Starting phenix.real_space_refine on Sun Jul 5 07:21:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rxb_54364/07_2026/9rxb_54364.map" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 Zn 1 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 123 5.16 5 C 16152 2.51 5 N 4379 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25421 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6562 Classifications: {'peptide': 810} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 38, 'TRANS': 768} Chain breaks: 2 Chain: "B" Number of atoms: 9518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9518 Classifications: {'peptide': 1197} Link IDs: {'CIS': 6, 'PCIS': 4, 'PTRANS': 52, 'TRANS': 1134} Chain breaks: 5 Chain: "C" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3120 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3456 Classifications: {'peptide': 423} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "E" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1333 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "F" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1321 Classifications: {'peptide': 168} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 163} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' MG': 1, 'MYR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16110 SG CYS C 18 42.476 135.766 40.623 1.00191.04 S ATOM 16136 SG CYS C 21 40.206 134.712 43.714 1.00196.96 S ATOM 16607 SG CYS C 137 38.912 137.804 42.561 1.00241.45 S ATOM 16631 SG CYS C 140 40.649 137.797 43.906 1.00251.77 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG F 300 " occ=0.72 residue: pdb=" C1' GTP F 301 " occ=0.92 ... (30 atoms not shown) pdb=" PG GTP F 301 " occ=0.92 Time building chain proxies: 5.48, per 1000 atoms: 0.22 Number of scatterers: 25421 At special positions: 0 Unit cell: (108.04, 181.04, 243.82, 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) Zn 1 29.99 S 123 16.00 P 8 15.00 Mg 3 11.99 O 4755 8.00 N 4379 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 21 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " Number of angles added : 6 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5990 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 30 sheets defined 49.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.872A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 190 through 212 removed outlier: 4.202A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.342A pdb=" N HIS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.624A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 325' Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.652A pdb=" N LYS A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.616A pdb=" N GLU A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.029A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.591A pdb=" N MET A 394 " --> pdb=" O ASP A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.602A pdb=" N GLN A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.540A pdb=" N ASN A 413 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.565A pdb=" N GLN A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.712A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.898A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.865A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 removed outlier: 4.303A pdb=" N ASP A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.951A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.600A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 788 Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.029A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.725A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 826 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 851 through 869 removed outlier: 3.798A pdb=" N ALA A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 121 through 143 removed outlier: 4.420A pdb=" N GLY B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 236 through 253 removed outlier: 4.009A pdb=" N ASP B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.518A pdb=" N ILE B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.706A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.621A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 removed outlier: 3.761A pdb=" N HIS B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.022A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.600A pdb=" N LEU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.650A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 418 through 425 removed outlier: 3.516A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.613A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.555A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.699A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.763A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.580A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.089A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 569 through 581 removed outlier: 4.589A pdb=" N LEU B 578 " --> pdb=" O ASN B 574 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 590 through 609 removed outlier: 3.808A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.716A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.890A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 666 " --> pdb=" O PHE B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.611A pdb=" N VAL B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.715A pdb=" N ASP B 700 " --> pdb=" O PRO B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 733 removed outlier: 3.848A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 removed outlier: 3.807A pdb=" N LEU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 removed outlier: 3.704A pdb=" N ALA B 768 " --> pdb=" O ASP B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 790 removed outlier: 3.708A pdb=" N GLU B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 786 " --> pdb=" O GLU B 782 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 790 " --> pdb=" O LYS B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.507A pdb=" N LYS B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.519A pdb=" N SER B 813 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 940 through 965 removed outlier: 3.733A pdb=" N GLN B 945 " --> pdb=" O LYS B 941 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 965 " --> pdb=" O ALA B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 1021 through 1027 removed outlier: 3.796A pdb=" N LYS B1024 " --> pdb=" O ASN B1021 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B1025 " --> pdb=" O SER B1022 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B1026 " --> pdb=" O GLN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.696A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.558A pdb=" N PHE C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 137 through 170 removed outlier: 3.953A pdb=" N ASP C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 219 removed outlier: 3.710A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 245 removed outlier: 3.737A pdb=" N GLN C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 267 removed outlier: 4.374A pdb=" N GLU C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.647A pdb=" N ALA C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 308 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.505A pdb=" N PHE C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.178A pdb=" N MET C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA C 371 " --> pdb=" O HIS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 375 through 384 removed outlier: 4.011A pdb=" N PHE C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.544A pdb=" N PHE C 419 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 420 " --> pdb=" O THR C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 421 through 427 Processing helix chain 'C' and resid 428 through 438 removed outlier: 3.617A pdb=" N MET C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'C' and resid 447 through 450 Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.676A pdb=" N HIS D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.970A pdb=" N GLU D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 164 through 168' Processing helix chain 'D' and resid 192 through 226 Processing helix chain 'D' and resid 227 through 278 removed outlier: 4.057A pdb=" N LYS D 243 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 324 removed outlier: 4.290A pdb=" N GLU D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 359 through 378 removed outlier: 3.963A pdb=" N ALA D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.538A pdb=" N THR D 404 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 419 through 439 Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.822A pdb=" N LYS D 455 " --> pdb=" O PRO D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 removed outlier: 3.647A pdb=" N LEU E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.557A pdb=" N ARG E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 121 removed outlier: 3.929A pdb=" N PHE E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 4.168A pdb=" N ASN E 139 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 153 removed outlier: 3.911A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 181 removed outlier: 3.552A pdb=" N ILE E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 79 through 84 removed outlier: 3.773A pdb=" N TYR F 82 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER F 84 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.940A pdb=" N ARG F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 121 removed outlier: 3.557A pdb=" N PHE F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 4.748A pdb=" N ASN F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.550A pdb=" N ILE F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 4.914A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N LYS A 6 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLY A 232 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 831 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 9 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 96 removed outlier: 6.763A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 23 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 69 removed outlier: 6.509A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA7, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.054A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 98 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 93 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 removed outlier: 5.788A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 999 through 1001 removed outlier: 3.893A pdb=" N ARG B1000 " --> pdb=" O ALA B1009 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1017 through 1019 removed outlier: 3.566A pdb=" N VAL B1017 " --> pdb=" O TYR B1038 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B1038 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B1019 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 3.737A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B1060 " --> pdb=" O THR B1047 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B1049 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B1061 " --> pdb=" O ALA B1065 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1097 through 1103 removed outlier: 4.266A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B1114 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B1122 " --> pdb=" O TYR B1114 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1144 through 1146 removed outlier: 7.142A pdb=" N GLY B1159 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B1174 " --> pdb=" O ASP B1169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 6.552A pdb=" N ALA B1203 " --> pdb=" O ARG B1188 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B1190 " --> pdb=" O ILE B1201 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B1201 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET B1192 " --> pdb=" O TRP B1199 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP B1199 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1242 through 1247 removed outlier: 4.597A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1256 " --> pdb=" O TRP B1268 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B1260 " --> pdb=" O LYS B1264 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS B1264 " --> pdb=" O GLY B1260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1332 through 1339 removed outlier: 4.205A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AC2, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AC3, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.531A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 394 through 397 Processing sheet with id=AC5, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.795A pdb=" N TYR D 161 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.512A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.512A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 65 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE D 113 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS D 132 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL D 115 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU D 130 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 117 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.574A pdb=" N ASP D 338 " --> pdb=" O ASN D 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 394 through 396 Processing sheet with id=AD1, first strand: chain 'E' and resid 56 through 60 removed outlier: 3.755A pdb=" N GLN E 60 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER E 19 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLU E 72 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE E 21 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRP E 74 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 23 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ALA E 95 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS E 22 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE E 97 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 24 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL E 99 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU E 26 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ASP E 101 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA E 96 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER E 131 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL E 98 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASN E 133 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR E 100 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 20 removed outlier: 6.470A pdb=" N SER F 19 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 62 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 73 through 75 removed outlier: 6.323A pdb=" N VAL F 24 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL F 99 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU F 26 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASP F 101 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY F 132 " --> pdb=" O MET F 160 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3174 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: 5.73 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8293 1.34 - 1.46: 4646 1.46 - 1.58: 12787 1.58 - 1.69: 13 1.69 - 1.81: 194 Bond restraints: 25933 Sorted by residual: bond pdb=" C ASP B 700 " pdb=" N PRO B 701 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.44e-02 4.82e+03 7.02e+00 bond pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.86e+00 bond pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.58e+00 bond pdb=" N GLU E 161 " pdb=" CA GLU E 161 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.23e-02 6.61e+03 3.58e+00 bond pdb=" CA ASP B 737 " pdb=" C ASP B 737 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.14e-02 7.69e+03 3.47e+00 ... (remaining 25928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 34751 2.66 - 5.33: 263 5.33 - 7.99: 34 7.99 - 10.66: 7 10.66 - 13.32: 5 Bond angle restraints: 35060 Sorted by residual: angle pdb=" C GLU A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 121.70 134.59 -12.89 1.80e+00 3.09e-01 5.13e+01 angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 134.16 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 133.81 -12.11 1.80e+00 3.09e-01 4.53e+01 angle pdb=" C MET E 160 " pdb=" CA MET E 160 " pdb=" CB MET E 160 " ideal model delta sigma weight residual 110.42 123.74 -13.32 1.99e+00 2.53e-01 4.48e+01 angle pdb=" C SER B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta sigma weight residual 121.70 131.05 -9.35 1.80e+00 3.09e-01 2.70e+01 ... (remaining 35055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 15324 31.71 - 63.42: 369 63.42 - 95.12: 60 95.12 - 126.83: 3 126.83 - 158.54: 4 Dihedral angle restraints: 15760 sinusoidal: 6530 harmonic: 9230 Sorted by residual: dihedral pdb=" CA MET E 160 " pdb=" C MET E 160 " pdb=" N GLU E 161 " pdb=" CA GLU E 161 " ideal model delta harmonic sigma weight residual 180.00 58.97 121.03 0 5.00e+00 4.00e-02 5.86e+02 dihedral pdb=" C MET E 160 " pdb=" N MET E 160 " pdb=" CA MET E 160 " pdb=" CB MET E 160 " ideal model delta harmonic sigma weight residual -122.60 -144.05 21.45 0 2.50e+00 1.60e-01 7.36e+01 dihedral pdb=" CA HIS A 141 " pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta harmonic sigma weight residual 0.00 35.28 -35.28 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 15757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3887 0.150 - 0.300: 9 0.300 - 0.450: 1 0.450 - 0.600: 0 0.600 - 0.750: 1 Chirality restraints: 3898 Sorted by residual: chirality pdb=" CA MET E 160 " pdb=" N MET E 160 " pdb=" C MET E 160 " pdb=" CB MET E 160 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CB ILE B 23 " pdb=" CA ILE B 23 " pdb=" CG1 ILE B 23 " pdb=" CG2 ILE B 23 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 294 " pdb=" CA ILE B 294 " pdb=" CG1 ILE B 294 " pdb=" CG2 ILE B 294 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 3895 not shown) Planarity restraints: 4484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO B 667 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 547 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO B 548 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 771 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 772 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 772 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 772 " 0.036 5.00e-02 4.00e+02 ... (remaining 4481 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 179 2.58 - 3.16: 19280 3.16 - 3.74: 38088 3.74 - 4.32: 50298 4.32 - 4.90: 83962 Nonbonded interactions: 191807 Sorted by model distance: nonbonded pdb=" O3A GDP B1401 " pdb="MG MG B1402 " model vdw 2.001 2.170 nonbonded pdb="MG MG E 300 " pdb=" O1G GTP E 301 " model vdw 2.079 2.170 nonbonded pdb="MG MG E 300 " pdb=" O2B GTP E 301 " model vdw 2.087 2.170 nonbonded pdb="MG MG F 300 " pdb=" O2B GTP F 301 " model vdw 2.105 2.170 nonbonded pdb=" OH TYR B 196 " pdb=" OE1 GLU B 250 " model vdw 2.244 3.040 ... (remaining 191802 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 'E' and resid 17 through 301) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.72 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25938 Z= 0.163 Angle : 0.806 53.327 35066 Z= 0.414 Chirality : 0.044 0.750 3898 Planarity : 0.005 0.075 4484 Dihedral : 14.660 158.539 9770 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.89 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3115 helix: 0.37 (0.13), residues: 1313 sheet: -0.04 (0.27), residues: 389 loop : -0.88 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.029 0.001 TYR A 803 PHE 0.017 0.001 PHE A 703 TRP 0.019 0.001 TRP B1155 HIS 0.008 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (25933) covalent geometry : angle 0.69805 / 0.41 (35060) hydrogen bonds : bond 0.20370 / 13.01 ( 1125) hydrogen bonds : angle 6.05483 / 4.19 ( 3174) metal coordination : bond 0.05192 / 2.19 ( 4) metal coordination : angle 30.81069 / 18.86 ( 6) Misc. bond : bond 0.00682 / 0.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 1.048 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: A 52 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8810 (mp0) REVERT: A 180 LYS cc_start: 0.9687 (tttt) cc_final: 0.9017 (tppt) REVERT: A 215 MET cc_start: 0.8380 (mtm) cc_final: 0.8115 (mtt) REVERT: A 238 LYS cc_start: 0.8823 (mttt) cc_final: 0.8523 (mttm) REVERT: A 318 LYS cc_start: 0.8932 (tptt) cc_final: 0.8718 (tptp) REVERT: A 319 PHE cc_start: 0.8770 (m-80) cc_final: 0.7596 (m-80) REVERT: A 323 LEU cc_start: 0.9109 (mt) cc_final: 0.8824 (mt) REVERT: A 332 LYS cc_start: 0.8357 (mptt) cc_final: 0.7830 (mttm) REVERT: A 358 MET cc_start: 0.7956 (mtt) cc_final: 0.7313 (ttm) REVERT: A 359 ASP cc_start: 0.8700 (t0) cc_final: 0.7896 (p0) REVERT: A 516 MET cc_start: 0.8361 (tmm) cc_final: 0.7916 (tmm) REVERT: A 538 MET cc_start: 0.8318 (mtm) cc_final: 0.7967 (ttp) REVERT: A 583 MET cc_start: 0.8451 (mmm) cc_final: 0.7843 (tmm) REVERT: A 650 ILE cc_start: 0.9381 (tp) cc_final: 0.9156 (mt) REVERT: A 684 PHE cc_start: 0.8561 (t80) cc_final: 0.8191 (t80) REVERT: A 704 PHE cc_start: 0.8693 (m-10) cc_final: 0.8492 (m-80) REVERT: A 722 MET cc_start: 0.9130 (tpt) cc_final: 0.8521 (mtm) REVERT: A 743 ASP cc_start: 0.8555 (t0) cc_final: 0.8287 (t0) REVERT: A 798 PHE cc_start: 0.9425 (t80) cc_final: 0.9207 (t80) REVERT: A 799 ARG cc_start: 0.9293 (mtp-110) cc_final: 0.8814 (mtp-110) REVERT: A 803 TYR cc_start: 0.9054 (p90) cc_final: 0.8788 (p90) REVERT: A 806 PHE cc_start: 0.9415 (t80) cc_final: 0.9104 (t80) REVERT: A 819 LEU cc_start: 0.9325 (mt) cc_final: 0.9082 (mt) REVERT: A 846 PHE cc_start: 0.9069 (m-80) cc_final: 0.8707 (m-80) REVERT: A 854 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8873 (mt-10) REVERT: A 859 MET cc_start: 0.8881 (ppp) cc_final: 0.8570 (ppp) REVERT: B 22 ASP cc_start: 0.8833 (m-30) cc_final: 0.8573 (p0) REVERT: B 134 THR cc_start: 0.9087 (m) cc_final: 0.8855 (p) REVERT: B 179 ASN cc_start: 0.9120 (t0) cc_final: 0.8862 (t0) REVERT: B 202 PHE cc_start: 0.8148 (m-80) cc_final: 0.7858 (m-80) REVERT: B 243 SER cc_start: 0.9314 (m) cc_final: 0.8847 (t) REVERT: B 267 TYR cc_start: 0.8477 (t80) cc_final: 0.8224 (t80) REVERT: B 284 HIS cc_start: 0.8707 (m-70) cc_final: 0.7741 (m90) REVERT: B 289 LEU cc_start: 0.8889 (tp) cc_final: 0.8197 (tt) REVERT: B 328 MET cc_start: 0.9351 (mmm) cc_final: 0.9082 (tpp) REVERT: B 436 GLU cc_start: 0.8533 (tp30) cc_final: 0.8331 (tp30) REVERT: B 439 ARG cc_start: 0.8015 (ptp-110) cc_final: 0.7582 (ptp90) REVERT: B 543 THR cc_start: 0.8768 (m) cc_final: 0.8282 (p) REVERT: B 557 MET cc_start: 0.8171 (mmm) cc_final: 0.7953 (mmm) REVERT: B 587 ASP cc_start: 0.9055 (t0) cc_final: 0.8571 (t0) REVERT: B 659 ASP cc_start: 0.8876 (m-30) cc_final: 0.8589 (t0) REVERT: B 695 LEU cc_start: 0.9345 (tp) cc_final: 0.9106 (tt) REVERT: B 711 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8163 (tm-30) REVERT: B 720 LEU cc_start: 0.9376 (mt) cc_final: 0.9163 (mt) REVERT: B 751 LYS cc_start: 0.9443 (tttm) cc_final: 0.9179 (ttpt) REVERT: B 777 GLN cc_start: 0.9246 (mm-40) cc_final: 0.9033 (mm110) REVERT: B 821 LEU cc_start: 0.9165 (tp) cc_final: 0.8942 (tp) REVERT: B 958 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 959 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7845 (mtm-85) REVERT: B 1008 PHE cc_start: 0.8172 (m-80) cc_final: 0.7910 (m-80) REVERT: B 1036 LEU cc_start: 0.8786 (mt) cc_final: 0.8385 (mt) REVERT: B 1192 MET cc_start: 0.9046 (mmm) cc_final: 0.8735 (mpp) REVERT: B 1235 LEU cc_start: 0.9357 (tp) cc_final: 0.9039 (tp) REVERT: B 1295 ILE cc_start: 0.8814 (mt) cc_final: 0.8537 (mp) REVERT: C 162 TYR cc_start: 0.9222 (m-80) cc_final: 0.8548 (m-80) REVERT: C 165 CYS cc_start: 0.8889 (m) cc_final: 0.8142 (p) REVERT: C 256 TYR cc_start: 0.9212 (t80) cc_final: 0.8925 (t80) REVERT: C 396 MET cc_start: 0.2306 (ptt) cc_final: 0.1448 (tpt) REVERT: D 61 LEU cc_start: 0.4872 (mt) cc_final: 0.4659 (mt) REVERT: D 97 LEU cc_start: 0.9080 (mt) cc_final: 0.8846 (tt) REVERT: D 107 ASP cc_start: 0.8939 (t0) cc_final: 0.8645 (t0) REVERT: D 116 LYS cc_start: 0.9068 (mttt) cc_final: 0.8805 (mppt) REVERT: D 118 TRP cc_start: 0.8838 (m-90) cc_final: 0.7825 (m-90) REVERT: D 204 CYS cc_start: 0.9171 (m) cc_final: 0.8683 (m) REVERT: D 221 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8000 (mm-30) REVERT: D 329 TYR cc_start: 0.9319 (m-80) cc_final: 0.8363 (m-80) REVERT: D 431 LYS cc_start: 0.8826 (tttt) cc_final: 0.8516 (mmtm) REVERT: E 42 LYS cc_start: 0.9547 (mmtp) cc_final: 0.9141 (mmmm) REVERT: E 44 GLN cc_start: 0.9365 (mp10) cc_final: 0.9163 (mp10) REVERT: E 57 PHE cc_start: 0.9147 (t80) cc_final: 0.8854 (t80) REVERT: E 89 TYR cc_start: 0.9060 (m-80) cc_final: 0.8678 (m-80) REVERT: E 91 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8044 (mtm-85) REVERT: E 94 GLN cc_start: 0.8834 (mt0) cc_final: 0.8545 (mt0) REVERT: E 97 ILE cc_start: 0.8939 (mt) cc_final: 0.8682 (mm) REVERT: E 133 ASN cc_start: 0.8358 (t0) cc_final: 0.7948 (t0) REVERT: E 137 LEU cc_start: 0.9274 (mt) cc_final: 0.9054 (mt) REVERT: E 144 ASP cc_start: 0.8561 (t70) cc_final: 0.8220 (t70) REVERT: E 153 ASP cc_start: 0.8293 (m-30) cc_final: 0.7648 (m-30) REVERT: E 160 MET cc_start: 0.8694 (mmt) cc_final: 0.7903 (tpp) REVERT: E 162 THR cc_start: 0.8705 (p) cc_final: 0.8303 (t) REVERT: E 168 MET cc_start: 0.8580 (tmm) cc_final: 0.8157 (tmm) REVERT: E 175 MET cc_start: 0.9175 (mmm) cc_final: 0.8861 (mmm) REVERT: F 46 HIS cc_start: 0.9047 (m170) cc_final: 0.7883 (m-70) REVERT: F 73 ILE cc_start: 0.8673 (tp) cc_final: 0.8362 (mp) REVERT: F 89 TYR cc_start: 0.8199 (m-80) cc_final: 0.7910 (m-80) REVERT: F 133 ASN cc_start: 0.8673 (t0) cc_final: 0.7951 (t0) REVERT: F 145 PHE cc_start: 0.8082 (t80) cc_final: 0.7783 (t80) REVERT: F 149 GLN cc_start: 0.8982 (tp40) cc_final: 0.8513 (tp-100) REVERT: F 153 ASP cc_start: 0.8933 (m-30) cc_final: 0.8090 (m-30) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.1959 time to fit residues: 195.0731 Evaluate side-chains 470 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 554 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 292 GLN B 387 GLN B 531 GLN B 571 GLN B 954 GLN B1102 HIS B1109 GLN ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 335 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 158 ASN D 208 GLN D 254 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 GLN D 435 GLN E 46 HIS F 121 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.095105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071279 restraints weight = 118063.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073245 restraints weight = 64389.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074667 restraints weight = 42882.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075552 restraints weight = 32094.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076219 restraints weight = 26333.485| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25938 Z= 0.149 Angle : 0.652 25.636 35066 Z= 0.330 Chirality : 0.042 0.170 3898 Planarity : 0.005 0.072 4484 Dihedral : 8.175 155.495 3454 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3115 helix: 1.16 (0.14), residues: 1340 sheet: 0.16 (0.27), residues: 372 loop : -0.73 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 39 TYR 0.018 0.002 TYR D 191 PHE 0.029 0.002 PHE B 38 TRP 0.015 0.001 TRP F 114 HIS 0.010 0.001 HIS C 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (25933) covalent geometry : angle 0.62995 / 0.33 (35060) hydrogen bonds : bond 0.05161 / 3.31 ( 1125) hydrogen bonds : angle 4.70689 / 3.26 ( 3174) metal coordination : bond 0.01474 / 0.76 ( 4) metal coordination : angle 12.98458 / 7.84 ( 6) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 0.894 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: A 180 LYS cc_start: 0.9564 (tttt) cc_final: 0.8559 (tptp) REVERT: A 264 ASN cc_start: 0.8149 (t0) cc_final: 0.7933 (t0) REVERT: A 295 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 319 PHE cc_start: 0.8629 (m-80) cc_final: 0.7709 (m-80) REVERT: A 335 LYS cc_start: 0.9377 (mttt) cc_final: 0.9034 (mptt) REVERT: A 358 MET cc_start: 0.7626 (mtt) cc_final: 0.7401 (ttm) REVERT: A 492 TYR cc_start: 0.8291 (m-10) cc_final: 0.7965 (m-80) REVERT: A 516 MET cc_start: 0.8282 (tmm) cc_final: 0.7622 (tmm) REVERT: A 583 MET cc_start: 0.8451 (mmm) cc_final: 0.7848 (tmm) REVERT: A 681 PHE cc_start: 0.8733 (m-10) cc_final: 0.8459 (m-10) REVERT: A 777 MET cc_start: 0.8085 (pmm) cc_final: 0.7462 (pmm) REVERT: A 799 ARG cc_start: 0.9295 (mtp-110) cc_final: 0.9058 (mtp-110) REVERT: A 806 PHE cc_start: 0.9398 (t80) cc_final: 0.9053 (t80) REVERT: A 808 HIS cc_start: 0.8354 (m90) cc_final: 0.8145 (m90) REVERT: A 840 LYS cc_start: 0.9307 (mmtm) cc_final: 0.9039 (ttpt) REVERT: A 846 PHE cc_start: 0.9070 (m-80) cc_final: 0.8833 (m-80) REVERT: A 868 HIS cc_start: 0.8326 (m170) cc_final: 0.8077 (m170) REVERT: B 202 PHE cc_start: 0.8246 (m-80) cc_final: 0.7449 (m-80) REVERT: B 243 SER cc_start: 0.9276 (m) cc_final: 0.8746 (t) REVERT: B 289 LEU cc_start: 0.9138 (tp) cc_final: 0.8828 (tp) REVERT: B 416 ASP cc_start: 0.8611 (m-30) cc_final: 0.8344 (m-30) REVERT: B 587 ASP cc_start: 0.9065 (t0) cc_final: 0.8640 (t0) REVERT: B 751 LYS cc_start: 0.9416 (tttm) cc_final: 0.9202 (ttpt) REVERT: B 792 ASP cc_start: 0.8933 (p0) cc_final: 0.8591 (p0) REVERT: B 821 LEU cc_start: 0.9034 (tp) cc_final: 0.8812 (tp) REVERT: B 958 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 1008 PHE cc_start: 0.8107 (m-80) cc_final: 0.7841 (m-80) REVERT: B 1025 MET cc_start: 0.7687 (mtm) cc_final: 0.7229 (mtm) REVERT: B 1141 SER cc_start: 0.8931 (m) cc_final: 0.8578 (p) REVERT: B 1245 ILE cc_start: 0.9159 (mt) cc_final: 0.8888 (pt) REVERT: B 1290 TYR cc_start: 0.7997 (m-80) cc_final: 0.7787 (m-10) REVERT: B 1295 ILE cc_start: 0.8692 (mt) cc_final: 0.8437 (mp) REVERT: C 254 MET cc_start: 0.9275 (tpp) cc_final: 0.8988 (tpt) REVERT: C 256 TYR cc_start: 0.9140 (t80) cc_final: 0.8637 (t80) REVERT: C 277 TRP cc_start: 0.8173 (t-100) cc_final: 0.7922 (t-100) REVERT: C 396 MET cc_start: 0.2307 (ptt) cc_final: 0.1509 (tpt) REVERT: D 107 ASP cc_start: 0.8924 (t0) cc_final: 0.8610 (t0) REVERT: D 204 CYS cc_start: 0.8968 (m) cc_final: 0.8674 (m) REVERT: D 207 LYS cc_start: 0.8882 (tttt) cc_final: 0.8567 (ttpt) REVERT: D 320 GLN cc_start: 0.8916 (pt0) cc_final: 0.8591 (pm20) REVERT: D 329 TYR cc_start: 0.9223 (m-80) cc_final: 0.8337 (m-80) REVERT: D 380 VAL cc_start: 0.9030 (t) cc_final: 0.8654 (p) REVERT: D 388 HIS cc_start: 0.8075 (p-80) cc_final: 0.7408 (p-80) REVERT: D 389 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8445 (mmmt) REVERT: E 52 THR cc_start: 0.8523 (m) cc_final: 0.8100 (p) REVERT: E 89 TYR cc_start: 0.8930 (m-80) cc_final: 0.8716 (m-80) REVERT: E 91 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8172 (mtm-85) REVERT: E 133 ASN cc_start: 0.8025 (t0) cc_final: 0.7462 (t0) REVERT: E 175 MET cc_start: 0.9112 (mmm) cc_final: 0.8828 (mmm) REVERT: F 46 HIS cc_start: 0.8790 (m170) cc_final: 0.7695 (m-70) REVERT: F 70 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8645 (tppt) REVERT: F 75 ASP cc_start: 0.7861 (t70) cc_final: 0.7596 (t0) REVERT: F 108 PHE cc_start: 0.9038 (t80) cc_final: 0.8263 (t80) REVERT: F 133 ASN cc_start: 0.8466 (t0) cc_final: 0.7864 (t0) REVERT: F 145 PHE cc_start: 0.8003 (t80) cc_final: 0.7533 (t80) REVERT: F 149 GLN cc_start: 0.8864 (tp40) cc_final: 0.8404 (tp-100) REVERT: F 153 ASP cc_start: 0.8757 (m-30) cc_final: 0.7723 (m-30) outliers start: 1 outliers final: 1 residues processed: 498 average time/residue: 0.1732 time to fit residues: 129.8369 Evaluate side-chains 401 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 276 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 184 optimal weight: 0.0000 chunk 158 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 233 optimal weight: 40.0000 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 255 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS B 531 GLN B1153 GLN ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS D 158 ASN D 208 GLN D 266 HIS ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 320 GLN D 435 GLN E 83 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.090556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066593 restraints weight = 120399.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068488 restraints weight = 66629.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069843 restraints weight = 44886.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070724 restraints weight = 33996.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071337 restraints weight = 28183.185| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25938 Z= 0.129 Angle : 0.614 20.504 35066 Z= 0.310 Chirality : 0.041 0.197 3898 Planarity : 0.004 0.071 4484 Dihedral : 7.936 159.144 3454 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3115 helix: 1.40 (0.14), residues: 1341 sheet: 0.19 (0.27), residues: 390 loop : -0.72 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 959 TYR 0.015 0.001 TYR A 725 PHE 0.019 0.001 PHE B 38 TRP 0.013 0.001 TRP B 670 HIS 0.009 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (25933) covalent geometry : angle 0.59912 / 0.31 (35060) hydrogen bonds : bond 0.04551 / 2.91 ( 1125) hydrogen bonds : angle 4.50363 / 3.10 ( 3174) metal coordination : bond 0.01122 / 0.58 ( 4) metal coordination : angle 10.18982 / 6.14 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 448 time to evaluate : 0.663 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: A 180 LYS cc_start: 0.9459 (tttt) cc_final: 0.9110 (mtmm) REVERT: A 183 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8237 (ptp90) REVERT: A 295 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 319 PHE cc_start: 0.8487 (m-80) cc_final: 0.8225 (m-80) REVERT: A 335 LYS cc_start: 0.9344 (mttt) cc_final: 0.8859 (mtmm) REVERT: A 394 MET cc_start: 0.8627 (mmt) cc_final: 0.8252 (mmt) REVERT: A 492 TYR cc_start: 0.8329 (m-10) cc_final: 0.7984 (m-80) REVERT: A 516 MET cc_start: 0.8346 (tmm) cc_final: 0.7940 (tmm) REVERT: A 556 MET cc_start: 0.8367 (tmm) cc_final: 0.8150 (ppp) REVERT: A 583 MET cc_start: 0.8372 (mmm) cc_final: 0.7815 (tmm) REVERT: A 649 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8389 (tp40) REVERT: A 681 PHE cc_start: 0.8599 (m-10) cc_final: 0.8307 (m-10) REVERT: A 722 MET cc_start: 0.9096 (tpt) cc_final: 0.8215 (tpt) REVERT: A 745 HIS cc_start: 0.7502 (m-70) cc_final: 0.7300 (m-70) REVERT: A 799 ARG cc_start: 0.9220 (mtp-110) cc_final: 0.8772 (mtt-85) REVERT: A 806 PHE cc_start: 0.9357 (t80) cc_final: 0.9122 (t80) REVERT: A 817 LEU cc_start: 0.9549 (mp) cc_final: 0.9277 (mm) REVERT: A 846 PHE cc_start: 0.9072 (m-80) cc_final: 0.8830 (m-80) REVERT: B 202 PHE cc_start: 0.8272 (m-80) cc_final: 0.7474 (m-80) REVERT: B 243 SER cc_start: 0.9288 (m) cc_final: 0.8799 (t) REVERT: B 289 LEU cc_start: 0.9179 (tp) cc_final: 0.8746 (tp) REVERT: B 328 MET cc_start: 0.9299 (tpp) cc_final: 0.8878 (mpp) REVERT: B 416 ASP cc_start: 0.8618 (m-30) cc_final: 0.8355 (m-30) REVERT: B 525 ASN cc_start: 0.8615 (t0) cc_final: 0.8150 (t0) REVERT: B 587 ASP cc_start: 0.9040 (t0) cc_final: 0.8638 (t0) REVERT: B 751 LYS cc_start: 0.9427 (tttm) cc_final: 0.9185 (ttpt) REVERT: B 792 ASP cc_start: 0.8907 (p0) cc_final: 0.8679 (p0) REVERT: B 958 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 1008 PHE cc_start: 0.8062 (m-80) cc_final: 0.7701 (m-80) REVERT: B 1025 MET cc_start: 0.7666 (mtm) cc_final: 0.7304 (mtm) REVERT: B 1141 SER cc_start: 0.8946 (m) cc_final: 0.8624 (p) REVERT: B 1245 ILE cc_start: 0.9135 (mt) cc_final: 0.8886 (pt) REVERT: B 1295 ILE cc_start: 0.8731 (mt) cc_final: 0.8475 (mp) REVERT: C 254 MET cc_start: 0.9301 (tpp) cc_final: 0.8955 (tpt) REVERT: C 271 ASN cc_start: 0.9232 (m110) cc_final: 0.9024 (m-40) REVERT: C 277 TRP cc_start: 0.8252 (t-100) cc_final: 0.8015 (t-100) REVERT: C 369 MET cc_start: 0.1596 (mpp) cc_final: 0.1238 (mtt) REVERT: C 396 MET cc_start: 0.2366 (ptt) cc_final: 0.1583 (tpt) REVERT: D 107 ASP cc_start: 0.8902 (t0) cc_final: 0.8572 (t0) REVERT: D 207 LYS cc_start: 0.8965 (tttt) cc_final: 0.8734 (tttt) REVERT: D 221 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7251 (pt0) REVERT: D 329 TYR cc_start: 0.9239 (m-80) cc_final: 0.8333 (m-80) REVERT: D 373 MET cc_start: 0.8336 (mmt) cc_final: 0.8086 (mmt) REVERT: D 388 HIS cc_start: 0.8191 (p-80) cc_final: 0.7382 (p-80) REVERT: D 389 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8491 (mmmt) REVERT: E 133 ASN cc_start: 0.8204 (t0) cc_final: 0.7644 (t0) REVERT: E 137 LEU cc_start: 0.9184 (mt) cc_final: 0.8952 (mt) REVERT: E 175 MET cc_start: 0.9110 (mmm) cc_final: 0.8706 (mmm) REVERT: F 46 HIS cc_start: 0.8839 (m170) cc_final: 0.7783 (m-70) REVERT: F 75 ASP cc_start: 0.7735 (t70) cc_final: 0.7517 (t0) REVERT: F 133 ASN cc_start: 0.8541 (t0) cc_final: 0.7700 (t0) REVERT: F 145 PHE cc_start: 0.8036 (t80) cc_final: 0.7449 (t80) REVERT: F 149 GLN cc_start: 0.8814 (tp40) cc_final: 0.8387 (tp-100) REVERT: F 153 ASP cc_start: 0.8709 (m-30) cc_final: 0.7596 (m-30) outliers start: 2 outliers final: 1 residues processed: 449 average time/residue: 0.1827 time to fit residues: 124.0726 Evaluate side-chains 375 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 6 optimal weight: 0.0060 chunk 124 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 759 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 457 ASN B 956 ASN ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 181 GLN D 146 HIS D 283 HIS D 313 GLN D 435 GLN ** D 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS F 20 GLN F 113 ASN F 155 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.099154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080687 restraints weight = 149248.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080599 restraints weight = 84049.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.081238 restraints weight = 63155.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081365 restraints weight = 52298.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081445 restraints weight = 48540.257| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25938 Z= 0.190 Angle : 0.641 19.937 35066 Z= 0.327 Chirality : 0.042 0.163 3898 Planarity : 0.004 0.067 4484 Dihedral : 7.971 163.201 3454 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.59 % Favored : 95.28 % Rotamer: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3115 helix: 1.44 (0.14), residues: 1347 sheet: 0.01 (0.26), residues: 402 loop : -0.72 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1044 TYR 0.029 0.002 TYR F 90 PHE 0.020 0.002 PHE B 38 TRP 0.017 0.002 TRP D 131 HIS 0.008 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (25933) covalent geometry : angle 0.62778 / 0.33 (35060) hydrogen bonds : bond 0.04711 / 3.00 ( 1125) hydrogen bonds : angle 4.58252 / 3.16 ( 3174) metal coordination : bond 0.01062 / 0.55 ( 4) metal coordination : angle 9.82969 / 5.88 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 0.953 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: A 140 MET cc_start: 0.8189 (mtp) cc_final: 0.7925 (mtp) REVERT: A 142 ASP cc_start: 0.8534 (m-30) cc_final: 0.8278 (m-30) REVERT: A 180 LYS cc_start: 0.9542 (tttt) cc_final: 0.8969 (tptp) REVERT: A 183 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8346 (ptt-90) REVERT: A 319 PHE cc_start: 0.8565 (m-80) cc_final: 0.8360 (m-80) REVERT: A 335 LYS cc_start: 0.9391 (mttt) cc_final: 0.8983 (mppt) REVERT: A 339 TRP cc_start: 0.8841 (m100) cc_final: 0.8514 (m100) REVERT: A 358 MET cc_start: 0.8026 (tpp) cc_final: 0.7135 (tpp) REVERT: A 359 ASP cc_start: 0.8545 (t0) cc_final: 0.8158 (p0) REVERT: A 492 TYR cc_start: 0.8431 (m-10) cc_final: 0.8094 (m-80) REVERT: A 516 MET cc_start: 0.8476 (tmm) cc_final: 0.8137 (tmm) REVERT: A 583 MET cc_start: 0.8412 (mmm) cc_final: 0.7778 (tmm) REVERT: A 649 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8660 (tp-100) REVERT: A 658 LEU cc_start: 0.9512 (mt) cc_final: 0.9088 (tp) REVERT: A 722 MET cc_start: 0.9179 (tpt) cc_final: 0.8502 (tpt) REVERT: A 799 ARG cc_start: 0.9146 (mtp-110) cc_final: 0.8763 (mtt-85) REVERT: A 806 PHE cc_start: 0.9443 (t80) cc_final: 0.9225 (t80) REVERT: A 817 LEU cc_start: 0.9558 (mp) cc_final: 0.9313 (mm) REVERT: A 830 ASP cc_start: 0.8334 (m-30) cc_final: 0.7345 (t0) REVERT: A 842 VAL cc_start: 0.9494 (t) cc_final: 0.9109 (m) REVERT: A 846 PHE cc_start: 0.9258 (m-80) cc_final: 0.8815 (m-80) REVERT: A 868 HIS cc_start: 0.8417 (m170) cc_final: 0.8200 (m-70) REVERT: B 68 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8242 (mttt) REVERT: B 164 LEU cc_start: 0.8903 (tp) cc_final: 0.8629 (tp) REVERT: B 202 PHE cc_start: 0.8689 (m-80) cc_final: 0.7793 (m-80) REVERT: B 243 SER cc_start: 0.9364 (m) cc_final: 0.8885 (t) REVERT: B 288 GLU cc_start: 0.8945 (mp0) cc_final: 0.8632 (mp0) REVERT: B 289 LEU cc_start: 0.9220 (tp) cc_final: 0.8789 (tp) REVERT: B 416 ASP cc_start: 0.8629 (m-30) cc_final: 0.8372 (m-30) REVERT: B 587 ASP cc_start: 0.9082 (t0) cc_final: 0.8689 (t0) REVERT: B 751 LYS cc_start: 0.9465 (tttm) cc_final: 0.9160 (ttpt) REVERT: B 958 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 1008 PHE cc_start: 0.8231 (m-80) cc_final: 0.7812 (m-80) REVERT: B 1141 SER cc_start: 0.9031 (m) cc_final: 0.8730 (p) REVERT: B 1245 ILE cc_start: 0.9161 (mt) cc_final: 0.8864 (pt) REVERT: B 1293 LYS cc_start: 0.8909 (mttt) cc_final: 0.8651 (mppt) REVERT: B 1295 ILE cc_start: 0.8798 (mt) cc_final: 0.8526 (mp) REVERT: B 1357 TRP cc_start: 0.8971 (m100) cc_final: 0.8517 (m100) REVERT: C 254 MET cc_start: 0.9356 (tpp) cc_final: 0.8923 (tpt) REVERT: C 256 TYR cc_start: 0.9270 (t80) cc_final: 0.8881 (t80) REVERT: C 277 TRP cc_start: 0.8397 (t-100) cc_final: 0.8158 (t-100) REVERT: C 396 MET cc_start: 0.2513 (ptt) cc_final: 0.1775 (tpt) REVERT: D 107 ASP cc_start: 0.8959 (t0) cc_final: 0.8571 (t0) REVERT: D 221 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7412 (pt0) REVERT: D 309 LYS cc_start: 0.9443 (tttt) cc_final: 0.9183 (tptp) REVERT: D 329 TYR cc_start: 0.9405 (m-80) cc_final: 0.8521 (m-80) REVERT: D 373 MET cc_start: 0.8480 (mmt) cc_final: 0.8262 (mmt) REVERT: D 388 HIS cc_start: 0.8560 (p-80) cc_final: 0.7781 (p-80) REVERT: D 389 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8675 (mmmt) REVERT: D 438 TYR cc_start: 0.8791 (t80) cc_final: 0.8479 (t80) REVERT: E 44 GLN cc_start: 0.9232 (mp10) cc_final: 0.8944 (mp10) REVERT: E 52 THR cc_start: 0.8866 (m) cc_final: 0.8493 (p) REVERT: E 53 ILE cc_start: 0.8621 (mm) cc_final: 0.8190 (tp) REVERT: E 133 ASN cc_start: 0.8470 (t0) cc_final: 0.7991 (t0) REVERT: E 137 LEU cc_start: 0.9217 (mt) cc_final: 0.8994 (mt) REVERT: E 168 MET cc_start: 0.8566 (tmm) cc_final: 0.8003 (tmm) REVERT: E 175 MET cc_start: 0.9091 (mmm) cc_final: 0.8582 (mmm) REVERT: F 46 HIS cc_start: 0.9009 (m170) cc_final: 0.8702 (m-70) REVERT: F 75 ASP cc_start: 0.7862 (t70) cc_final: 0.7646 (t0) REVERT: F 133 ASN cc_start: 0.8716 (t0) cc_final: 0.7929 (t0) REVERT: F 145 PHE cc_start: 0.7992 (t80) cc_final: 0.7598 (t80) REVERT: F 146 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8802 (tm-30) REVERT: F 149 GLN cc_start: 0.8981 (tp40) cc_final: 0.8467 (tp-100) REVERT: F 160 MET cc_start: 0.8239 (ttt) cc_final: 0.7936 (ttt) REVERT: F 169 ASN cc_start: 0.8385 (m-40) cc_final: 0.8038 (m-40) outliers start: 1 outliers final: 1 residues processed: 442 average time/residue: 0.1798 time to fit residues: 120.5530 Evaluate side-chains 369 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 120 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 252 optimal weight: 0.0770 chunk 174 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 709 GLN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 271 ASN D 146 HIS D 158 ASN D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN E 46 HIS E 169 ASN F 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081699 restraints weight = 150430.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.081521 restraints weight = 81374.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081439 restraints weight = 62557.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.081829 restraints weight = 60380.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.081994 restraints weight = 49690.323| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25938 Z= 0.151 Angle : 0.617 17.517 35066 Z= 0.313 Chirality : 0.042 0.199 3898 Planarity : 0.004 0.063 4484 Dihedral : 7.829 165.243 3454 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3115 helix: 1.57 (0.15), residues: 1347 sheet: -0.01 (0.26), residues: 403 loop : -0.67 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 81 TYR 0.025 0.002 TYR F 90 PHE 0.024 0.001 PHE F 21 TRP 0.020 0.001 TRP F 114 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (25933) covalent geometry : angle 0.60631 / 0.31 (35060) hydrogen bonds : bond 0.04372 / 2.78 ( 1125) hydrogen bonds : angle 4.45587 / 3.08 ( 3174) metal coordination : bond 0.00938 / 0.49 ( 4) metal coordination : angle 8.68261 / 5.20 ( 6) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.892 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: A 180 LYS cc_start: 0.9512 (tttt) cc_final: 0.8956 (tptp) REVERT: A 183 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8332 (ptt-90) REVERT: A 262 MET cc_start: 0.8390 (mpp) cc_final: 0.8123 (mpp) REVERT: A 264 ASN cc_start: 0.8235 (m-40) cc_final: 0.7819 (m-40) REVERT: A 314 ASP cc_start: 0.9192 (t0) cc_final: 0.8962 (t0) REVERT: A 335 LYS cc_start: 0.9358 (mttt) cc_final: 0.8941 (mtmm) REVERT: A 359 ASP cc_start: 0.8621 (t0) cc_final: 0.8384 (t70) REVERT: A 398 GLN cc_start: 0.9336 (mp10) cc_final: 0.8139 (mm-40) REVERT: A 492 TYR cc_start: 0.8450 (m-10) cc_final: 0.8120 (m-80) REVERT: A 556 MET cc_start: 0.8444 (tmm) cc_final: 0.8184 (ppp) REVERT: A 583 MET cc_start: 0.8426 (mmm) cc_final: 0.7812 (tmm) REVERT: A 649 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8567 (tp-100) REVERT: A 658 LEU cc_start: 0.9542 (mt) cc_final: 0.9091 (tp) REVERT: A 722 MET cc_start: 0.9204 (tpt) cc_final: 0.8471 (tpt) REVERT: A 799 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8800 (mtt-85) REVERT: A 817 LEU cc_start: 0.9555 (mp) cc_final: 0.9306 (mm) REVERT: A 823 MET cc_start: 0.8404 (mmp) cc_final: 0.7699 (mmm) REVERT: A 830 ASP cc_start: 0.8240 (m-30) cc_final: 0.7293 (t0) REVERT: A 846 PHE cc_start: 0.9145 (m-80) cc_final: 0.8634 (m-80) REVERT: A 868 HIS cc_start: 0.8464 (m170) cc_final: 0.8220 (m-70) REVERT: B 202 PHE cc_start: 0.8615 (m-80) cc_final: 0.7704 (m-80) REVERT: B 243 SER cc_start: 0.9389 (m) cc_final: 0.8850 (t) REVERT: B 288 GLU cc_start: 0.9021 (mp0) cc_final: 0.8578 (mp0) REVERT: B 416 ASP cc_start: 0.8627 (m-30) cc_final: 0.8369 (m-30) REVERT: B 587 ASP cc_start: 0.9052 (t0) cc_final: 0.8679 (t0) REVERT: B 751 LYS cc_start: 0.9460 (tttm) cc_final: 0.9167 (ttpt) REVERT: B 958 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 1245 ILE cc_start: 0.9135 (mt) cc_final: 0.8846 (pt) REVERT: B 1357 TRP cc_start: 0.8920 (m100) cc_final: 0.8457 (m100) REVERT: C 254 MET cc_start: 0.9357 (tpp) cc_final: 0.8929 (tpt) REVERT: C 260 GLN cc_start: 0.8944 (mt0) cc_final: 0.8735 (pt0) REVERT: C 277 TRP cc_start: 0.8288 (t-100) cc_final: 0.8003 (t-100) REVERT: C 396 MET cc_start: 0.2436 (ptt) cc_final: 0.1781 (mmm) REVERT: D 107 ASP cc_start: 0.8913 (t0) cc_final: 0.8541 (t0) REVERT: D 204 CYS cc_start: 0.8868 (m) cc_final: 0.8600 (m) REVERT: D 221 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7685 (pt0) REVERT: D 329 TYR cc_start: 0.9352 (m-80) cc_final: 0.8455 (m-80) REVERT: D 373 MET cc_start: 0.8628 (mmt) cc_final: 0.8311 (mmt) REVERT: D 388 HIS cc_start: 0.8665 (p-80) cc_final: 0.7732 (p-80) REVERT: D 389 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8647 (mmmt) REVERT: D 438 TYR cc_start: 0.8690 (t80) cc_final: 0.8405 (t80) REVERT: E 44 GLN cc_start: 0.9130 (mp10) cc_final: 0.8884 (mp10) REVERT: E 52 THR cc_start: 0.8903 (m) cc_final: 0.8468 (p) REVERT: E 53 ILE cc_start: 0.8742 (mm) cc_final: 0.8324 (tp) REVERT: E 133 ASN cc_start: 0.8433 (t0) cc_final: 0.7895 (t0) REVERT: E 137 LEU cc_start: 0.9182 (mt) cc_final: 0.8971 (mt) REVERT: E 175 MET cc_start: 0.8904 (mmm) cc_final: 0.8639 (mmm) REVERT: F 20 GLN cc_start: 0.8580 (mm110) cc_final: 0.8209 (mm-40) REVERT: F 70 LYS cc_start: 0.8427 (pttm) cc_final: 0.8129 (pttm) REVERT: F 75 ASP cc_start: 0.7920 (t70) cc_final: 0.7653 (t0) REVERT: F 133 ASN cc_start: 0.8710 (t0) cc_final: 0.7910 (t0) REVERT: F 144 ASP cc_start: 0.9075 (t0) cc_final: 0.8798 (t0) REVERT: F 145 PHE cc_start: 0.7893 (t80) cc_final: 0.7690 (t80) REVERT: F 146 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8732 (tm-30) REVERT: F 149 GLN cc_start: 0.8912 (tp40) cc_final: 0.8544 (tp-100) REVERT: F 153 ASP cc_start: 0.8813 (m-30) cc_final: 0.8564 (m-30) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1774 time to fit residues: 118.7961 Evaluate side-chains 366 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 245 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 857 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 798 ASN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN D 146 HIS D 158 ASN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065162 restraints weight = 119016.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067075 restraints weight = 65352.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068395 restraints weight = 43463.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069233 restraints weight = 32682.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069809 restraints weight = 27026.968| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25938 Z= 0.135 Angle : 0.618 15.793 35066 Z= 0.312 Chirality : 0.042 0.179 3898 Planarity : 0.004 0.063 4484 Dihedral : 7.698 168.883 3454 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.59 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1336 sheet: 0.10 (0.26), residues: 401 loop : -0.66 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 91 TYR 0.025 0.001 TYR E 90 PHE 0.035 0.001 PHE B 38 TRP 0.019 0.001 TRP B1213 HIS 0.010 0.001 HIS A 857 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25933) covalent geometry : angle 0.60953 / 0.31 (35060) hydrogen bonds : bond 0.04197 / 2.67 ( 1125) hydrogen bonds : angle 4.40504 / 3.05 ( 3174) metal coordination : bond 0.00912 / 0.47 ( 4) metal coordination : angle 7.96044 / 4.77 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 1.053 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: A 142 ASP cc_start: 0.8524 (m-30) cc_final: 0.8245 (m-30) REVERT: A 180 LYS cc_start: 0.9505 (tttt) cc_final: 0.8927 (tptp) REVERT: A 183 ARG cc_start: 0.8675 (ptt-90) cc_final: 0.8318 (ptt-90) REVERT: A 262 MET cc_start: 0.8427 (mpp) cc_final: 0.8145 (mpp) REVERT: A 264 ASN cc_start: 0.8288 (m-40) cc_final: 0.7875 (m-40) REVERT: A 314 ASP cc_start: 0.9187 (t0) cc_final: 0.8877 (p0) REVERT: A 335 LYS cc_start: 0.9361 (mttt) cc_final: 0.8976 (mtmm) REVERT: A 359 ASP cc_start: 0.8805 (t0) cc_final: 0.8363 (t70) REVERT: A 395 TYR cc_start: 0.8919 (m-80) cc_final: 0.8591 (m-80) REVERT: A 398 GLN cc_start: 0.9331 (mp10) cc_final: 0.8132 (mm-40) REVERT: A 583 MET cc_start: 0.8370 (mmm) cc_final: 0.7858 (tmm) REVERT: A 649 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8626 (tm-30) REVERT: A 658 LEU cc_start: 0.9570 (mt) cc_final: 0.9130 (tp) REVERT: A 703 PHE cc_start: 0.8177 (t80) cc_final: 0.7932 (t80) REVERT: A 722 MET cc_start: 0.9174 (tpt) cc_final: 0.8382 (tpt) REVERT: A 799 ARG cc_start: 0.9227 (mtp-110) cc_final: 0.8940 (mtt-85) REVERT: A 817 LEU cc_start: 0.9579 (mp) cc_final: 0.9325 (mm) REVERT: A 823 MET cc_start: 0.8412 (mmp) cc_final: 0.7660 (mmm) REVERT: A 830 ASP cc_start: 0.8189 (m-30) cc_final: 0.7267 (t0) REVERT: A 834 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7835 (mm-30) REVERT: A 846 PHE cc_start: 0.9039 (m-80) cc_final: 0.8644 (m-80) REVERT: A 868 HIS cc_start: 0.8452 (m170) cc_final: 0.8180 (m-70) REVERT: B 202 PHE cc_start: 0.8315 (m-80) cc_final: 0.7499 (m-80) REVERT: B 243 SER cc_start: 0.9410 (m) cc_final: 0.8810 (t) REVERT: B 289 LEU cc_start: 0.9293 (tp) cc_final: 0.9061 (tp) REVERT: B 307 TYR cc_start: 0.7610 (t80) cc_final: 0.7146 (t80) REVERT: B 416 ASP cc_start: 0.8656 (m-30) cc_final: 0.8387 (m-30) REVERT: B 587 ASP cc_start: 0.9072 (t0) cc_final: 0.8778 (t0) REVERT: B 700 ASP cc_start: 0.8670 (m-30) cc_final: 0.8320 (m-30) REVERT: B 751 LYS cc_start: 0.9409 (tttm) cc_final: 0.9163 (ttpt) REVERT: B 958 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 1192 MET cc_start: 0.9061 (tpp) cc_final: 0.8152 (mpp) REVERT: B 1245 ILE cc_start: 0.9134 (mt) cc_final: 0.8819 (pt) REVERT: B 1262 ASP cc_start: 0.8459 (m-30) cc_final: 0.8098 (m-30) REVERT: B 1329 HIS cc_start: 0.8672 (m-70) cc_final: 0.8344 (m-70) REVERT: B 1357 TRP cc_start: 0.8900 (m100) cc_final: 0.8489 (m100) REVERT: C 165 CYS cc_start: 0.9095 (m) cc_final: 0.8761 (m) REVERT: C 254 MET cc_start: 0.9352 (tpp) cc_final: 0.8924 (tpt) REVERT: C 396 MET cc_start: 0.2416 (ptt) cc_final: 0.1781 (mmm) REVERT: D 63 ASP cc_start: 0.8602 (m-30) cc_final: 0.8357 (m-30) REVERT: D 107 ASP cc_start: 0.8829 (t0) cc_final: 0.8482 (t0) REVERT: D 121 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7725 (mmtt) REVERT: D 204 CYS cc_start: 0.8857 (m) cc_final: 0.8535 (m) REVERT: D 221 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7706 (pt0) REVERT: D 309 LYS cc_start: 0.9411 (tttt) cc_final: 0.9159 (tptt) REVERT: D 329 TYR cc_start: 0.9232 (m-80) cc_final: 0.8415 (m-80) REVERT: D 373 MET cc_start: 0.8583 (mmt) cc_final: 0.8251 (mmt) REVERT: D 380 VAL cc_start: 0.9189 (t) cc_final: 0.8879 (t) REVERT: D 388 HIS cc_start: 0.8666 (p-80) cc_final: 0.7625 (p-80) REVERT: D 389 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8583 (mmmt) REVERT: D 436 LEU cc_start: 0.9417 (tt) cc_final: 0.9192 (pp) REVERT: E 52 THR cc_start: 0.9018 (m) cc_final: 0.8441 (p) REVERT: E 53 ILE cc_start: 0.8729 (mm) cc_final: 0.8182 (tp) REVERT: E 133 ASN cc_start: 0.8449 (t0) cc_final: 0.7887 (t0) REVERT: E 137 LEU cc_start: 0.9154 (mt) cc_final: 0.8928 (mt) REVERT: E 175 MET cc_start: 0.8956 (mmm) cc_final: 0.8684 (mmm) REVERT: F 133 ASN cc_start: 0.8621 (t0) cc_final: 0.7652 (t0) REVERT: F 144 ASP cc_start: 0.9089 (t0) cc_final: 0.8833 (t0) REVERT: F 180 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8491 (tptp) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.1928 time to fit residues: 126.8035 Evaluate side-chains 365 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 280 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 292 GLN B 531 GLN B 580 HIS B 798 ASN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN D 146 HIS D 208 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 169 ASN F 46 HIS F 149 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.100024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.081974 restraints weight = 149128.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.081902 restraints weight = 86432.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082638 restraints weight = 61459.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.082807 restraints weight = 48939.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082835 restraints weight = 45577.920| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25938 Z= 0.127 Angle : 0.625 14.667 35066 Z= 0.317 Chirality : 0.042 0.167 3898 Planarity : 0.004 0.063 4484 Dihedral : 7.584 172.382 3454 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 0.04 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3115 helix: 1.65 (0.15), residues: 1339 sheet: 0.12 (0.26), residues: 405 loop : -0.64 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 561 TYR 0.022 0.001 TYR A 322 PHE 0.033 0.001 PHE B 38 TRP 0.020 0.001 TRP B1213 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (25933) covalent geometry : angle 0.61714 / 0.32 (35060) hydrogen bonds : bond 0.04073 / 2.62 ( 1125) hydrogen bonds : angle 4.42726 / 3.05 ( 3174) metal coordination : bond 0.00871 / 0.45 ( 4) metal coordination : angle 7.48055 / 4.49 ( 6) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 422 time to evaluate : 1.012 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: A 140 MET cc_start: 0.8157 (mtp) cc_final: 0.7952 (mtm) REVERT: A 180 LYS cc_start: 0.9507 (tttt) cc_final: 0.8907 (tptp) REVERT: A 183 ARG cc_start: 0.8676 (ptt-90) cc_final: 0.8299 (ptt-90) REVERT: A 187 MET cc_start: 0.8595 (mtm) cc_final: 0.8368 (mtm) REVERT: A 262 MET cc_start: 0.8389 (mpp) cc_final: 0.8122 (mpp) REVERT: A 264 ASN cc_start: 0.8243 (m-40) cc_final: 0.7841 (m-40) REVERT: A 314 ASP cc_start: 0.9181 (t0) cc_final: 0.8897 (p0) REVERT: A 319 PHE cc_start: 0.8679 (m-80) cc_final: 0.8414 (m-80) REVERT: A 335 LYS cc_start: 0.9365 (mttt) cc_final: 0.9014 (mtmm) REVERT: A 358 MET cc_start: 0.8697 (tpt) cc_final: 0.8293 (tpt) REVERT: A 359 ASP cc_start: 0.8853 (t0) cc_final: 0.8323 (p0) REVERT: A 394 MET cc_start: 0.8670 (mmt) cc_final: 0.8420 (mmt) REVERT: A 395 TYR cc_start: 0.8998 (m-80) cc_final: 0.8640 (m-80) REVERT: A 398 GLN cc_start: 0.9366 (mp10) cc_final: 0.8172 (mm-40) REVERT: A 408 PHE cc_start: 0.8465 (m-80) cc_final: 0.8210 (m-10) REVERT: A 516 MET cc_start: 0.9239 (mmm) cc_final: 0.8943 (mmm) REVERT: A 538 MET cc_start: 0.7875 (mtp) cc_final: 0.7574 (mtt) REVERT: A 556 MET cc_start: 0.8355 (tmm) cc_final: 0.8132 (ppp) REVERT: A 583 MET cc_start: 0.8393 (mmm) cc_final: 0.7787 (tmm) REVERT: A 635 PHE cc_start: 0.6697 (t80) cc_final: 0.6373 (t80) REVERT: A 643 GLN cc_start: 0.9068 (tt0) cc_final: 0.8760 (mt0) REVERT: A 649 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8676 (tm-30) REVERT: A 658 LEU cc_start: 0.9555 (mt) cc_final: 0.9049 (tp) REVERT: A 681 PHE cc_start: 0.8379 (m-10) cc_final: 0.8057 (m-10) REVERT: A 722 MET cc_start: 0.9220 (tpt) cc_final: 0.8483 (tpt) REVERT: A 798 PHE cc_start: 0.9286 (t80) cc_final: 0.9074 (t80) REVERT: A 799 ARG cc_start: 0.9324 (mtp-110) cc_final: 0.9026 (mtp85) REVERT: A 809 LEU cc_start: 0.9409 (mm) cc_final: 0.9088 (pp) REVERT: A 817 LEU cc_start: 0.9573 (mp) cc_final: 0.9325 (mm) REVERT: A 823 MET cc_start: 0.8500 (mmp) cc_final: 0.7732 (mmm) REVERT: A 830 ASP cc_start: 0.8305 (m-30) cc_final: 0.7444 (t0) REVERT: A 834 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7873 (mm-30) REVERT: A 842 VAL cc_start: 0.9472 (t) cc_final: 0.9202 (t) REVERT: A 846 PHE cc_start: 0.9111 (m-80) cc_final: 0.8719 (m-80) REVERT: A 868 HIS cc_start: 0.8509 (m170) cc_final: 0.8248 (m-70) REVERT: B 202 PHE cc_start: 0.8601 (m-80) cc_final: 0.7683 (m-80) REVERT: B 243 SER cc_start: 0.9390 (m) cc_final: 0.8808 (t) REVERT: B 289 LEU cc_start: 0.9337 (tp) cc_final: 0.8885 (tp) REVERT: B 292 GLN cc_start: 0.9082 (mp10) cc_final: 0.8776 (mp10) REVERT: B 328 MET cc_start: 0.9362 (tpp) cc_final: 0.8749 (mpp) REVERT: B 416 ASP cc_start: 0.8638 (m-30) cc_final: 0.8378 (m-30) REVERT: B 587 ASP cc_start: 0.9066 (t0) cc_final: 0.8751 (t0) REVERT: B 700 ASP cc_start: 0.8687 (m-30) cc_final: 0.8317 (m-30) REVERT: B 751 LYS cc_start: 0.9450 (tttm) cc_final: 0.9152 (ttpt) REVERT: B 952 ARG cc_start: 0.9036 (mmp80) cc_final: 0.8806 (mmp80) REVERT: B 958 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 1025 MET cc_start: 0.7558 (ptp) cc_final: 0.6938 (ptp) REVERT: B 1101 MET cc_start: 0.8545 (ttm) cc_final: 0.8203 (ttp) REVERT: B 1192 MET cc_start: 0.8985 (mmt) cc_final: 0.8629 (mpp) REVERT: B 1245 ILE cc_start: 0.9167 (mt) cc_final: 0.8791 (pt) REVERT: B 1262 ASP cc_start: 0.8537 (m-30) cc_final: 0.8120 (m-30) REVERT: B 1263 MET cc_start: 0.9084 (mmt) cc_final: 0.8636 (mmm) REVERT: B 1329 HIS cc_start: 0.8790 (m-70) cc_final: 0.8371 (m-70) REVERT: B 1357 TRP cc_start: 0.8870 (m100) cc_final: 0.8466 (m100) REVERT: C 254 MET cc_start: 0.9345 (tpp) cc_final: 0.8918 (tpt) REVERT: C 271 ASN cc_start: 0.9471 (m110) cc_final: 0.9068 (p0) REVERT: C 396 MET cc_start: 0.2597 (ptt) cc_final: 0.1849 (tpt) REVERT: D 62 LEU cc_start: 0.8870 (tp) cc_final: 0.8448 (tp) REVERT: D 107 ASP cc_start: 0.8883 (t0) cc_final: 0.8500 (t0) REVERT: D 121 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7760 (mmtt) REVERT: D 204 CYS cc_start: 0.8966 (m) cc_final: 0.8585 (m) REVERT: D 221 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7582 (pt0) REVERT: D 325 LEU cc_start: 0.9566 (tp) cc_final: 0.9345 (mt) REVERT: D 329 TYR cc_start: 0.9339 (m-80) cc_final: 0.8396 (m-80) REVERT: D 373 MET cc_start: 0.8659 (mmt) cc_final: 0.8380 (mmt) REVERT: D 388 HIS cc_start: 0.8776 (p-80) cc_final: 0.7809 (p-80) REVERT: D 389 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8758 (mmmt) REVERT: D 436 LEU cc_start: 0.9378 (tt) cc_final: 0.9143 (pp) REVERT: E 52 THR cc_start: 0.8930 (m) cc_final: 0.8473 (p) REVERT: E 53 ILE cc_start: 0.8715 (mm) cc_final: 0.8115 (tp) REVERT: E 57 PHE cc_start: 0.8904 (t80) cc_final: 0.8613 (t80) REVERT: E 133 ASN cc_start: 0.8487 (t0) cc_final: 0.7903 (t0) REVERT: E 137 LEU cc_start: 0.9167 (mt) cc_final: 0.8914 (mt) REVERT: E 175 MET cc_start: 0.9022 (mmm) cc_final: 0.8513 (mmm) REVERT: F 22 LYS cc_start: 0.8722 (mppt) cc_final: 0.8469 (mmtm) REVERT: F 70 LYS cc_start: 0.8407 (pttm) cc_final: 0.8025 (pttm) REVERT: F 133 ASN cc_start: 0.8526 (t0) cc_final: 0.7548 (t0) REVERT: F 144 ASP cc_start: 0.9097 (t0) cc_final: 0.8827 (t0) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.1912 time to fit residues: 123.5839 Evaluate side-chains 353 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 81 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 36 optimal weight: 0.0050 chunk 257 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 129 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 overall best weight: 1.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 798 ASN B 811 HIS ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 146 HIS ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 169 ASN F 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079884 restraints weight = 149387.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.079957 restraints weight = 92074.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080847 restraints weight = 64146.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.080947 restraints weight = 48350.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.080971 restraints weight = 46647.693| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25938 Z= 0.153 Angle : 0.642 15.371 35066 Z= 0.326 Chirality : 0.043 0.222 3898 Planarity : 0.004 0.062 4484 Dihedral : 7.572 175.496 3454 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.78 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 3115 helix: 1.65 (0.15), residues: 1344 sheet: 0.06 (0.26), residues: 407 loop : -0.66 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.037 0.002 TYR F 90 PHE 0.029 0.001 PHE B 38 TRP 0.023 0.001 TRP B1213 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (25933) covalent geometry : angle 0.63570 / 0.33 (35060) hydrogen bonds : bond 0.04188 / 2.66 ( 1125) hydrogen bonds : angle 4.47378 / 3.11 ( 3174) metal coordination : bond 0.00828 / 0.43 ( 4) metal coordination : angle 6.88583 / 4.14 ( 6) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.048 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: A 180 LYS cc_start: 0.9519 (tttt) cc_final: 0.8870 (tptp) REVERT: A 183 ARG cc_start: 0.8671 (ptt-90) cc_final: 0.8252 (ptt-90) REVERT: A 262 MET cc_start: 0.8402 (mpp) cc_final: 0.8088 (mpp) REVERT: A 264 ASN cc_start: 0.8257 (m-40) cc_final: 0.7836 (m-40) REVERT: A 319 PHE cc_start: 0.8528 (m-80) cc_final: 0.8211 (m-80) REVERT: A 335 LYS cc_start: 0.9410 (mttt) cc_final: 0.9052 (mtmm) REVERT: A 359 ASP cc_start: 0.8931 (t0) cc_final: 0.8450 (t70) REVERT: A 395 TYR cc_start: 0.9071 (m-80) cc_final: 0.8758 (m-80) REVERT: A 398 GLN cc_start: 0.9385 (mp10) cc_final: 0.8214 (mm-40) REVERT: A 408 PHE cc_start: 0.8526 (m-80) cc_final: 0.7987 (m-10) REVERT: A 492 TYR cc_start: 0.8610 (m-10) cc_final: 0.8355 (m-80) REVERT: A 516 MET cc_start: 0.9318 (mmm) cc_final: 0.8922 (mmm) REVERT: A 538 MET cc_start: 0.7859 (mtp) cc_final: 0.7596 (mtt) REVERT: A 583 MET cc_start: 0.8301 (mmm) cc_final: 0.7547 (ttm) REVERT: A 635 PHE cc_start: 0.6716 (t80) cc_final: 0.6269 (t80) REVERT: A 643 GLN cc_start: 0.9216 (tt0) cc_final: 0.8907 (mt0) REVERT: A 658 LEU cc_start: 0.9585 (mt) cc_final: 0.9098 (tp) REVERT: A 681 PHE cc_start: 0.8551 (m-10) cc_final: 0.8101 (m-10) REVERT: A 722 MET cc_start: 0.9245 (tpt) cc_final: 0.8575 (tpt) REVERT: A 780 ASN cc_start: 0.7470 (t0) cc_final: 0.7194 (t0) REVERT: A 799 ARG cc_start: 0.9300 (mtp-110) cc_final: 0.9004 (mtp85) REVERT: A 809 LEU cc_start: 0.9419 (mm) cc_final: 0.9074 (pp) REVERT: A 823 MET cc_start: 0.8582 (mmp) cc_final: 0.8046 (mmm) REVERT: A 830 ASP cc_start: 0.8418 (m-30) cc_final: 0.7558 (t0) REVERT: A 834 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7923 (mm-30) REVERT: A 842 VAL cc_start: 0.9469 (t) cc_final: 0.9165 (t) REVERT: A 846 PHE cc_start: 0.9177 (m-80) cc_final: 0.8730 (m-80) REVERT: A 868 HIS cc_start: 0.8532 (m170) cc_final: 0.8290 (m-70) REVERT: B 202 PHE cc_start: 0.8658 (m-80) cc_final: 0.7738 (m-80) REVERT: B 289 LEU cc_start: 0.9274 (tp) cc_final: 0.8542 (tp) REVERT: B 307 TYR cc_start: 0.7605 (t80) cc_final: 0.7358 (t80) REVERT: B 416 ASP cc_start: 0.8648 (m-30) cc_final: 0.8390 (m-30) REVERT: B 529 GLU cc_start: 0.8429 (pt0) cc_final: 0.8195 (pt0) REVERT: B 587 ASP cc_start: 0.9082 (t0) cc_final: 0.8792 (t0) REVERT: B 700 ASP cc_start: 0.8654 (m-30) cc_final: 0.8316 (m-30) REVERT: B 751 LYS cc_start: 0.9440 (tttm) cc_final: 0.9145 (ttpt) REVERT: B 958 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 1025 MET cc_start: 0.7605 (ptp) cc_final: 0.7025 (ptp) REVERT: B 1165 MET cc_start: 0.8237 (mtm) cc_final: 0.7912 (mtm) REVERT: B 1192 MET cc_start: 0.8892 (mmt) cc_final: 0.8648 (mpp) REVERT: B 1245 ILE cc_start: 0.9228 (mt) cc_final: 0.8963 (pt) REVERT: B 1262 ASP cc_start: 0.8466 (m-30) cc_final: 0.8175 (m-30) REVERT: B 1263 MET cc_start: 0.9135 (mmt) cc_final: 0.8662 (mmm) REVERT: B 1293 LYS cc_start: 0.8965 (mttt) cc_final: 0.8686 (mppt) REVERT: B 1329 HIS cc_start: 0.8857 (m-70) cc_final: 0.8348 (m-70) REVERT: B 1357 TRP cc_start: 0.8878 (m100) cc_final: 0.8444 (m100) REVERT: C 254 MET cc_start: 0.9384 (tpp) cc_final: 0.8939 (tpt) REVERT: C 396 MET cc_start: 0.2857 (ptt) cc_final: 0.2119 (tpt) REVERT: D 107 ASP cc_start: 0.8852 (t0) cc_final: 0.8452 (t0) REVERT: D 204 CYS cc_start: 0.8758 (m) cc_final: 0.8316 (m) REVERT: D 221 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7552 (pt0) REVERT: D 309 LYS cc_start: 0.9460 (tttt) cc_final: 0.9183 (tptp) REVERT: D 325 LEU cc_start: 0.9614 (tp) cc_final: 0.9366 (mt) REVERT: D 329 TYR cc_start: 0.9409 (m-80) cc_final: 0.8495 (m-80) REVERT: D 373 MET cc_start: 0.8761 (mmt) cc_final: 0.8497 (mmt) REVERT: D 387 ILE cc_start: 0.7878 (mm) cc_final: 0.7325 (tp) REVERT: D 388 HIS cc_start: 0.8779 (p-80) cc_final: 0.8013 (p-80) REVERT: E 52 THR cc_start: 0.9074 (m) cc_final: 0.8536 (p) REVERT: E 53 ILE cc_start: 0.8801 (mm) cc_final: 0.8191 (tp) REVERT: E 133 ASN cc_start: 0.8486 (t0) cc_final: 0.7898 (t0) REVERT: E 140 LYS cc_start: 0.9089 (mptt) cc_final: 0.8821 (mmtm) REVERT: E 175 MET cc_start: 0.8938 (mmm) cc_final: 0.8732 (mmm) REVERT: F 70 LYS cc_start: 0.8518 (pttm) cc_final: 0.8181 (pttm) REVERT: F 75 ASP cc_start: 0.7823 (t70) cc_final: 0.7595 (t0) REVERT: F 133 ASN cc_start: 0.8574 (t0) cc_final: 0.7726 (t0) REVERT: F 144 ASP cc_start: 0.9117 (t0) cc_final: 0.8839 (t0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1970 time to fit residues: 127.1672 Evaluate side-chains 359 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 117 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 301 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 186 optimal weight: 0.0270 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 531 GLN B 744 HIS B 798 ASN B 811 HIS ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 271 ASN D 146 HIS ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.100022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.081248 restraints weight = 149598.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081545 restraints weight = 88766.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.082354 restraints weight = 63322.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082409 restraints weight = 47802.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082421 restraints weight = 45551.949| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25938 Z= 0.117 Angle : 0.643 16.374 35066 Z= 0.323 Chirality : 0.043 0.251 3898 Planarity : 0.004 0.089 4484 Dihedral : 7.417 179.096 3454 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 0.04 % Allowed : 0.64 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 3115 helix: 1.75 (0.15), residues: 1341 sheet: 0.11 (0.26), residues: 410 loop : -0.62 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 191 TYR 0.036 0.001 TYR F 90 PHE 0.031 0.001 PHE A 704 TRP 0.022 0.001 TRP B1213 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (25933) covalent geometry : angle 0.63689 / 0.32 (35060) hydrogen bonds : bond 0.03942 / 2.52 ( 1125) hydrogen bonds : angle 4.34697 / 3.01 ( 3174) metal coordination : bond 0.00821 / 0.43 ( 4) metal coordination : angle 6.66161 / 4.00 ( 6) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.063 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: A 180 LYS cc_start: 0.9512 (tttt) cc_final: 0.8893 (tptp) REVERT: A 183 ARG cc_start: 0.8659 (ptt-90) cc_final: 0.8295 (ptt-90) REVERT: A 262 MET cc_start: 0.8361 (mpp) cc_final: 0.8100 (mpp) REVERT: A 264 ASN cc_start: 0.8222 (m-40) cc_final: 0.7831 (m-40) REVERT: A 319 PHE cc_start: 0.8546 (m-80) cc_final: 0.8345 (m-80) REVERT: A 335 LYS cc_start: 0.9379 (mttt) cc_final: 0.9038 (mtmm) REVERT: A 359 ASP cc_start: 0.8930 (t0) cc_final: 0.8479 (t0) REVERT: A 395 TYR cc_start: 0.9086 (m-80) cc_final: 0.8816 (m-80) REVERT: A 397 LEU cc_start: 0.9258 (tp) cc_final: 0.9057 (tp) REVERT: A 408 PHE cc_start: 0.8589 (m-80) cc_final: 0.8161 (m-10) REVERT: A 492 TYR cc_start: 0.8598 (m-10) cc_final: 0.8356 (m-80) REVERT: A 516 MET cc_start: 0.9333 (mmm) cc_final: 0.8940 (mmm) REVERT: A 538 MET cc_start: 0.7906 (mtp) cc_final: 0.7662 (mtt) REVERT: A 583 MET cc_start: 0.8288 (mmm) cc_final: 0.7726 (tmm) REVERT: A 635 PHE cc_start: 0.6626 (t80) cc_final: 0.6370 (t80) REVERT: A 643 GLN cc_start: 0.9187 (tt0) cc_final: 0.8867 (mt0) REVERT: A 658 LEU cc_start: 0.9591 (mt) cc_final: 0.9107 (tp) REVERT: A 681 PHE cc_start: 0.8404 (m-10) cc_final: 0.8075 (m-10) REVERT: A 722 MET cc_start: 0.9247 (tpt) cc_final: 0.8569 (tpt) REVERT: A 780 ASN cc_start: 0.7456 (t0) cc_final: 0.7176 (t0) REVERT: A 799 ARG cc_start: 0.9240 (mtp-110) cc_final: 0.9037 (mtp85) REVERT: A 809 LEU cc_start: 0.9373 (mm) cc_final: 0.9061 (pp) REVERT: A 834 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7925 (mm-30) REVERT: A 842 VAL cc_start: 0.9419 (t) cc_final: 0.9206 (t) REVERT: A 846 PHE cc_start: 0.9170 (m-80) cc_final: 0.8813 (m-80) REVERT: A 868 HIS cc_start: 0.8532 (m170) cc_final: 0.8293 (m-70) REVERT: B 141 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8784 (mmmt) REVERT: B 202 PHE cc_start: 0.8633 (m-80) cc_final: 0.7704 (m-80) REVERT: B 416 ASP cc_start: 0.8637 (m-30) cc_final: 0.8373 (m-30) REVERT: B 503 LYS cc_start: 0.9272 (mmmt) cc_final: 0.9038 (mtmm) REVERT: B 529 GLU cc_start: 0.8387 (pt0) cc_final: 0.8181 (pt0) REVERT: B 587 ASP cc_start: 0.9044 (t0) cc_final: 0.8754 (t0) REVERT: B 700 ASP cc_start: 0.8657 (m-30) cc_final: 0.8301 (m-30) REVERT: B 751 LYS cc_start: 0.9438 (tttm) cc_final: 0.9144 (ttpt) REVERT: B 952 ARG cc_start: 0.9028 (mmp80) cc_final: 0.8787 (mmp80) REVERT: B 958 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 1025 MET cc_start: 0.7607 (ptp) cc_final: 0.7018 (ptp) REVERT: B 1101 MET cc_start: 0.8541 (ttm) cc_final: 0.8267 (ttp) REVERT: B 1165 MET cc_start: 0.8140 (mtm) cc_final: 0.7861 (mtm) REVERT: B 1192 MET cc_start: 0.8948 (mmt) cc_final: 0.8600 (mpp) REVERT: B 1212 MET cc_start: 0.8569 (ptt) cc_final: 0.8204 (ptm) REVERT: B 1245 ILE cc_start: 0.9221 (mt) cc_final: 0.8966 (pt) REVERT: B 1262 ASP cc_start: 0.8404 (m-30) cc_final: 0.8132 (m-30) REVERT: B 1263 MET cc_start: 0.9072 (mmt) cc_final: 0.8659 (mmm) REVERT: B 1293 LYS cc_start: 0.8922 (mttt) cc_final: 0.8645 (mppt) REVERT: B 1357 TRP cc_start: 0.8862 (m100) cc_final: 0.8541 (m100) REVERT: C 254 MET cc_start: 0.9387 (tpp) cc_final: 0.8947 (tpt) REVERT: C 271 ASN cc_start: 0.9480 (m110) cc_final: 0.9082 (p0) REVERT: C 396 MET cc_start: 0.2953 (ptt) cc_final: 0.2207 (tpt) REVERT: D 62 LEU cc_start: 0.8821 (tp) cc_final: 0.8495 (tp) REVERT: D 107 ASP cc_start: 0.8826 (t0) cc_final: 0.8418 (t0) REVERT: D 204 CYS cc_start: 0.8736 (m) cc_final: 0.8453 (m) REVERT: D 221 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7549 (pt0) REVERT: D 309 LYS cc_start: 0.9459 (tttt) cc_final: 0.9180 (tptp) REVERT: D 325 LEU cc_start: 0.9618 (tp) cc_final: 0.9377 (mt) REVERT: D 329 TYR cc_start: 0.9398 (m-80) cc_final: 0.8463 (m-80) REVERT: D 373 MET cc_start: 0.8752 (mmt) cc_final: 0.8509 (mmt) REVERT: D 387 ILE cc_start: 0.7913 (mm) cc_final: 0.7294 (tp) REVERT: D 388 HIS cc_start: 0.8732 (p-80) cc_final: 0.7926 (p-80) REVERT: D 389 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8597 (mmmt) REVERT: D 436 LEU cc_start: 0.9238 (tt) cc_final: 0.9031 (pp) REVERT: E 53 ILE cc_start: 0.8727 (mm) cc_final: 0.8161 (tp) REVERT: E 75 ASP cc_start: 0.8577 (t70) cc_final: 0.8376 (t0) REVERT: E 90 TYR cc_start: 0.8725 (p90) cc_final: 0.8475 (p90) REVERT: E 133 ASN cc_start: 0.8471 (t0) cc_final: 0.7830 (t0) REVERT: E 160 MET cc_start: 0.8111 (tpt) cc_final: 0.7592 (tmm) REVERT: E 175 MET cc_start: 0.9002 (mmm) cc_final: 0.8535 (mmm) REVERT: F 70 LYS cc_start: 0.8433 (pttm) cc_final: 0.8166 (pttm) REVERT: F 133 ASN cc_start: 0.8440 (t0) cc_final: 0.7442 (t0) REVERT: F 144 ASP cc_start: 0.9074 (t0) cc_final: 0.8785 (t0) REVERT: F 162 THR cc_start: 0.8682 (p) cc_final: 0.8445 (p) REVERT: F 169 ASN cc_start: 0.8527 (m-40) cc_final: 0.8252 (m-40) REVERT: F 180 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8461 (tptp) outliers start: 1 outliers final: 0 residues processed: 421 average time/residue: 0.1898 time to fit residues: 122.2150 Evaluate side-chains 356 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 149 optimal weight: 0.7980 chunk 230 optimal weight: 40.0000 chunk 157 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 107 optimal weight: 0.0670 chunk 164 optimal weight: 0.0000 chunk 106 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 798 ASN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS D 146 HIS D 313 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 83 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.100363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081685 restraints weight = 149107.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.081729 restraints weight = 93000.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.082761 restraints weight = 64295.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.082609 restraints weight = 49701.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.082758 restraints weight = 48177.183| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25938 Z= 0.122 Angle : 0.648 17.108 35066 Z= 0.325 Chirality : 0.043 0.389 3898 Planarity : 0.004 0.065 4484 Dihedral : 7.221 177.228 3454 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 3115 helix: 1.74 (0.15), residues: 1342 sheet: 0.22 (0.26), residues: 423 loop : -0.55 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 20 TYR 0.036 0.001 TYR F 90 PHE 0.025 0.001 PHE B 38 TRP 0.021 0.001 TRP B1213 HIS 0.011 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (25933) covalent geometry : angle 0.64272 / 0.32 (35060) hydrogen bonds : bond 0.03893 / 2.48 ( 1125) hydrogen bonds : angle 4.31957 / 2.97 ( 3174) metal coordination : bond 0.00777 / 0.40 ( 4) metal coordination : angle 6.47818 / 3.89 ( 6) Misc. bond : bond 0.00024 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.991 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: A 180 LYS cc_start: 0.9508 (tttt) cc_final: 0.8885 (tptp) REVERT: A 183 ARG cc_start: 0.8648 (ptt-90) cc_final: 0.8280 (ptt-90) REVERT: A 187 MET cc_start: 0.8661 (mtm) cc_final: 0.8441 (mtm) REVERT: A 262 MET cc_start: 0.8341 (mpp) cc_final: 0.8073 (mpp) REVERT: A 264 ASN cc_start: 0.8228 (m-40) cc_final: 0.7836 (m-40) REVERT: A 319 PHE cc_start: 0.8583 (m-80) cc_final: 0.8379 (m-80) REVERT: A 335 LYS cc_start: 0.9369 (mttt) cc_final: 0.9021 (mtmm) REVERT: A 395 TYR cc_start: 0.9064 (m-80) cc_final: 0.8722 (m-80) REVERT: A 397 LEU cc_start: 0.9396 (tp) cc_final: 0.9155 (tp) REVERT: A 408 PHE cc_start: 0.8612 (m-80) cc_final: 0.7932 (m-10) REVERT: A 492 TYR cc_start: 0.8600 (m-10) cc_final: 0.8356 (m-80) REVERT: A 516 MET cc_start: 0.9345 (mmm) cc_final: 0.8831 (mmm) REVERT: A 538 MET cc_start: 0.7875 (mtp) cc_final: 0.7635 (mtt) REVERT: A 583 MET cc_start: 0.8304 (mmm) cc_final: 0.7745 (tmm) REVERT: A 658 LEU cc_start: 0.9589 (mt) cc_final: 0.9152 (tp) REVERT: A 681 PHE cc_start: 0.8416 (m-10) cc_final: 0.8105 (m-10) REVERT: A 722 MET cc_start: 0.9266 (tpt) cc_final: 0.8641 (tpt) REVERT: A 798 PHE cc_start: 0.9304 (t80) cc_final: 0.9089 (t80) REVERT: A 799 ARG cc_start: 0.9301 (mtp-110) cc_final: 0.8961 (mtt-85) REVERT: A 834 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7957 (mm-30) REVERT: A 846 PHE cc_start: 0.9157 (m-80) cc_final: 0.8816 (m-80) REVERT: A 868 HIS cc_start: 0.8526 (m170) cc_final: 0.8290 (m-70) REVERT: B 69 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8841 (tp-100) REVERT: B 141 LYS cc_start: 0.8988 (mmpt) cc_final: 0.8731 (mmmt) REVERT: B 202 PHE cc_start: 0.8651 (m-80) cc_final: 0.7697 (m-80) REVERT: B 243 SER cc_start: 0.9412 (m) cc_final: 0.8796 (t) REVERT: B 272 PHE cc_start: 0.7904 (t80) cc_final: 0.7284 (t80) REVERT: B 274 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7449 (Cg_exo) REVERT: B 288 GLU cc_start: 0.9101 (mp0) cc_final: 0.8576 (mp0) REVERT: B 289 LEU cc_start: 0.9330 (tp) cc_final: 0.8957 (tp) REVERT: B 292 GLN cc_start: 0.9128 (mp10) cc_final: 0.8779 (pm20) REVERT: B 416 ASP cc_start: 0.8647 (m-30) cc_final: 0.8382 (m-30) REVERT: B 503 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9037 (mtmm) REVERT: B 587 ASP cc_start: 0.9049 (t0) cc_final: 0.8720 (t0) REVERT: B 700 ASP cc_start: 0.8602 (m-30) cc_final: 0.8249 (m-30) REVERT: B 751 LYS cc_start: 0.9445 (tttm) cc_final: 0.9145 (ttpt) REVERT: B 958 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 1025 MET cc_start: 0.7637 (ptp) cc_final: 0.7047 (ptp) REVERT: B 1101 MET cc_start: 0.8594 (ttm) cc_final: 0.8298 (ttp) REVERT: B 1141 SER cc_start: 0.9118 (m) cc_final: 0.8783 (p) REVERT: B 1192 MET cc_start: 0.8973 (mmt) cc_final: 0.8645 (mpp) REVERT: B 1212 MET cc_start: 0.8537 (ptt) cc_final: 0.8173 (ptm) REVERT: B 1245 ILE cc_start: 0.9196 (mt) cc_final: 0.8934 (pt) REVERT: B 1262 ASP cc_start: 0.8433 (m-30) cc_final: 0.8193 (m-30) REVERT: B 1329 HIS cc_start: 0.8819 (m-70) cc_final: 0.8300 (m-70) REVERT: B 1357 TRP cc_start: 0.8871 (m100) cc_final: 0.8560 (m100) REVERT: C 162 TYR cc_start: 0.9036 (m-10) cc_final: 0.8517 (m-10) REVERT: C 254 MET cc_start: 0.9381 (tpp) cc_final: 0.8926 (tpt) REVERT: C 396 MET cc_start: 0.3014 (ptt) cc_final: 0.2194 (tpt) REVERT: D 107 ASP cc_start: 0.8808 (t0) cc_final: 0.8404 (t0) REVERT: D 113 PHE cc_start: 0.9009 (p90) cc_final: 0.8777 (p90) REVERT: D 204 CYS cc_start: 0.8730 (m) cc_final: 0.8487 (m) REVERT: D 221 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7506 (pt0) REVERT: D 240 LEU cc_start: 0.9238 (mt) cc_final: 0.9018 (tt) REVERT: D 373 MET cc_start: 0.8758 (mmt) cc_final: 0.8526 (mmt) REVERT: D 387 ILE cc_start: 0.7915 (mm) cc_final: 0.7299 (tp) REVERT: D 388 HIS cc_start: 0.8737 (p-80) cc_final: 0.7930 (p-80) REVERT: D 389 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8600 (mmmt) REVERT: D 436 LEU cc_start: 0.9208 (tt) cc_final: 0.8773 (pp) REVERT: E 53 ILE cc_start: 0.8738 (mm) cc_final: 0.8143 (tp) REVERT: E 75 ASP cc_start: 0.8540 (t70) cc_final: 0.8334 (t0) REVERT: E 90 TYR cc_start: 0.8725 (p90) cc_final: 0.8432 (p90) REVERT: E 110 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: E 133 ASN cc_start: 0.8500 (t0) cc_final: 0.7836 (t0) REVERT: E 160 MET cc_start: 0.8086 (tpt) cc_final: 0.7370 (tmm) REVERT: E 175 MET cc_start: 0.8935 (mmm) cc_final: 0.8706 (mmm) REVERT: F 70 LYS cc_start: 0.8484 (pttm) cc_final: 0.8232 (pttm) REVERT: F 133 ASN cc_start: 0.8346 (t0) cc_final: 0.7279 (t0) REVERT: F 144 ASP cc_start: 0.9059 (t0) cc_final: 0.8771 (t0) REVERT: F 162 THR cc_start: 0.8645 (p) cc_final: 0.8418 (p) REVERT: F 169 ASN cc_start: 0.8484 (m-40) cc_final: 0.8270 (m-40) REVERT: F 177 ILE cc_start: 0.9329 (tp) cc_final: 0.8978 (tp) REVERT: F 180 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8425 (ptmt) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1819 time to fit residues: 117.7451 Evaluate side-chains 352 residues out of total 2792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 121 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 232 optimal weight: 0.0370 chunk 212 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 248 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 281 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 745 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 798 ASN ** B 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN D 146 HIS D 313 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 83 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.099923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081463 restraints weight = 149356.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081068 restraints weight = 97321.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082105 restraints weight = 70125.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082145 restraints weight = 49454.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.082164 restraints weight = 48479.843| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25938 Z= 0.125 Angle : 0.654 18.238 35066 Z= 0.328 Chirality : 0.043 0.299 3898 Planarity : 0.004 0.062 4484 Dihedral : 7.136 178.161 3454 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.51 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 3115 helix: 1.69 (0.15), residues: 1339 sheet: 0.22 (0.26), residues: 419 loop : -0.56 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 952 TYR 0.023 0.001 TYR A 322 PHE 0.032 0.001 PHE A 704 TRP 0.024 0.001 TRP B1213 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (25933) covalent geometry : angle 0.64794 / 0.33 (35060) hydrogen bonds : bond 0.03905 / 2.50 ( 1125) hydrogen bonds : angle 4.38601 / 3.02 ( 3174) metal coordination : bond 0.00753 / 0.39 ( 4) metal coordination : angle 6.57853 / 3.94 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5043.48 seconds wall clock time: 87 minutes 57.87 seconds (5277.87 seconds total)