40.0000 chunk 213 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 528 HIS B 642 ASN C 325 GLN C 575 ASN C 606 ASN C 622 GLN D 579 GLN D 606 ASN F 422 ASN J 150 ASN K 191 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38562 Z= 0.193 Angle : 0.533 7.029 52104 Z= 0.275 Chirality : 0.039 0.157 5979 Planarity : 0.004 0.056 6722 Dihedral : 9.872 174.056 5406 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.68 % Allowed : 15.45 % Favored : 82.87 % 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: 0.16 (0.12), residues: 4789 helix: 1.04 (0.10), residues: 2490 sheet: -0.72 (0.18), residues: 714 loop : -0.88 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.034 0.001 HIS A 483 PHE 0.027 0.001 PHE A 640 TYR 0.013 0.001 TYR K 60 ARG 0.007 0.000 ARG C 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1186 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1118 time to evaluate : 4.409 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: A 264 GLU cc_start: 0.8183 (mp0) cc_final: 0.7970 (pm20) REVERT: A 306 LEU cc_start: 0.8527 (mt) cc_final: 0.8165 (mt) REVERT: A 307 ILE cc_start: 0.8501 (pt) cc_final: 0.8054 (mt) REVERT: A 321 SER cc_start: 0.8786 (m) cc_final: 0.8544 (p) REVERT: A 359 ASN cc_start: 0.7936 (m-40) cc_final: 0.7656 (m-40) REVERT: A 376 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7620 (mtpp) REVERT: A 387 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8652 (ttmm) REVERT: A 393 HIS cc_start: 0.6466 (m-70) cc_final: 0.6014 (m-70) REVERT: A 427 GLU cc_start: 0.7323 (pt0) cc_final: 0.6777 (pt0) REVERT: A 475 LYS cc_start: 0.8380 (mttt) cc_final: 0.8020 (mtpt) REVERT: A 503 GLU cc_start: 0.7229 (tp30) cc_final: 0.6794 (tp30) REVERT: B 206 ARG cc_start: 0.7302 (tpt170) cc_final: 0.7064 (mmt180) REVERT: B 247 SER cc_start: 0.8447 (t) cc_final: 0.8163 (p) REVERT: B 419 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8173 (tttt) REVERT: B 425 ASP cc_start: 0.7940 (t70) cc_final: 0.7406 (t0) REVERT: B 674 ASP cc_start: 0.7455 (m-30) cc_final: 0.7092 (m-30) REVERT: B 735 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8536 (tt) REVERT: C 207 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8717 (mtpt) REVERT: C 573 VAL cc_start: 0.9205 (t) cc_final: 0.8936 (m) REVERT: D 370 ASP cc_start: 0.7304 (t0) cc_final: 0.7054 (t0) REVERT: D 396 ASP cc_start: 0.8011 (t70) cc_final: 0.7606 (t0) REVERT: D 454 ASP cc_start: 0.8206 (m-30) cc_final: 0.7880 (m-30) REVERT: D 502 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8208 (p) REVERT: D 532 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7485 (mmm-85) REVERT: D 688 ASN cc_start: 0.8163 (m-40) cc_final: 0.7946 (m110) REVERT: E 225 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7999 (mt-10) REVERT: E 235 ASP cc_start: 0.7288 (t0) cc_final: 0.6938 (t0) REVERT: E 252 SER cc_start: 0.8923 (m) cc_final: 0.8690 (m) REVERT: E 348 GLU cc_start: 0.8133 (pt0) cc_final: 0.7423 (pt0) REVERT: E 532 ARG cc_start: 0.7192 (mmm160) cc_final: 0.6921 (mmm160) REVERT: E 617 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8743 (mt) REVERT: E 633 LYS cc_start: 0.7931 (mttt) cc_final: 0.7587 (mttp) REVERT: E 704 MET cc_start: 0.7243 (ttt) cc_final: 0.6972 (ttt) REVERT: F 268 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7799 (tttm) REVERT: F 272 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7960 (mmtm) REVERT: F 340 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.7295 (mmt90) REVERT: F 523 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 551 ASP cc_start: 0.7060 (m-30) cc_final: 0.6694 (m-30) REVERT: H 22 ARG cc_start: 0.8987 (tpt90) cc_final: 0.8354 (tpt90) REVERT: H 162 GLU cc_start: 0.6348 (tm-30) cc_final: 0.5856 (tm-30) REVERT: I 136 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6667 (tm-30) REVERT: I 151 GLU cc_start: 0.7347 (tt0) cc_final: 0.7125 (tt0) REVERT: K 15 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7114 (ttp-110) REVERT: K 17 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: L 140 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7230 (ttm110) REVERT: L 144 LYS cc_start: 0.8201 (mttm) cc_final: 0.7755 (mtpp) REVERT: L 172 ARG cc_start: 0.7568 (ttt90) cc_final: 0.7105 (ttt180) REVERT: M 89 THR cc_start: 0.8124 (p) cc_final: 0.7796 (p) REVERT: N 70 ILE cc_start: 0.8476 (mm) cc_final: 0.8068 (mm) REVERT: N 144 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8206 (mptt) outliers start: 68 outliers final: 59 residues processed: 1150 average time/residue: 1.1387 time to fit residues: 2059.1756 Evaluate side-chains 1163 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1100 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS C 325 GLN C 606 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 579 GLN D 606 ASN F 393 HIS H 41 ASN J 9 GLN J 150 ASN K 191 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 38562 Z= 0.296 Angle : 0.558 8.357 52104 Z= 0.289 Chirality : 0.041 0.155 5979 Planarity : 0.004 0.060 6722 Dihedral : 9.857 170.701 5406 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.80 % Allowed : 15.78 % Favored : 82.43 % 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: 0.12 (0.12), residues: 4789 helix: 1.01 (0.10), residues: 2493 sheet: -0.74 (0.18), residues: 727 loop : -0.89 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.013 0.001 HIS A 393 PHE 0.024 0.001 PHE A 640 TYR 0.016 0.001 TYR K 60 ARG 0.018 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1196 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1123 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: A 306 LEU cc_start: 0.8533 (mt) cc_final: 0.8172 (mt) REVERT: A 307 ILE cc_start: 0.8501 (pt) cc_final: 0.8055 (mt) REVERT: A 355 VAL cc_start: 0.8304 (m) cc_final: 0.8092 (p) REVERT: A 359 ASN cc_start: 0.7942 (m-40) cc_final: 0.7648 (m-40) REVERT: A 376 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7640 (mtpp) REVERT: A 387 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8658 (ttmm) REVERT: A 427 GLU cc_start: 0.7306 (pt0) cc_final: 0.6753 (pt0) REVERT: A 472 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 503 GLU cc_start: 0.7209 (tp30) cc_final: 0.6750 (tp30) REVERT: B 206 ARG cc_start: 0.7332 (tpt170) cc_final: 0.7092 (mmt180) REVERT: B 247 SER cc_start: 0.8454 (t) cc_final: 0.8160 (p) REVERT: B 425 ASP cc_start: 0.8012 (t70) cc_final: 0.7496 (t0) REVERT: B 674 ASP cc_start: 0.7464 (m-30) cc_final: 0.7085 (m-30) REVERT: B 735 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8529 (tt) REVERT: C 259 TYR cc_start: 0.8697 (m-80) cc_final: 0.7869 (m-80) REVERT: C 573 VAL cc_start: 0.9234 (t) cc_final: 0.8953 (m) REVERT: D 370 ASP cc_start: 0.7332 (t0) cc_final: 0.7078 (t0) REVERT: D 396 ASP cc_start: 0.8046 (t70) cc_final: 0.7654 (t0) REVERT: D 454 ASP cc_start: 0.8234 (m-30) cc_final: 0.7944 (m-30) REVERT: D 502 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8231 (p) REVERT: D 532 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7534 (mmm-85) REVERT: E 225 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8041 (mt-10) REVERT: E 235 ASP cc_start: 0.7368 (t0) cc_final: 0.7019 (t0) REVERT: E 532 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6930 (mmm160) REVERT: E 617 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (mt) REVERT: E 633 LYS cc_start: 0.8005 (mttt) cc_final: 0.7678 (mttp) REVERT: E 704 MET cc_start: 0.7259 (ttt) cc_final: 0.6997 (ttt) REVERT: F 268 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7876 (tttm) REVERT: F 272 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7968 (mmtm) REVERT: F 340 ARG cc_start: 0.7567 (mmt-90) cc_final: 0.7317 (mmt90) REVERT: F 392 ARG cc_start: 0.7723 (ptp-170) cc_final: 0.7202 (ptp90) REVERT: F 523 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8661 (tm-30) REVERT: F 551 ASP cc_start: 0.7082 (m-30) cc_final: 0.6712 (m-30) REVERT: H 22 ARG cc_start: 0.9005 (tpt90) cc_final: 0.8377 (tpt90) REVERT: H 162 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6014 (tm-30) REVERT: H 172 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6776 (tpp80) REVERT: I 136 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6691 (tm-30) REVERT: I 151 GLU cc_start: 0.7379 (tt0) cc_final: 0.7161 (tt0) REVERT: K 15 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7172 (ttp-110) REVERT: L 122 HIS cc_start: 0.7541 (p90) cc_final: 0.7254 (p90) REVERT: L 140 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7397 (ttm110) REVERT: L 148 ARG cc_start: 0.6827 (mmm160) cc_final: 0.6618 (mmm160) REVERT: L 172 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7118 (ttt180) REVERT: M 89 THR cc_start: 0.8163 (p) cc_final: 0.7841 (p) REVERT: N 70 ILE cc_start: 0.8505 (mm) cc_final: 0.8171 (mm) REVERT: N 144 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8194 (mptt) REVERT: N 148 ARG cc_start: 0.7214 (tpt170) cc_final: 0.6871 (mmm160) outliers start: 73 outliers final: 65 residues processed: 1157 average time/residue: 1.1607 time to fit residues: 2110.0289 Evaluate side-chains 1169 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1101 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 160 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.9990 chunk 443 optimal weight: 1.9990 chunk 404 optimal weight: 0.9980 chunk 431 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 389 optimal weight: 0.9980 chunk 407 optimal weight: 4.9990 chunk 429 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 507 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN C 325 GLN C 606 ASN D 579 GLN D 606 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN H 41 ASN J 9 GLN J 150 ASN J 159 GLN K 191 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 38562 Z= 0.154 Angle : 0.529 7.795 52104 Z= 0.270 Chirality : 0.039 0.162 5979 Planarity : 0.004 0.059 6722 Dihedral : 9.602 175.476 5406 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.58 % Allowed : 16.29 % Favored : 82.13 % 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: 0.32 (0.12), residues: 4789 helix: 1.18 (0.10), residues: 2500 sheet: -0.64 (0.18), residues: 700 loop : -0.84 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 229 HIS 0.029 0.001 HIS F 393 PHE 0.025 0.001 PHE A 640 TYR 0.012 0.001 TYR K 128 ARG 0.013 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1173 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1109 time to evaluate : 4.476 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: A 286 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6609 (mm-30) REVERT: A 306 LEU cc_start: 0.8532 (mt) cc_final: 0.8172 (mt) REVERT: A 307 ILE cc_start: 0.8478 (pt) cc_final: 0.8015 (mt) REVERT: A 321 SER cc_start: 0.8791 (m) cc_final: 0.8495 (p) REVERT: A 359 ASN cc_start: 0.7936 (m-40) cc_final: 0.7645 (m-40) REVERT: A 376 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7610 (mtpp) REVERT: A 387 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8653 (ttmm) REVERT: A 427 GLU cc_start: 0.7263 (pt0) cc_final: 0.6717 (pt0) REVERT: A 472 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 503 GLU cc_start: 0.7168 (tp30) cc_final: 0.6658 (tp30) REVERT: A 507 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: B 206 ARG cc_start: 0.7273 (tpt170) cc_final: 0.7058 (mmt180) REVERT: B 247 SER cc_start: 0.8442 (t) cc_final: 0.8168 (p) REVERT: B 419 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8207 (tttt) REVERT: B 425 ASP cc_start: 0.7921 (t70) cc_final: 0.7394 (t0) REVERT: B 674 ASP cc_start: 0.7441 (m-30) cc_final: 0.7094 (m-30) REVERT: B 735 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 573 VAL cc_start: 0.9179 (t) cc_final: 0.8898 (m) REVERT: D 370 ASP cc_start: 0.7278 (t0) cc_final: 0.7024 (t0) REVERT: D 396 ASP cc_start: 0.7955 (t70) cc_final: 0.7597 (t0) REVERT: D 532 ARG cc_start: 0.7738 (mmm-85) cc_final: 0.7466 (mmm-85) REVERT: D 674 ASP cc_start: 0.7320 (m-30) cc_final: 0.6873 (m-30) REVERT: E 225 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7902 (mt-10) REVERT: E 235 ASP cc_start: 0.7298 (t0) cc_final: 0.6995 (t0) REVERT: E 252 SER cc_start: 0.8920 (m) cc_final: 0.8697 (m) REVERT: E 348 GLU cc_start: 0.8141 (pt0) cc_final: 0.7414 (pt0) REVERT: E 532 ARG cc_start: 0.7195 (mmm160) cc_final: 0.6917 (mmm160) REVERT: E 617 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8665 (mt) REVERT: E 633 LYS cc_start: 0.7938 (mttt) cc_final: 0.7601 (mttp) REVERT: E 704 MET cc_start: 0.7249 (ttt) cc_final: 0.6969 (ttt) REVERT: F 220 LYS cc_start: 0.7466 (pttm) cc_final: 0.7223 (pttt) REVERT: F 225 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: F 268 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7807 (tttm) REVERT: F 272 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7958 (mmtm) REVERT: F 340 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7267 (mmt90) REVERT: F 393 HIS cc_start: 0.7627 (m-70) cc_final: 0.7408 (m-70) REVERT: F 523 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 551 ASP cc_start: 0.7061 (m-30) cc_final: 0.6683 (m-30) REVERT: H 22 ARG cc_start: 0.8977 (tpt90) cc_final: 0.8388 (tpt90) REVERT: H 162 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5961 (tm-30) REVERT: H 172 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6747 (tpp80) REVERT: H 178 GLU cc_start: 0.7674 (mp0) cc_final: 0.7410 (mp0) REVERT: I 136 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6722 (tm-30) REVERT: J 144 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8521 (mtpp) REVERT: K 148 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7996 (tpp80) REVERT: L 140 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7323 (ttm110) REVERT: L 144 LYS cc_start: 0.8174 (mttm) cc_final: 0.7745 (mtpp) REVERT: L 148 ARG cc_start: 0.6735 (mmm160) cc_final: 0.6527 (mmm160) REVERT: L 149 MET cc_start: 0.7842 (mmt) cc_final: 0.7262 (mmp) REVERT: L 172 ARG cc_start: 0.7578 (ttt90) cc_final: 0.7099 (ttt180) REVERT: M 89 THR cc_start: 0.8083 (p) cc_final: 0.7754 (p) REVERT: N 70 ILE cc_start: 0.8528 (mm) cc_final: 0.8094 (mm) REVERT: N 144 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8166 (mptt) REVERT: N 148 ARG cc_start: 0.7174 (tpt170) cc_final: 0.6720 (mmm160) outliers start: 64 outliers final: 51 residues processed: 1138 average time/residue: 1.1361 time to fit residues: 2019.4330 Evaluate side-chains 1150 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1095 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 160 SER 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: 10.0000 chunk 278 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 316 optimal weight: 50.0000 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 579 GLN D 606 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 606 ASN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 GLN K 191 HIS ** M 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 38562 Z= 0.239 Angle : 0.626 59.199 52104 Z= 0.343 Chirality : 0.040 0.169 5979 Planarity : 0.004 0.099 6722 Dihedral : 9.598 174.757 5406 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.55 % Allowed : 16.37 % Favored : 82.08 % Cbeta Deviations : 0.02 % 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: 0.32 (0.12), residues: 4789 helix: 1.18 (0.10), residues: 2500 sheet: -0.62 (0.18), residues: 700 loop : -0.84 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.019 0.001 HIS F 393 PHE 0.027 0.001 PHE B 327 TYR 0.011 0.001 TYR K 60 ARG 0.007 0.000 ARG A 643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1154 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1091 time to evaluate : 4.407 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: A 286 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6621 (mm-30) REVERT: A 306 LEU cc_start: 0.8534 (mt) cc_final: 0.8177 (mt) REVERT: A 307 ILE cc_start: 0.8482 (pt) cc_final: 0.8019 (mt) REVERT: A 321 SER cc_start: 0.8790 (m) cc_final: 0.8494 (p) REVERT: A 359 ASN cc_start: 0.7928 (m-40) cc_final: 0.7649 (m-40) REVERT: A 376 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7618 (mtpp) REVERT: A 387 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8658 (ttmm) REVERT: A 427 GLU cc_start: 0.7292 (pt0) cc_final: 0.6737 (pt0) REVERT: A 472 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 503 GLU cc_start: 0.7238 (tp30) cc_final: 0.6866 (tp30) REVERT: A 692 GLU cc_start: 0.6487 (tm-30) cc_final: 0.6256 (tp30) REVERT: B 206 ARG cc_start: 0.7275 (tpt170) cc_final: 0.7066 (mmt180) REVERT: B 247 SER cc_start: 0.8455 (t) cc_final: 0.8176 (p) REVERT: B 419 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8211 (tttt) REVERT: B 425 ASP cc_start: 0.7899 (t70) cc_final: 0.7409 (t0) REVERT: B 674 ASP cc_start: 0.7455 (m-30) cc_final: 0.7104 (m-30) REVERT: B 735 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8501 (tt) REVERT: C 573 VAL cc_start: 0.9182 (t) cc_final: 0.8909 (m) REVERT: D 370 ASP cc_start: 0.7293 (t0) cc_final: 0.7034 (t0) REVERT: D 396 ASP cc_start: 0.7969 (t70) cc_final: 0.7610 (t0) REVERT: D 502 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8308 (p) REVERT: D 532 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7486 (mmm-85) REVERT: D 674 ASP cc_start: 0.7328 (m-30) cc_final: 0.6884 (m-30) REVERT: E 225 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 235 ASP cc_start: 0.7309 (t0) cc_final: 0.7001 (t0) REVERT: E 252 SER cc_start: 0.8933 (m) cc_final: 0.8705 (m) REVERT: E 348 GLU cc_start: 0.8127 (pt0) cc_final: 0.7396 (pt0) REVERT: E 532 ARG cc_start: 0.7200 (mmm160) cc_final: 0.6924 (mmm160) REVERT: E 633 LYS cc_start: 0.7952 (mttt) cc_final: 0.7599 (mttp) REVERT: E 704 MET cc_start: 0.7254 (ttt) cc_final: 0.6975 (ttt) REVERT: F 220 LYS cc_start: 0.7475 (pttm) cc_final: 0.7241 (pttt) REVERT: F 225 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: F 268 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7815 (tttm) REVERT: F 272 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7962 (mmtm) REVERT: F 340 ARG cc_start: 0.7508 (mmt-90) cc_final: 0.7280 (mmt90) REVERT: F 523 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8649 (tm-30) REVERT: F 551 ASP cc_start: 0.7061 (m-30) cc_final: 0.6688 (m-30) REVERT: H 22 ARG cc_start: 0.8980 (tpt90) cc_final: 0.8761 (tpt90) REVERT: H 162 GLU cc_start: 0.6265 (tm-30) cc_final: 0.6021 (tm-30) REVERT: H 172 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6753 (tpp80) REVERT: I 136 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6728 (tm-30) REVERT: L 140 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7329 (ttm110) REVERT: L 144 LYS cc_start: 0.8178 (mttm) cc_final: 0.7760 (mtpp) REVERT: L 148 ARG cc_start: 0.6746 (mmm160) cc_final: 0.6533 (mmm160) REVERT: L 149 MET cc_start: 0.7855 (mmt) cc_final: 0.7387 (mmp) REVERT: L 172 ARG cc_start: 0.7582 (ttt90) cc_final: 0.7104 (ttt180) REVERT: M 89 THR cc_start: 0.8101 (p) cc_final: 0.7774 (p) REVERT: N 70 ILE cc_start: 0.8533 (mm) cc_final: 0.8112 (mm) REVERT: N 144 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8174 (mptt) REVERT: N 148 ARG cc_start: 0.7191 (tpt170) cc_final: 0.6735 (mmm160) outliers start: 63 outliers final: 51 residues processed: 1120 average time/residue: 1.1114 time to fit residues: 1931.1062 Evaluate side-chains 1142 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1088 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 708 ILE Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 391 ASP Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 657 VAL Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 160 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 10.0000 chunk 405 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 351 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 391 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 579 GLN D 606 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 606 ASN F 675 GLN ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114028 restraints weight = 142479.637| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.40 r_work: 0.2975 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 38562 Z= 0.255 Angle : 0.687 59.199 52104 Z= 0.421 Chirality : 0.040 0.427 5979 Planarity : 0.005 0.220 6722 Dihedral : 9.603 174.567 5406 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.53 % Allowed : 16.32 % Favored : 82.15 % Cbeta Deviations : 0.02 % 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: 0.32 (0.12), residues: 4789 helix: 1.18 (0.10), residues: 2500 sheet: -0.63 (0.18), residues: 700 loop : -0.84 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.426 0.002 HIS F 393 PHE 0.024 0.001 PHE A 640 TYR 0.014 0.001 TYR M 128 ARG 0.005 0.000 ARG A 643 =============================================================================== Job complete usr+sys time: 28932.93 seconds wall clock time: 491 minutes 49.09 seconds (29509.09 seconds total)