Starting phenix.real_space_refine on Sun Jul 5 02:19:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.map" model { file = "/net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx9_54362/07_2026/9rx9_54362.cif" } resolution = 3.99 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 5 5.49 5 Mg 2 5.21 5 S 119 5.16 5 C 15300 2.51 5 N 4151 2.21 5 O 4489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 24067 Number of models: 1 Model: "" Number of chains: 9 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16110 SG CYS C 18 40.676 135.840 40.881 1.00207.63 S ATOM 16136 SG CYS C 21 38.831 134.629 43.390 1.00215.48 S ATOM 16607 SG CYS C 137 37.008 138.044 42.470 1.00241.64 S ATOM 16631 SG CYS C 140 38.733 137.760 43.940 1.00243.87 S Time building chain proxies: 4.96, per 1000 atoms: 0.21 Number of scatterers: 24067 At special positions: 0 Unit cell: (104.39, 180.31, 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 119 16.00 P 5 15.00 Mg 2 11.99 O 4489 8.00 N 4151 7.00 C 15300 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.3 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 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5668 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 26 sheets defined 49.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.897A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.512A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) 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 184 Processing helix chain 'A' and resid 190 through 212 removed outlier: 4.224A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.575A 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: 4.186A pdb=" N HIS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.704A pdb=" N SER A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.554A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 341 through 353 removed outlier: 4.333A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.905A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.788A 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 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.828A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (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 503 through 510 removed outlier: 3.945A pdb=" N ARG A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 4.015A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.618A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.754A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.744A 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: 3.807A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 706 " --> pdb=" O ASN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.769A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS A 733 " --> pdb=" O CYS A 729 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 737 " --> pdb=" O CYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.713A pdb=" N MET A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.800A pdb=" N GLN A 791 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 792 " --> pdb=" O GLY A 789 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 788 through 792' Processing helix chain 'A' and resid 793 through 810 Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.847A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.763A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 3.949A pdb=" N LYS A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 869 removed outlier: 3.612A pdb=" N SER A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 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 142 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: 3.737A pdb=" N ASP B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.563A pdb=" N ASN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 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 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.655A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.212A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.863A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.643A pdb=" N ASP B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 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: 3.584A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (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 458 through 463 Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.514A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.630A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.579A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.695A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 3.943A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.767A pdb=" N LEU B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 569 " --> pdb=" O CYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.190A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.795A pdb=" N LYS B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.938A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 removed outlier: 3.514A pdb=" N GLU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.792A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 removed outlier: 4.117A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 682 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 696 through 700 removed outlier: 3.536A pdb=" N ASP B 700 " --> pdb=" O PRO B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.829A pdb=" N SER B 735 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 removed outlier: 4.089A pdb=" N ARG B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 780 through 790 removed outlier: 3.662A pdb=" N GLU B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.572A pdb=" N MET B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.921A 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 821 through 825 Processing helix chain 'B' and resid 940 through 965 removed outlier: 3.614A pdb=" N GLN B 945 " --> pdb=" O LYS B 941 " (cutoff:3.500A) removed outlier: 3.722A 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 1022 through 1027 removed outlier: 3.672A pdb=" N GLU B1026 " --> pdb=" O GLN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.836A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.562A pdb=" N ARG B1275 " --> pdb=" O TYR B1272 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1272 through 1276' Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.861A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.707A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 137 through 169 removed outlier: 3.763A pdb=" N ASP C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 219 removed outlier: 3.624A pdb=" N LEU C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 245 removed outlier: 3.725A pdb=" N GLN C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 267 removed outlier: 4.383A 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: 4.046A pdb=" N ALA C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 removed outlier: 4.208A pdb=" N HIS C 336 " --> pdb=" O TYR C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.550A pdb=" N PHE C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.241A pdb=" N MET C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA C 371 " --> pdb=" O HIS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.880A pdb=" N GLN C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.632A pdb=" N PHE C 419 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 3.649A 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 removed outlier: 3.628A pdb=" N LYS C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 444 removed outlier: 3.604A pdb=" N MET C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 5.783A pdb=" N TYR C 448 " --> pdb=" O SER C 445 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 450 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.822A 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 164 through 168 removed outlier: 4.137A pdb=" N GLU D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.562A 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 removed outlier: 3.525A pdb=" N ARG D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 324 removed outlier: 3.534A pdb=" N CYS D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS D 243 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 378 removed outlier: 3.921A pdb=" N GLY D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.656A 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 'E' and resid 32 through 42 removed outlier: 3.619A pdb=" N LEU E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.697A pdb=" N ARG E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 122 removed outlier: 4.037A pdb=" N PHE E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 4.839A pdb=" N ASN E 139 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 155 removed outlier: 3.596A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 181 removed outlier: 3.799A pdb=" N ILE E 173 " --> pdb=" O ASN E 169 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 7.110A pdb=" N CYS A 223 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LYS A 6 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY A 232 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 9 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 829 " --> pdb=" O TYR A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 96 removed outlier: 6.974A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.885A 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: 3.652A pdb=" N ILE A 110 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 123 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP A 112 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR A 114 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 119 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.631A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.631A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 680 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 673 " --> pdb=" O PHE A 681 " (cutoff:3.500A) 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: 6.412A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 51 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 103 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.201A 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: 6.063A 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 998 through 1001 removed outlier: 4.015A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS B1011 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B1000 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B1018 " --> pdb=" O THR B1010 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B1017 " --> pdb=" O TYR B1038 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B1038 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B1019 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 3.866A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1060 " --> pdb=" O THR B1047 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B1049 " --> pdb=" O ALA B1058 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1097 through 1103 removed outlier: 4.022A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B1124 " --> pdb=" O LEU B1112 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B1114 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B1121 " --> pdb=" O THR B1134 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B1134 " --> pdb=" O LEU B1121 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY B1123 " --> pdb=" O ALA B1132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 6.986A pdb=" N GLY B1159 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B1147 " --> pdb=" O CYS B1157 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS B1157 " --> pdb=" O PHE B1147 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B1149 " --> pdb=" O TRP B1155 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TRP B1155 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B1167 " --> pdb=" O SER B1177 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 6.464A pdb=" N ALA B1203 " --> pdb=" O ARG B1188 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B1190 " --> pdb=" O ILE B1201 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B1201 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N MET B1192 " --> pdb=" O TRP B1199 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TRP B1199 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B1303 " --> pdb=" O TRP B1225 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B1302 " --> pdb=" O TYR B1291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1242 through 1247 removed outlier: 4.563A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1256 " --> pdb=" O TRP B1268 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B1260 " --> pdb=" O LYS B1264 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS B1264 " --> pdb=" O GLY B1260 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B1280 " --> pdb=" O ILE B1265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1332 through 1339 removed outlier: 4.072A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B1348 " --> pdb=" O ASP B1334 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.537A pdb=" N PHE C 16 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AC2, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.948A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 394 through 397 Processing sheet with id=AC4, first strand: chain 'D' and resid 93 through 96 removed outlier: 3.887A pdb=" N TRP D 94 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE D 48 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR D 161 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.721A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 129 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY D 119 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU D 127 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS D 121 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TYR D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.790A pdb=" N ASP D 338 " --> pdb=" O ASN D 334 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 394 through 396 Processing sheet with id=AC8, first strand: chain 'E' and resid 55 through 58 removed outlier: 6.027A pdb=" N SER E 19 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU E 72 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE E 21 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP E 74 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 23 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 76 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU E 25 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL E 99 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA E 96 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER E 131 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL E 98 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN E 133 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR E 100 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 160 " --> pdb=" O LEU E 130 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2946 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: 5.14 Time building geometry restraints manager: 2.43 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: 7849 1.34 - 1.46: 5059 1.46 - 1.58: 11452 1.58 - 1.70: 9 1.70 - 1.82: 186 Bond restraints: 24555 Sorted by residual: bond pdb=" CD LYS E 134 " pdb=" CE LYS E 134 " ideal model delta sigma weight residual 1.520 1.592 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.56e+00 bond pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.22e+00 bond pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.08e+00 bond pdb=" C GLU A 263 " pdb=" N ASN A 264 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.40e-02 5.10e+03 3.91e+00 ... (remaining 24550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 32988 3.44 - 6.89: 175 6.89 - 10.33: 22 10.33 - 13.78: 4 13.78 - 17.22: 3 Bond angle restraints: 33192 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 121.70 135.63 -13.93 1.80e+00 3.09e-01 5.99e+01 angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 135.06 -13.36 1.80e+00 3.09e-01 5.51e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 134.67 -12.97 1.80e+00 3.09e-01 5.19e+01 angle pdb=" C SER B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta sigma weight residual 121.70 132.41 -10.71 1.80e+00 3.09e-01 3.54e+01 angle pdb=" CD LYS E 134 " pdb=" CE LYS E 134 " pdb=" NZ LYS E 134 " ideal model delta sigma weight residual 111.90 95.60 16.30 3.20e+00 9.77e-02 2.60e+01 ... (remaining 33187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 14474 30.67 - 61.33: 396 61.33 - 92.00: 59 92.00 - 122.67: 2 122.67 - 153.34: 3 Dihedral angle restraints: 14934 sinusoidal: 6198 harmonic: 8736 Sorted by residual: 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 36.19 -36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" O3B GTP E 301 " pdb=" O3A GTP E 301 " pdb=" PB GTP E 301 " pdb=" PA GTP E 301 " ideal model delta sinusoidal sigma weight residual 291.08 137.74 153.34 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" CA PRO B1182 " pdb=" C PRO B1182 " pdb=" N SER B1183 " pdb=" CA SER B1183 " ideal model delta harmonic sigma weight residual 180.00 -148.88 -31.12 0 5.00e+00 4.00e-02 3.87e+01 ... (remaining 14931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2721 0.044 - 0.087: 702 0.087 - 0.131: 214 0.131 - 0.174: 46 0.174 - 0.218: 5 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA VAL B1098 " pdb=" N VAL B1098 " pdb=" C VAL B1098 " pdb=" CB VAL B1098 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1' GTP E 301 " pdb=" C2' GTP E 301 " pdb=" N9 GTP E 301 " pdb=" O4' GTP E 301 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CB THR D 450 " pdb=" CA THR D 450 " pdb=" OG1 THR D 450 " pdb=" CG2 THR D 450 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 3685 not shown) Planarity restraints: 4251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP E 301 " 0.027 2.00e-02 2.50e+03 2.30e-02 1.59e+01 pdb=" C2 GTP E 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GTP E 301 " 0.015 2.00e-02 2.50e+03 pdb=" C5 GTP E 301 " 0.028 2.00e-02 2.50e+03 pdb=" C6 GTP E 301 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GTP E 301 " 0.009 2.00e-02 2.50e+03 pdb=" N1 GTP E 301 " -0.008 2.00e-02 2.50e+03 pdb=" N2 GTP E 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GTP E 301 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GTP E 301 " 0.001 2.00e-02 2.50e+03 pdb=" N9 GTP E 301 " -0.067 2.00e-02 2.50e+03 pdb=" O6 GTP E 301 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 650 " 0.063 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO B 651 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 651 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 651 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO B 667 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.038 5.00e-02 4.00e+02 ... (remaining 4248 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 299 2.66 - 3.22: 20424 3.22 - 3.78: 35457 3.78 - 4.34: 46780 4.34 - 4.90: 77582 Nonbonded interactions: 180542 Sorted by model distance: nonbonded pdb="MG MG E 300 " pdb=" O2B GTP E 301 " model vdw 2.097 2.170 nonbonded pdb=" O1B GDP B1401 " pdb="MG MG B1402 " model vdw 2.106 2.170 nonbonded pdb="MG MG E 300 " pdb=" O3B GTP E 301 " model vdw 2.112 2.170 nonbonded pdb=" O5' GDP B1401 " pdb="MG MG B1402 " model vdw 2.171 2.170 nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1402 " model vdw 2.198 2.170 ... (remaining 180537 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 0.096 24562 Z= 0.193 Angle : 0.885 50.437 33198 Z= 0.457 Chirality : 0.045 0.218 3688 Planarity : 0.006 0.094 4251 Dihedral : 14.621 153.337 9266 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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: -1.35 (0.14), residues: 2949 helix: -0.90 (0.13), residues: 1271 sheet: 0.01 (0.27), residues: 364 loop : -1.01 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.035 0.002 TYR A 803 PHE 0.017 0.002 PHE B1267 TRP 0.023 0.002 TRP B1213 HIS 0.013 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (24555) covalent geometry : angle 0.78129 / 0.45 (33192) hydrogen bonds : bond 0.20349 / 13.41 ( 1031) hydrogen bonds : angle 6.15760 / 4.25 ( 2946) metal coordination : bond 0.05349 / 2.46 ( 4) metal coordination : angle 30.95869 / 18.68 ( 6) Misc. bond : bond 0.05607 / 2.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.930 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: A 16 ASP cc_start: 0.9168 (t0) cc_final: 0.8837 (t0) REVERT: A 92 LYS cc_start: 0.8764 (tttt) cc_final: 0.8474 (tttp) REVERT: A 135 MET cc_start: 0.8456 (mtp) cc_final: 0.8195 (ttt) REVERT: A 140 MET cc_start: 0.8391 (ttm) cc_final: 0.7938 (ttp) REVERT: A 180 LYS cc_start: 0.9446 (tttt) cc_final: 0.9142 (tppt) REVERT: A 296 LEU cc_start: 0.9191 (mt) cc_final: 0.8795 (pp) REVERT: A 308 LEU cc_start: 0.9083 (mt) cc_final: 0.8198 (mp) REVERT: A 312 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8600 (tm-30) REVERT: A 338 ASN cc_start: 0.8884 (t0) cc_final: 0.8261 (t0) REVERT: A 361 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8126 (tm-30) REVERT: A 393 LEU cc_start: 0.9335 (mt) cc_final: 0.9105 (pt) REVERT: A 494 TYR cc_start: 0.8697 (t80) cc_final: 0.8497 (t80) REVERT: A 556 MET cc_start: 0.8573 (tpp) cc_final: 0.7979 (tmm) REVERT: A 642 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8441 (mpp-170) REVERT: A 651 ILE cc_start: 0.9351 (mt) cc_final: 0.8953 (tp) REVERT: A 668 THR cc_start: 0.8865 (m) cc_final: 0.8650 (p) REVERT: A 795 TYR cc_start: 0.9146 (t80) cc_final: 0.8607 (t80) REVERT: A 800 LYS cc_start: 0.9179 (mtmt) cc_final: 0.8960 (ptpp) REVERT: A 803 TYR cc_start: 0.8740 (p90) cc_final: 0.8319 (p90) REVERT: A 809 LEU cc_start: 0.9480 (mt) cc_final: 0.9252 (pp) REVERT: A 816 ILE cc_start: 0.9444 (mt) cc_final: 0.9195 (pt) REVERT: A 837 LYS cc_start: 0.8964 (mttp) cc_final: 0.8446 (mttm) REVERT: A 842 VAL cc_start: 0.9177 (t) cc_final: 0.8775 (m) REVERT: A 846 PHE cc_start: 0.8803 (m-80) cc_final: 0.8234 (m-80) REVERT: A 850 LEU cc_start: 0.8468 (mt) cc_final: 0.8227 (mt) REVERT: A 854 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9051 (mm-30) REVERT: A 857 HIS cc_start: 0.9224 (m170) cc_final: 0.9001 (m-70) REVERT: A 859 MET cc_start: 0.9361 (ppp) cc_final: 0.9052 (ppp) REVERT: B 30 LYS cc_start: 0.9051 (tttt) cc_final: 0.8844 (ttpt) REVERT: B 70 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9058 (pt0) REVERT: B 74 LEU cc_start: 0.8889 (mt) cc_final: 0.8607 (tp) REVERT: B 77 ARG cc_start: 0.8738 (mtt-85) cc_final: 0.8463 (ttm-80) REVERT: B 78 LEU cc_start: 0.9149 (mt) cc_final: 0.8733 (mm) REVERT: B 108 ASP cc_start: 0.7986 (t0) cc_final: 0.7697 (t0) REVERT: B 196 TYR cc_start: 0.8027 (m-80) cc_final: 0.7665 (m-80) REVERT: B 240 ASP cc_start: 0.9157 (t70) cc_final: 0.8916 (t0) REVERT: B 272 PHE cc_start: 0.8247 (t80) cc_final: 0.7587 (t80) REVERT: B 273 PHE cc_start: 0.8505 (t80) cc_final: 0.8077 (t80) REVERT: B 278 LEU cc_start: 0.9430 (mt) cc_final: 0.8910 (tt) REVERT: B 289 LEU cc_start: 0.8851 (tp) cc_final: 0.8203 (tp) REVERT: B 290 VAL cc_start: 0.9362 (t) cc_final: 0.8960 (p) REVERT: B 294 ILE cc_start: 0.9266 (mm) cc_final: 0.9059 (tt) REVERT: B 309 LYS cc_start: 0.9293 (mttt) cc_final: 0.9039 (mmtp) REVERT: B 400 GLU cc_start: 0.8738 (tt0) cc_final: 0.8224 (tm-30) REVERT: B 436 GLU cc_start: 0.9008 (tp30) cc_final: 0.8684 (tp30) REVERT: B 587 ASP cc_start: 0.9201 (t0) cc_final: 0.8671 (t0) REVERT: B 730 ASP cc_start: 0.9098 (m-30) cc_final: 0.8879 (m-30) REVERT: B 774 LEU cc_start: 0.9602 (mt) cc_final: 0.9266 (tp) REVERT: B 791 LYS cc_start: 0.8665 (tttt) cc_final: 0.8372 (ptmm) REVERT: B 795 MET cc_start: 0.9106 (mtp) cc_final: 0.8787 (mpp) REVERT: B 959 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7817 (ttm110) REVERT: B 1007 LEU cc_start: 0.9353 (mt) cc_final: 0.9118 (mm) REVERT: B 1019 ILE cc_start: 0.9043 (mt) cc_final: 0.8829 (tp) REVERT: B 1209 GLU cc_start: 0.8731 (tt0) cc_final: 0.8476 (tm-30) REVERT: B 1216 GLU cc_start: 0.8378 (tp30) cc_final: 0.8109 (tp30) REVERT: B 1262 ASP cc_start: 0.8709 (t0) cc_final: 0.8400 (t0) REVERT: B 1263 MET cc_start: 0.9043 (mpp) cc_final: 0.7915 (mtt) REVERT: B 1264 LYS cc_start: 0.9391 (mttt) cc_final: 0.8900 (mmmt) REVERT: C 144 LEU cc_start: 0.9499 (tp) cc_final: 0.9287 (tp) REVERT: C 156 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9129 (tm-30) REVERT: C 159 CYS cc_start: 0.9511 (t) cc_final: 0.9283 (p) REVERT: C 165 CYS cc_start: 0.9143 (m) cc_final: 0.8513 (p) REVERT: C 251 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9092 (mp0) REVERT: C 260 GLN cc_start: 0.9138 (tt0) cc_final: 0.8859 (pt0) REVERT: C 263 LYS cc_start: 0.9473 (mttt) cc_final: 0.9258 (pttt) REVERT: C 264 LEU cc_start: 0.9174 (mt) cc_final: 0.8906 (mt) REVERT: C 271 ASN cc_start: 0.9162 (m110) cc_final: 0.8714 (p0) REVERT: C 274 PHE cc_start: 0.8262 (m-80) cc_final: 0.8019 (m-80) REVERT: C 312 LEU cc_start: 0.9537 (pp) cc_final: 0.9284 (mm) REVERT: C 396 MET cc_start: 0.4122 (ptt) cc_final: 0.2958 (tpt) REVERT: D 64 THR cc_start: 0.8113 (p) cc_final: 0.7719 (t) REVERT: D 80 PHE cc_start: 0.7738 (t80) cc_final: 0.7484 (t80) REVERT: D 116 LYS cc_start: 0.8945 (mttt) cc_final: 0.8627 (mtpt) REVERT: D 204 CYS cc_start: 0.9351 (m) cc_final: 0.9009 (m) REVERT: D 221 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8273 (pt0) REVERT: D 315 THR cc_start: 0.9175 (m) cc_final: 0.7956 (p) REVERT: D 329 TYR cc_start: 0.8808 (m-80) cc_final: 0.8538 (m-80) REVERT: D 428 LEU cc_start: 0.9439 (mt) cc_final: 0.8821 (tp) REVERT: D 431 LYS cc_start: 0.9477 (tttt) cc_final: 0.8899 (mttt) REVERT: D 435 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9134 (pt0) REVERT: D 440 HIS cc_start: 0.8759 (m-70) cc_final: 0.8531 (t-170) REVERT: E 21 PHE cc_start: 0.8535 (m-80) cc_final: 0.8238 (m-10) REVERT: E 28 GLU cc_start: 0.8483 (tp30) cc_final: 0.7985 (pm20) REVERT: E 53 ILE cc_start: 0.8938 (mm) cc_final: 0.8419 (tp) REVERT: E 60 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8118 (tp-100) REVERT: E 72 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8363 (pt0) REVERT: E 75 ASP cc_start: 0.8630 (t0) cc_final: 0.8323 (p0) REVERT: E 100 TYR cc_start: 0.8874 (p90) cc_final: 0.8481 (p90) REVERT: E 104 ASN cc_start: 0.8464 (t0) cc_final: 0.8120 (t0) REVERT: E 107 SER cc_start: 0.8861 (t) cc_final: 0.7927 (p) REVERT: E 112 LYS cc_start: 0.9399 (mttt) cc_final: 0.9154 (mttm) REVERT: E 113 ASN cc_start: 0.9148 (m-40) cc_final: 0.8917 (m110) REVERT: E 133 ASN cc_start: 0.8620 (t0) cc_final: 0.8085 (t0) REVERT: E 145 PHE cc_start: 0.8305 (t80) cc_final: 0.8044 (t80) REVERT: E 159 PHE cc_start: 0.8405 (t80) cc_final: 0.6611 (t80) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.2114 time to fit residues: 191.3161 Evaluate side-chains 419 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 386 GLN A 554 HIS ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A 794 GLN B 314 ASN B 457 ASN B 525 ASN B 798 ASN ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 158 ASN E 121 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.093349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069623 restraints weight = 110324.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071600 restraints weight = 59655.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072958 restraints weight = 39360.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073871 restraints weight = 29454.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074501 restraints weight = 24132.575| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24562 Z= 0.142 Angle : 0.701 15.754 33198 Z= 0.344 Chirality : 0.043 0.212 3688 Planarity : 0.005 0.097 4251 Dihedral : 7.258 156.291 3262 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 1.47 % Allowed : 12.49 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.17 (0.15), residues: 2949 helix: 0.56 (0.14), residues: 1300 sheet: 0.30 (0.28), residues: 343 loop : -0.85 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 117 TYR 0.025 0.002 TYR A 35 PHE 0.026 0.002 PHE B 38 TRP 0.017 0.001 TRP B 159 HIS 0.023 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (24555) covalent geometry : angle 0.68758 / 0.34 (33192) hydrogen bonds : bond 0.05042 / 3.21 ( 1031) hydrogen bonds : angle 4.60498 / 3.18 ( 2946) metal coordination : bond 0.01053 / 0.53 ( 4) metal coordination : angle 10.27293 / 6.31 ( 6) Misc. bond : bond 0.00537 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 434 time to evaluate : 0.643 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: A 16 ASP cc_start: 0.8787 (t0) cc_final: 0.8344 (t0) REVERT: A 92 LYS cc_start: 0.8682 (tttt) cc_final: 0.8450 (tttp) REVERT: A 135 MET cc_start: 0.8140 (mtp) cc_final: 0.7880 (ttt) REVERT: A 296 LEU cc_start: 0.9293 (mt) cc_final: 0.8846 (pp) REVERT: A 312 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 338 ASN cc_start: 0.8986 (t0) cc_final: 0.8428 (t0) REVERT: A 359 ASP cc_start: 0.8726 (t70) cc_final: 0.8512 (t70) REVERT: A 377 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.9163 (mtp180) REVERT: A 492 TYR cc_start: 0.9058 (m-10) cc_final: 0.8772 (m-10) REVERT: A 494 TYR cc_start: 0.8887 (t80) cc_final: 0.8341 (t80) REVERT: A 556 MET cc_start: 0.8488 (tpp) cc_final: 0.7859 (tmm) REVERT: A 651 ILE cc_start: 0.9326 (mt) cc_final: 0.9044 (tp) REVERT: A 663 LEU cc_start: 0.8489 (mm) cc_final: 0.7893 (mm) REVERT: A 670 TYR cc_start: 0.7771 (m-80) cc_final: 0.7437 (m-80) REVERT: A 722 MET cc_start: 0.7651 (mtp) cc_final: 0.7174 (ptp) REVERT: A 732 TYR cc_start: 0.8254 (m-80) cc_final: 0.7956 (m-80) REVERT: A 795 TYR cc_start: 0.8711 (t80) cc_final: 0.8283 (t80) REVERT: A 803 TYR cc_start: 0.8701 (p90) cc_final: 0.8469 (p90) REVERT: A 808 HIS cc_start: 0.8922 (m-70) cc_final: 0.8382 (m90) REVERT: A 809 LEU cc_start: 0.9393 (mt) cc_final: 0.9168 (pp) REVERT: A 837 LYS cc_start: 0.8877 (mttp) cc_final: 0.8571 (mttm) REVERT: A 842 VAL cc_start: 0.9468 (t) cc_final: 0.8920 (p) REVERT: A 846 PHE cc_start: 0.8852 (m-80) cc_final: 0.8411 (m-80) REVERT: B 74 LEU cc_start: 0.8773 (mt) cc_final: 0.8500 (mm) REVERT: B 78 LEU cc_start: 0.9039 (mt) cc_final: 0.8665 (mm) REVERT: B 108 ASP cc_start: 0.8088 (t0) cc_final: 0.7619 (t0) REVERT: B 162 VAL cc_start: 0.9102 (t) cc_final: 0.8837 (m) REVERT: B 174 TYR cc_start: 0.8853 (m-80) cc_final: 0.8633 (m-80) REVERT: B 196 TYR cc_start: 0.8403 (m-80) cc_final: 0.7639 (m-80) REVERT: B 204 ASP cc_start: 0.7737 (t0) cc_final: 0.7365 (t0) REVERT: B 273 PHE cc_start: 0.8168 (t80) cc_final: 0.7867 (t80) REVERT: B 278 LEU cc_start: 0.9265 (mt) cc_final: 0.8833 (tt) REVERT: B 289 LEU cc_start: 0.8512 (tp) cc_final: 0.8145 (tp) REVERT: B 290 VAL cc_start: 0.9298 (t) cc_final: 0.8872 (p) REVERT: B 309 LYS cc_start: 0.9246 (mttt) cc_final: 0.8981 (mmtp) REVERT: B 357 LEU cc_start: 0.9362 (mm) cc_final: 0.9137 (tp) REVERT: B 400 GLU cc_start: 0.8363 (tt0) cc_final: 0.8160 (tm-30) REVERT: B 580 HIS cc_start: 0.8657 (t70) cc_final: 0.8222 (t70) REVERT: B 587 ASP cc_start: 0.9017 (t0) cc_final: 0.8589 (t0) REVERT: B 747 MET cc_start: 0.8301 (mtt) cc_final: 0.8097 (ptp) REVERT: B 783 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8597 (mt-10) REVERT: B 801 LYS cc_start: 0.9126 (tmmt) cc_final: 0.8897 (tptm) REVERT: B 941 LYS cc_start: 0.8420 (pttt) cc_final: 0.8218 (ptpt) REVERT: B 944 LEU cc_start: 0.8972 (mt) cc_final: 0.8642 (tp) REVERT: B 1101 MET cc_start: 0.7888 (ttp) cc_final: 0.7561 (ttp) REVERT: B 1192 MET cc_start: 0.8813 (mmt) cc_final: 0.7904 (mmm) REVERT: B 1216 GLU cc_start: 0.8034 (tp30) cc_final: 0.7704 (tp30) REVERT: B 1264 LYS cc_start: 0.9423 (mttt) cc_final: 0.9196 (mtpt) REVERT: C 144 LEU cc_start: 0.9455 (tp) cc_final: 0.9246 (tt) REVERT: C 271 ASN cc_start: 0.9009 (m110) cc_final: 0.8557 (p0) REVERT: C 312 LEU cc_start: 0.9408 (pp) cc_final: 0.9152 (mm) REVERT: C 315 HIS cc_start: 0.8659 (m-70) cc_final: 0.8459 (m90) REVERT: C 369 MET cc_start: 0.2375 (mtt) cc_final: 0.1668 (ppp) REVERT: C 379 PHE cc_start: 0.6552 (m-10) cc_final: 0.6251 (m-80) REVERT: C 396 MET cc_start: 0.3934 (ptt) cc_final: 0.3073 (tpt) REVERT: D 64 THR cc_start: 0.7565 (p) cc_final: 0.7185 (t) REVERT: D 204 CYS cc_start: 0.9180 (m) cc_final: 0.8802 (m) REVERT: D 329 TYR cc_start: 0.8763 (m-80) cc_final: 0.8535 (m-80) REVERT: D 428 LEU cc_start: 0.9428 (mt) cc_final: 0.9204 (mt) REVERT: D 431 LYS cc_start: 0.9414 (tttt) cc_final: 0.8881 (mttt) REVERT: E 42 LYS cc_start: 0.9436 (mmmm) cc_final: 0.9082 (tptp) REVERT: E 70 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8262 (mmmt) REVERT: E 100 TYR cc_start: 0.8700 (p90) cc_final: 0.8414 (p90) REVERT: E 112 LYS cc_start: 0.9415 (mttt) cc_final: 0.9181 (mtmm) REVERT: E 113 ASN cc_start: 0.9167 (m-40) cc_final: 0.8777 (m110) REVERT: E 119 GLN cc_start: 0.8944 (mt0) cc_final: 0.8740 (mt0) REVERT: E 159 PHE cc_start: 0.7698 (t80) cc_final: 0.7462 (t80) outliers start: 39 outliers final: 19 residues processed: 455 average time/residue: 0.1842 time to fit residues: 124.1521 Evaluate side-chains 381 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 361 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 424 TYR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 165 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 139 optimal weight: 0.0670 chunk 210 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN B1153 GLN ** B1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 ASN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 HIS D 453 ASN E 121 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.084804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062356 restraints weight = 114992.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064222 restraints weight = 62702.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065440 restraints weight = 41446.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.066263 restraints weight = 31235.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066832 restraints weight = 25733.786| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24562 Z= 0.155 Angle : 0.711 13.268 33198 Z= 0.349 Chirality : 0.043 0.199 3688 Planarity : 0.005 0.096 4251 Dihedral : 7.120 163.332 3262 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.63 % Favored : 96.24 % Rotamer: Outliers : 2.23 % Allowed : 13.88 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.21 (0.15), residues: 2949 helix: 1.04 (0.15), residues: 1309 sheet: 0.33 (0.27), residues: 349 loop : -0.81 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 36 TYR 0.031 0.001 TYR E 90 PHE 0.024 0.002 PHE B 38 TRP 0.021 0.001 TRP A 355 HIS 0.008 0.001 HIS C 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (24555) covalent geometry : angle 0.70381 / 0.35 (33192) hydrogen bonds : bond 0.04481 / 2.88 ( 1031) hydrogen bonds : angle 4.41451 / 3.06 ( 2946) metal coordination : bond 0.00771 / 0.39 ( 4) metal coordination : angle 7.58191 / 4.61 ( 6) Misc. bond : bond 0.00510 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 402 time to evaluate : 0.828 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 16 ASP cc_start: 0.8763 (t0) cc_final: 0.8352 (t0) REVERT: A 92 LYS cc_start: 0.8687 (tttt) cc_final: 0.8451 (tttp) REVERT: A 135 MET cc_start: 0.8195 (mtp) cc_final: 0.7891 (ttt) REVERT: A 171 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8326 (mp10) REVERT: A 296 LEU cc_start: 0.9289 (mt) cc_final: 0.8830 (pp) REVERT: A 312 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 338 ASN cc_start: 0.9047 (t0) cc_final: 0.8777 (t0) REVERT: A 492 TYR cc_start: 0.9068 (m-10) cc_final: 0.8766 (m-10) REVERT: A 494 TYR cc_start: 0.8925 (t80) cc_final: 0.8646 (t80) REVERT: A 522 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8500 (ttp80) REVERT: A 556 MET cc_start: 0.8439 (tpp) cc_final: 0.7819 (tmm) REVERT: A 670 TYR cc_start: 0.7738 (m-80) cc_final: 0.7280 (m-10) REVERT: A 682 MET cc_start: 0.8020 (tpt) cc_final: 0.7724 (tpp) REVERT: A 795 TYR cc_start: 0.8718 (t80) cc_final: 0.8265 (t80) REVERT: A 803 TYR cc_start: 0.8763 (p90) cc_final: 0.8318 (p90) REVERT: A 823 MET cc_start: 0.7962 (mmm) cc_final: 0.7753 (mmm) REVERT: A 846 PHE cc_start: 0.8916 (m-80) cc_final: 0.8404 (m-80) REVERT: B 3 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8212 (p0) REVERT: B 74 LEU cc_start: 0.8805 (mt) cc_final: 0.8545 (tp) REVERT: B 78 LEU cc_start: 0.9020 (mt) cc_final: 0.8687 (mm) REVERT: B 108 ASP cc_start: 0.8108 (t0) cc_final: 0.7624 (t0) REVERT: B 162 VAL cc_start: 0.9115 (t) cc_final: 0.8882 (m) REVERT: B 165 THR cc_start: 0.7666 (p) cc_final: 0.7291 (t) REVERT: B 196 TYR cc_start: 0.8385 (m-80) cc_final: 0.7604 (m-80) REVERT: B 204 ASP cc_start: 0.7703 (t0) cc_final: 0.7366 (t0) REVERT: B 273 PHE cc_start: 0.8296 (t80) cc_final: 0.7847 (t80) REVERT: B 278 LEU cc_start: 0.9267 (mt) cc_final: 0.9031 (mm) REVERT: B 309 LYS cc_start: 0.9261 (mttt) cc_final: 0.8995 (mmtp) REVERT: B 357 LEU cc_start: 0.9356 (mm) cc_final: 0.9154 (tp) REVERT: B 580 HIS cc_start: 0.8688 (t70) cc_final: 0.8190 (t70) REVERT: B 587 ASP cc_start: 0.8997 (t0) cc_final: 0.8583 (t0) REVERT: B 730 ASP cc_start: 0.8834 (m-30) cc_final: 0.8543 (p0) REVERT: B 774 LEU cc_start: 0.9461 (mm) cc_final: 0.9104 (tp) REVERT: B 783 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8593 (mt-10) REVERT: B 801 LYS cc_start: 0.9125 (tmmt) cc_final: 0.8881 (tptm) REVERT: B 941 LYS cc_start: 0.8530 (pttt) cc_final: 0.8299 (ptpt) REVERT: B 944 LEU cc_start: 0.9020 (mt) cc_final: 0.8721 (tp) REVERT: B 1101 MET cc_start: 0.7946 (ttp) cc_final: 0.7716 (ttp) REVERT: B 1216 GLU cc_start: 0.8114 (tp30) cc_final: 0.7782 (tp30) REVERT: B 1262 ASP cc_start: 0.8314 (t0) cc_final: 0.7986 (t0) REVERT: C 144 LEU cc_start: 0.9478 (tp) cc_final: 0.9275 (tt) REVERT: C 271 ASN cc_start: 0.8955 (m110) cc_final: 0.8478 (p0) REVERT: C 312 LEU cc_start: 0.9433 (pp) cc_final: 0.9187 (mm) REVERT: C 314 LEU cc_start: 0.9445 (tp) cc_final: 0.9213 (mm) REVERT: C 315 HIS cc_start: 0.8785 (m-70) cc_final: 0.8568 (m90) REVERT: C 369 MET cc_start: 0.2405 (mtt) cc_final: 0.1668 (ppp) REVERT: C 396 MET cc_start: 0.3985 (ptt) cc_final: 0.3100 (tpt) REVERT: D 64 THR cc_start: 0.7569 (p) cc_final: 0.7183 (t) REVERT: D 191 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7671 (t80) REVERT: D 204 CYS cc_start: 0.9267 (m) cc_final: 0.8886 (m) REVERT: D 428 LEU cc_start: 0.9486 (mt) cc_final: 0.9167 (mt) REVERT: D 431 LYS cc_start: 0.9305 (tttt) cc_final: 0.8977 (mttt) REVERT: E 48 PHE cc_start: 0.8847 (m-10) cc_final: 0.8634 (m-10) REVERT: E 100 TYR cc_start: 0.8673 (p90) cc_final: 0.8417 (p90) REVERT: E 110 ARG cc_start: 0.9129 (mmm160) cc_final: 0.8883 (mmm160) REVERT: E 113 ASN cc_start: 0.9136 (m-40) cc_final: 0.8902 (m110) REVERT: E 119 GLN cc_start: 0.8970 (mt0) cc_final: 0.8732 (mt0) REVERT: E 159 PHE cc_start: 0.7965 (t80) cc_final: 0.7717 (t80) outliers start: 59 outliers final: 37 residues processed: 436 average time/residue: 0.1874 time to fit residues: 122.3981 Evaluate side-chains 402 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 363 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 220 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 413 ASN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN B 292 GLN B 538 GLN B 769 GLN B 777 GLN B 798 ASN B1179 HIS ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 HIS D 453 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.084957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062509 restraints weight = 114557.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064363 restraints weight = 62019.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065534 restraints weight = 40892.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066364 restraints weight = 30932.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066688 restraints weight = 25538.096| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24562 Z= 0.126 Angle : 0.691 12.592 33198 Z= 0.337 Chirality : 0.043 0.227 3688 Planarity : 0.004 0.099 4251 Dihedral : 7.100 165.537 3262 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 2.49 % Allowed : 15.31 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.37 (0.16), residues: 2949 helix: 1.27 (0.15), residues: 1296 sheet: 0.25 (0.27), residues: 360 loop : -0.78 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 378 TYR 0.032 0.001 TYR E 90 PHE 0.038 0.002 PHE B 272 TRP 0.031 0.001 TRP A 355 HIS 0.007 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (24555) covalent geometry : angle 0.68585 / 0.34 (33192) hydrogen bonds : bond 0.04083 / 2.63 ( 1031) hydrogen bonds : angle 4.23018 / 2.92 ( 2946) metal coordination : bond 0.00604 / 0.31 ( 4) metal coordination : angle 6.25142 / 3.81 ( 6) Misc. bond : bond 0.00592 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 0.963 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: A 16 ASP cc_start: 0.8754 (t0) cc_final: 0.8366 (t0) REVERT: A 79 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8565 (ttpp) REVERT: A 92 LYS cc_start: 0.8644 (tttt) cc_final: 0.8410 (tttp) REVERT: A 135 MET cc_start: 0.8147 (mtp) cc_final: 0.7853 (ttt) REVERT: A 296 LEU cc_start: 0.9262 (mt) cc_final: 0.8795 (pp) REVERT: A 311 GLU cc_start: 0.8811 (pm20) cc_final: 0.8285 (pm20) REVERT: A 312 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8665 (mm-30) REVERT: A 338 ASN cc_start: 0.9085 (t0) cc_final: 0.8526 (t0) REVERT: A 344 GLU cc_start: 0.7805 (tt0) cc_final: 0.7364 (tt0) REVERT: A 492 TYR cc_start: 0.9074 (m-10) cc_final: 0.8761 (m-10) REVERT: A 494 TYR cc_start: 0.8801 (t80) cc_final: 0.8591 (t80) REVERT: A 516 MET cc_start: 0.8400 (ppp) cc_final: 0.7826 (ppp) REVERT: A 521 MET cc_start: 0.8991 (tmm) cc_final: 0.8667 (ppp) REVERT: A 548 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8849 (m-10) REVERT: A 556 MET cc_start: 0.8467 (tpp) cc_final: 0.7868 (tmm) REVERT: A 646 LEU cc_start: 0.9481 (mm) cc_final: 0.9271 (pp) REVERT: A 648 LEU cc_start: 0.9296 (mt) cc_final: 0.8889 (pp) REVERT: A 651 ILE cc_start: 0.9430 (mm) cc_final: 0.9022 (tp) REVERT: A 670 TYR cc_start: 0.7739 (m-80) cc_final: 0.7430 (m-10) REVERT: A 682 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7587 (tpp) REVERT: A 722 MET cc_start: 0.7710 (mtp) cc_final: 0.7398 (ptp) REVERT: A 795 TYR cc_start: 0.8745 (t80) cc_final: 0.8350 (t80) REVERT: A 823 MET cc_start: 0.8041 (mmm) cc_final: 0.7759 (mmm) REVERT: A 833 LEU cc_start: 0.8567 (mt) cc_final: 0.8121 (pt) REVERT: A 846 PHE cc_start: 0.8835 (m-80) cc_final: 0.8549 (m-80) REVERT: B 36 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.8070 (mtm110) REVERT: B 74 LEU cc_start: 0.8818 (mt) cc_final: 0.8554 (tp) REVERT: B 78 LEU cc_start: 0.9048 (mt) cc_final: 0.8670 (mt) REVERT: B 108 ASP cc_start: 0.8125 (t0) cc_final: 0.7567 (t0) REVERT: B 196 TYR cc_start: 0.8376 (m-80) cc_final: 0.7630 (m-80) REVERT: B 273 PHE cc_start: 0.8432 (t80) cc_final: 0.7943 (t80) REVERT: B 292 GLN cc_start: 0.8592 (pt0) cc_final: 0.8372 (pm20) REVERT: B 309 LYS cc_start: 0.9239 (mttt) cc_final: 0.9030 (mttm) REVERT: B 587 ASP cc_start: 0.8998 (t0) cc_final: 0.8551 (t0) REVERT: B 590 ASP cc_start: 0.8157 (t0) cc_final: 0.7928 (t0) REVERT: B 744 HIS cc_start: 0.8988 (t70) cc_final: 0.8595 (t-90) REVERT: B 747 MET cc_start: 0.8400 (mtt) cc_final: 0.8114 (ptp) REVERT: B 783 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 797 SER cc_start: 0.9554 (t) cc_final: 0.9142 (p) REVERT: B 941 LYS cc_start: 0.8574 (pttt) cc_final: 0.8333 (ptpp) REVERT: B 944 LEU cc_start: 0.9027 (mt) cc_final: 0.8763 (tp) REVERT: B 1192 MET cc_start: 0.8767 (mmm) cc_final: 0.7634 (mmm) REVERT: B 1216 GLU cc_start: 0.8078 (tp30) cc_final: 0.7782 (tp30) REVERT: B 1263 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.7493 (mmm) REVERT: B 1264 LYS cc_start: 0.9402 (mttt) cc_final: 0.8892 (mmmt) REVERT: C 158 GLU cc_start: 0.8919 (tp30) cc_final: 0.7598 (tp30) REVERT: C 162 TYR cc_start: 0.8771 (m-10) cc_final: 0.8145 (m-80) REVERT: C 271 ASN cc_start: 0.8988 (m110) cc_final: 0.8495 (p0) REVERT: C 312 LEU cc_start: 0.9383 (pp) cc_final: 0.9176 (mm) REVERT: C 369 MET cc_start: 0.2615 (mtt) cc_final: 0.2036 (ppp) REVERT: C 396 MET cc_start: 0.4073 (ptt) cc_final: 0.3126 (tpt) REVERT: D 191 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7691 (t80) REVERT: D 204 CYS cc_start: 0.9248 (m) cc_final: 0.8711 (m) REVERT: D 314 LEU cc_start: 0.9526 (pp) cc_final: 0.9235 (pp) REVERT: D 318 CYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8251 (p) REVERT: D 319 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8653 (mmm-85) REVERT: D 329 TYR cc_start: 0.8741 (m-80) cc_final: 0.7729 (m-80) REVERT: D 428 LEU cc_start: 0.9494 (mt) cc_final: 0.9156 (mt) REVERT: D 431 LYS cc_start: 0.9313 (tttt) cc_final: 0.9009 (mttt) REVERT: D 458 MET cc_start: 0.8327 (pmm) cc_final: 0.8047 (pmm) REVERT: E 47 GLU cc_start: 0.8810 (pm20) cc_final: 0.8176 (pm20) REVERT: E 48 PHE cc_start: 0.8926 (m-10) cc_final: 0.8703 (m-10) REVERT: E 100 TYR cc_start: 0.8723 (p90) cc_final: 0.8456 (p90) REVERT: E 110 ARG cc_start: 0.9109 (mmm160) cc_final: 0.8775 (mmm160) REVERT: E 113 ASN cc_start: 0.9132 (m-40) cc_final: 0.8795 (m110) REVERT: E 117 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8645 (mp0) REVERT: E 159 PHE cc_start: 0.7866 (t80) cc_final: 0.7308 (t80) outliers start: 66 outliers final: 36 residues processed: 419 average time/residue: 0.1778 time to fit residues: 112.5433 Evaluate side-chains 393 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 319 ARG Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 454 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 263 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 267 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B1092 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 260 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 453 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060581 restraints weight = 115334.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062341 restraints weight = 62470.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063544 restraints weight = 41334.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064345 restraints weight = 31179.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064866 restraints weight = 25791.376| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24562 Z= 0.214 Angle : 0.743 11.827 33198 Z= 0.371 Chirality : 0.045 0.269 3688 Planarity : 0.005 0.092 4251 Dihedral : 7.185 166.968 3262 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 2.57 % Allowed : 16.30 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.32 (0.16), residues: 2949 helix: 1.26 (0.15), residues: 1294 sheet: 0.09 (0.27), residues: 362 loop : -0.79 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 551 TYR 0.045 0.002 TYR A 58 PHE 0.033 0.002 PHE B 567 TRP 0.021 0.002 TRP B1213 HIS 0.029 0.002 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (24555) covalent geometry : angle 0.73895 / 0.37 (33192) hydrogen bonds : bond 0.04641 / 3.01 ( 1031) hydrogen bonds : angle 4.44629 / 3.08 ( 2946) metal coordination : bond 0.00544 / 0.28 ( 4) metal coordination : angle 6.13220 / 3.71 ( 6) Misc. bond : bond 0.00464 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 370 time to evaluate : 1.011 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: A 16 ASP cc_start: 0.8746 (t0) cc_final: 0.8389 (t0) REVERT: A 79 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8595 (ttpp) REVERT: A 92 LYS cc_start: 0.8691 (tttt) cc_final: 0.8453 (tttp) REVERT: A 296 LEU cc_start: 0.9306 (mt) cc_final: 0.8812 (pp) REVERT: A 311 GLU cc_start: 0.8824 (pm20) cc_final: 0.8349 (pm20) REVERT: A 338 ASN cc_start: 0.9035 (t0) cc_final: 0.8389 (t0) REVERT: A 344 GLU cc_start: 0.7943 (tt0) cc_final: 0.7436 (tt0) REVERT: A 394 MET cc_start: 0.9383 (mpp) cc_final: 0.9154 (mpp) REVERT: A 492 TYR cc_start: 0.9042 (m-10) cc_final: 0.8732 (m-10) REVERT: A 494 TYR cc_start: 0.8860 (t80) cc_final: 0.8557 (t80) REVERT: A 548 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8919 (m-10) REVERT: A 556 MET cc_start: 0.8523 (tpp) cc_final: 0.7916 (tmm) REVERT: A 646 LEU cc_start: 0.9494 (mm) cc_final: 0.9272 (pp) REVERT: A 670 TYR cc_start: 0.8008 (m-80) cc_final: 0.7740 (m-10) REVERT: A 682 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7683 (tpp) REVERT: A 722 MET cc_start: 0.7748 (mtp) cc_final: 0.7414 (mtp) REVERT: A 795 TYR cc_start: 0.8750 (t80) cc_final: 0.8433 (t80) REVERT: A 802 CYS cc_start: 0.9417 (m) cc_final: 0.9107 (m) REVERT: A 803 TYR cc_start: 0.8706 (p90) cc_final: 0.8171 (p90) REVERT: A 823 MET cc_start: 0.8235 (mmm) cc_final: 0.7902 (mmm) REVERT: A 833 LEU cc_start: 0.8702 (mt) cc_final: 0.8248 (pt) REVERT: A 845 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8721 (mmmm) REVERT: A 846 PHE cc_start: 0.9033 (m-80) cc_final: 0.8707 (m-80) REVERT: B 74 LEU cc_start: 0.8941 (mt) cc_final: 0.8732 (mm) REVERT: B 78 LEU cc_start: 0.9161 (mt) cc_final: 0.8825 (mm) REVERT: B 103 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.8001 (ptp90) REVERT: B 108 ASP cc_start: 0.8179 (t0) cc_final: 0.7716 (t0) REVERT: B 193 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8630 (mmm-85) REVERT: B 196 TYR cc_start: 0.8399 (m-80) cc_final: 0.7654 (m-80) REVERT: B 272 PHE cc_start: 0.8145 (t80) cc_final: 0.7813 (t80) REVERT: B 273 PHE cc_start: 0.8561 (t80) cc_final: 0.8071 (t80) REVERT: B 309 LYS cc_start: 0.9178 (mttt) cc_final: 0.8919 (mmtp) REVERT: B 340 ASP cc_start: 0.8865 (m-30) cc_final: 0.8287 (p0) REVERT: B 587 ASP cc_start: 0.9061 (t0) cc_final: 0.8757 (t0) REVERT: B 730 ASP cc_start: 0.8833 (m-30) cc_final: 0.8551 (p0) REVERT: B 783 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8665 (mt-10) REVERT: B 941 LYS cc_start: 0.8651 (pttt) cc_final: 0.8383 (ptpt) REVERT: B 1030 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8856 (t) REVERT: B 1101 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7844 (ptt) REVERT: B 1192 MET cc_start: 0.8700 (mmm) cc_final: 0.7912 (mmm) REVERT: B 1216 GLU cc_start: 0.8130 (tp30) cc_final: 0.7778 (tp30) REVERT: B 1236 GLN cc_start: 0.8669 (mp10) cc_final: 0.8401 (tm-30) REVERT: B 1331 ILE cc_start: 0.9176 (mp) cc_final: 0.8910 (tp) REVERT: C 165 CYS cc_start: 0.8917 (m) cc_final: 0.8587 (m) REVERT: C 271 ASN cc_start: 0.9091 (m110) cc_final: 0.8637 (p0) REVERT: C 369 MET cc_start: 0.2262 (mtt) cc_final: 0.1678 (ppp) REVERT: C 396 MET cc_start: 0.4141 (ptt) cc_final: 0.3159 (tpt) REVERT: D 64 THR cc_start: 0.7613 (p) cc_final: 0.7186 (t) REVERT: D 191 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7717 (t80) REVERT: D 204 CYS cc_start: 0.9294 (m) cc_final: 0.8940 (m) REVERT: D 318 CYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8199 (p) REVERT: D 319 ARG cc_start: 0.9013 (ptp-110) cc_final: 0.8777 (mmm-85) REVERT: D 329 TYR cc_start: 0.8783 (m-80) cc_final: 0.7781 (m-80) REVERT: D 378 LEU cc_start: 0.8955 (mt) cc_final: 0.8641 (mt) REVERT: D 380 VAL cc_start: 0.8927 (t) cc_final: 0.8653 (m) REVERT: D 428 LEU cc_start: 0.9509 (mt) cc_final: 0.9151 (mt) REVERT: D 431 LYS cc_start: 0.9355 (tttt) cc_final: 0.9029 (mttt) REVERT: D 448 ARG cc_start: 0.8898 (ttp-110) cc_final: 0.8601 (tpt90) REVERT: E 44 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8676 (tm-30) REVERT: E 75 ASP cc_start: 0.8464 (t0) cc_final: 0.8078 (p0) REVERT: E 110 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8808 (mmm160) REVERT: E 113 ASN cc_start: 0.9202 (m-40) cc_final: 0.8772 (m110) REVERT: E 146 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8920 (tp40) REVERT: E 159 PHE cc_start: 0.7899 (t80) cc_final: 0.7586 (t80) outliers start: 68 outliers final: 39 residues processed: 414 average time/residue: 0.1802 time to fit residues: 113.4058 Evaluate side-chains 386 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1030 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1101 MET Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1338 PHE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 92 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 132 optimal weight: 0.0010 chunk 129 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN B 292 GLN B 777 GLN B 798 ASN B1103 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 453 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.084234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061868 restraints weight = 114183.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063714 restraints weight = 61393.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064926 restraints weight = 40232.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065741 restraints weight = 30197.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066118 restraints weight = 24855.226| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24562 Z= 0.125 Angle : 0.718 13.608 33198 Z= 0.350 Chirality : 0.043 0.298 3688 Planarity : 0.004 0.091 4251 Dihedral : 7.039 168.576 3262 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 2.41 % Allowed : 16.60 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.42 (0.16), residues: 2949 helix: 1.35 (0.15), residues: 1284 sheet: 0.22 (0.27), residues: 359 loop : -0.76 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 378 TYR 0.031 0.001 TYR E 90 PHE 0.045 0.001 PHE E 108 TRP 0.019 0.001 TRP B1213 HIS 0.005 0.001 HIS C 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24555) covalent geometry : angle 0.71210 / 0.35 (33192) hydrogen bonds : bond 0.04103 / 2.68 ( 1031) hydrogen bonds : angle 4.25626 / 2.94 ( 2946) metal coordination : bond 0.00913 / 0.45 ( 4) metal coordination : angle 7.14544 / 4.30 ( 6) Misc. bond : bond 0.00467 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 368 time to evaluate : 1.002 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: A 16 ASP cc_start: 0.8715 (t0) cc_final: 0.8354 (t0) REVERT: A 79 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: A 92 LYS cc_start: 0.8637 (tttt) cc_final: 0.8402 (tttp) REVERT: A 296 LEU cc_start: 0.9281 (mt) cc_final: 0.8784 (pp) REVERT: A 311 GLU cc_start: 0.8676 (pm20) cc_final: 0.8466 (pm20) REVERT: A 338 ASN cc_start: 0.9044 (t0) cc_final: 0.8403 (t0) REVERT: A 344 GLU cc_start: 0.7981 (tt0) cc_final: 0.7484 (tt0) REVERT: A 361 GLU cc_start: 0.8934 (mp0) cc_final: 0.8725 (mp0) REVERT: A 394 MET cc_start: 0.9314 (mpp) cc_final: 0.9047 (mpp) REVERT: A 494 TYR cc_start: 0.8848 (t80) cc_final: 0.8535 (t80) REVERT: A 548 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8886 (m-10) REVERT: A 556 MET cc_start: 0.8524 (tpp) cc_final: 0.7930 (tmm) REVERT: A 646 LEU cc_start: 0.9489 (mm) cc_final: 0.9263 (pp) REVERT: A 722 MET cc_start: 0.7855 (mtp) cc_final: 0.7453 (mpp) REVERT: A 795 TYR cc_start: 0.8769 (t80) cc_final: 0.8452 (t80) REVERT: A 803 TYR cc_start: 0.8664 (p90) cc_final: 0.8310 (p90) REVERT: A 823 MET cc_start: 0.8220 (mmm) cc_final: 0.7920 (mmm) REVERT: A 833 LEU cc_start: 0.8730 (mt) cc_final: 0.8311 (pt) REVERT: A 845 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8830 (mmtm) REVERT: A 846 PHE cc_start: 0.8925 (m-80) cc_final: 0.8484 (m-80) REVERT: B 74 LEU cc_start: 0.8929 (mt) cc_final: 0.8711 (tp) REVERT: B 78 LEU cc_start: 0.9150 (mt) cc_final: 0.8816 (mm) REVERT: B 108 ASP cc_start: 0.8128 (t0) cc_final: 0.7565 (t0) REVERT: B 159 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8119 (p-90) REVERT: B 193 ARG cc_start: 0.8918 (mmm-85) cc_final: 0.8614 (mmm-85) REVERT: B 196 TYR cc_start: 0.8379 (m-80) cc_final: 0.7596 (m-80) REVERT: B 272 PHE cc_start: 0.8166 (t80) cc_final: 0.7799 (t80) REVERT: B 273 PHE cc_start: 0.8453 (t80) cc_final: 0.7979 (t80) REVERT: B 436 GLU cc_start: 0.8804 (tp30) cc_final: 0.8544 (tp30) REVERT: B 581 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: B 587 ASP cc_start: 0.9019 (t0) cc_final: 0.8574 (t0) REVERT: B 590 ASP cc_start: 0.8242 (t0) cc_final: 0.8042 (t0) REVERT: B 783 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8631 (mt-10) REVERT: B 797 SER cc_start: 0.9527 (t) cc_final: 0.9130 (p) REVERT: B 941 LYS cc_start: 0.8648 (pttt) cc_final: 0.8433 (ptpt) REVERT: B 964 MET cc_start: 0.8417 (mmm) cc_final: 0.8148 (mpp) REVERT: B 1192 MET cc_start: 0.8647 (mmm) cc_final: 0.8288 (mmm) REVERT: B 1216 GLU cc_start: 0.8114 (tp30) cc_final: 0.7798 (tp30) REVERT: C 144 LEU cc_start: 0.9505 (tt) cc_final: 0.9239 (pp) REVERT: C 158 GLU cc_start: 0.8946 (tp30) cc_final: 0.7614 (tp30) REVERT: C 162 TYR cc_start: 0.8729 (m-10) cc_final: 0.8237 (m-80) REVERT: C 165 CYS cc_start: 0.8952 (m) cc_final: 0.8622 (m) REVERT: C 271 ASN cc_start: 0.9042 (m110) cc_final: 0.8596 (p0) REVERT: C 369 MET cc_start: 0.2224 (mtt) cc_final: 0.1642 (ppp) REVERT: C 396 MET cc_start: 0.4145 (ptt) cc_final: 0.2756 (tpt) REVERT: D 191 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7711 (t80) REVERT: D 204 CYS cc_start: 0.9301 (m) cc_final: 0.8943 (m) REVERT: D 304 ARG cc_start: 0.8723 (ptp-110) cc_final: 0.8506 (ptt-90) REVERT: D 318 CYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8160 (p) REVERT: D 329 TYR cc_start: 0.8722 (m-80) cc_final: 0.7711 (m-80) REVERT: D 378 LEU cc_start: 0.8942 (mt) cc_final: 0.8640 (mt) REVERT: D 380 VAL cc_start: 0.8909 (t) cc_final: 0.8643 (m) REVERT: D 428 LEU cc_start: 0.9492 (mt) cc_final: 0.9229 (mt) REVERT: D 431 LYS cc_start: 0.9354 (tttt) cc_final: 0.9048 (mttt) REVERT: D 448 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8637 (tpt90) REVERT: E 44 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8661 (tm-30) REVERT: E 47 GLU cc_start: 0.8578 (pm20) cc_final: 0.8221 (pm20) REVERT: E 48 PHE cc_start: 0.8733 (m-10) cc_final: 0.8305 (m-10) REVERT: E 113 ASN cc_start: 0.9113 (m-40) cc_final: 0.8351 (m110) REVERT: E 120 ARG cc_start: 0.8474 (ptt-90) cc_final: 0.8154 (mtm110) REVERT: E 159 PHE cc_start: 0.7825 (t80) cc_final: 0.7545 (t80) outliers start: 64 outliers final: 36 residues processed: 409 average time/residue: 0.1880 time to fit residues: 116.1302 Evaluate side-chains 383 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1069 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 454 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 158 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 209 optimal weight: 0.5980 chunk 287 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 370 HIS ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 ASN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 253 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 453 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.083920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061203 restraints weight = 113569.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063020 restraints weight = 61261.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064213 restraints weight = 40379.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064958 restraints weight = 30368.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065480 restraints weight = 25287.120| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24562 Z= 0.165 Angle : 0.741 13.942 33198 Z= 0.364 Chirality : 0.044 0.306 3688 Planarity : 0.004 0.089 4251 Dihedral : 7.015 171.857 3262 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 2.60 % Allowed : 17.31 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.39 (0.16), residues: 2949 helix: 1.37 (0.15), residues: 1291 sheet: 0.07 (0.26), residues: 375 loop : -0.81 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 378 TYR 0.027 0.001 TYR A 803 PHE 0.027 0.002 PHE E 108 TRP 0.020 0.001 TRP B1213 HIS 0.006 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (24555) covalent geometry : angle 0.73573 / 0.36 (33192) hydrogen bonds : bond 0.04265 / 2.79 ( 1031) hydrogen bonds : angle 4.33119 / 2.99 ( 2946) metal coordination : bond 0.00671 / 0.33 ( 4) metal coordination : angle 6.86391 / 4.11 ( 6) Misc. bond : bond 0.00466 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 357 time to evaluate : 1.018 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: A 16 ASP cc_start: 0.8678 (t0) cc_final: 0.8296 (t0) REVERT: A 79 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8560 (ttpp) REVERT: A 92 LYS cc_start: 0.8649 (tttt) cc_final: 0.8429 (tttp) REVERT: A 296 LEU cc_start: 0.9278 (mt) cc_final: 0.8783 (pp) REVERT: A 338 ASN cc_start: 0.9047 (t0) cc_final: 0.8385 (t0) REVERT: A 344 GLU cc_start: 0.8031 (tt0) cc_final: 0.7505 (tt0) REVERT: A 361 GLU cc_start: 0.8908 (mp0) cc_final: 0.8694 (mp0) REVERT: A 394 MET cc_start: 0.9324 (mpp) cc_final: 0.9110 (mpp) REVERT: A 494 TYR cc_start: 0.8896 (t80) cc_final: 0.8532 (t80) REVERT: A 548 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8836 (m-10) REVERT: A 556 MET cc_start: 0.8452 (tpp) cc_final: 0.7840 (tmm) REVERT: A 646 LEU cc_start: 0.9495 (mm) cc_final: 0.9278 (pp) REVERT: A 648 LEU cc_start: 0.9294 (mt) cc_final: 0.9037 (pp) REVERT: A 722 MET cc_start: 0.7679 (mtp) cc_final: 0.7368 (mpp) REVERT: A 795 TYR cc_start: 0.8724 (t80) cc_final: 0.8393 (t80) REVERT: A 823 MET cc_start: 0.8306 (mmm) cc_final: 0.7995 (mmm) REVERT: A 833 LEU cc_start: 0.8862 (mt) cc_final: 0.8417 (pt) REVERT: A 845 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8904 (mmtm) REVERT: A 846 PHE cc_start: 0.8999 (m-80) cc_final: 0.8553 (m-80) REVERT: B 74 LEU cc_start: 0.9039 (mt) cc_final: 0.8830 (tp) REVERT: B 78 LEU cc_start: 0.9200 (mt) cc_final: 0.8887 (mm) REVERT: B 108 ASP cc_start: 0.8228 (t0) cc_final: 0.7807 (t0) REVERT: B 193 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8644 (mmm-85) REVERT: B 196 TYR cc_start: 0.8362 (m-80) cc_final: 0.7614 (m-80) REVERT: B 272 PHE cc_start: 0.8148 (t80) cc_final: 0.7890 (t80) REVERT: B 273 PHE cc_start: 0.8399 (t80) cc_final: 0.8002 (t80) REVERT: B 293 MET cc_start: 0.8531 (mmm) cc_final: 0.8198 (mmm) REVERT: B 305 GLU cc_start: 0.8701 (tt0) cc_final: 0.8337 (tt0) REVERT: B 309 LYS cc_start: 0.8929 (mttm) cc_final: 0.8588 (mmtp) REVERT: B 340 ASP cc_start: 0.8815 (m-30) cc_final: 0.8237 (p0) REVERT: B 581 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: B 587 ASP cc_start: 0.8989 (t0) cc_final: 0.8681 (t0) REVERT: B 730 ASP cc_start: 0.8771 (m-30) cc_final: 0.8486 (p0) REVERT: B 783 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 797 SER cc_start: 0.9551 (t) cc_final: 0.9144 (p) REVERT: B 1192 MET cc_start: 0.8694 (mmm) cc_final: 0.8322 (mmm) REVERT: B 1216 GLU cc_start: 0.8040 (tp30) cc_final: 0.7731 (tp30) REVERT: C 144 LEU cc_start: 0.9508 (tt) cc_final: 0.9243 (pp) REVERT: C 165 CYS cc_start: 0.8901 (m) cc_final: 0.8583 (m) REVERT: C 271 ASN cc_start: 0.9067 (m110) cc_final: 0.8645 (p0) REVERT: C 396 MET cc_start: 0.4159 (ptt) cc_final: 0.2807 (tpt) REVERT: D 191 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7591 (t80) REVERT: D 204 CYS cc_start: 0.9281 (m) cc_final: 0.8925 (m) REVERT: D 327 TYR cc_start: 0.8066 (m-10) cc_final: 0.7850 (m-10) REVERT: D 329 TYR cc_start: 0.8718 (m-80) cc_final: 0.7723 (m-80) REVERT: D 378 LEU cc_start: 0.9049 (mt) cc_final: 0.8848 (mm) REVERT: D 380 VAL cc_start: 0.8997 (t) cc_final: 0.8758 (m) REVERT: D 428 LEU cc_start: 0.9494 (mt) cc_final: 0.9214 (mt) REVERT: D 431 LYS cc_start: 0.9355 (tttt) cc_final: 0.9036 (mttt) REVERT: E 44 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8409 (tm-30) REVERT: E 75 ASP cc_start: 0.8384 (t0) cc_final: 0.8105 (p0) REVERT: E 159 PHE cc_start: 0.7923 (t80) cc_final: 0.7685 (t80) REVERT: E 179 LYS cc_start: 0.9243 (mtmm) cc_final: 0.9031 (mmtm) outliers start: 69 outliers final: 47 residues processed: 401 average time/residue: 0.1833 time to fit residues: 111.8776 Evaluate side-chains 387 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 700 ASP Chi-restraints excluded: chain B residue 731 TYR Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1069 LEU Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1338 PHE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 150 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 277 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS A 370 HIS ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.084834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061917 restraints weight = 113533.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063796 restraints weight = 61248.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064983 restraints weight = 40244.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065781 restraints weight = 30419.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066090 restraints weight = 25202.852| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24562 Z= 0.129 Angle : 0.752 15.985 33198 Z= 0.364 Chirality : 0.044 0.435 3688 Planarity : 0.004 0.089 4251 Dihedral : 6.930 175.763 3262 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 1.92 % Allowed : 18.79 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.16), residues: 2949 helix: 1.43 (0.15), residues: 1291 sheet: 0.21 (0.27), residues: 350 loop : -0.80 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 304 TYR 0.026 0.001 TYR E 90 PHE 0.032 0.001 PHE E 108 TRP 0.018 0.001 TRP B1213 HIS 0.014 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (24555) covalent geometry : angle 0.74730 / 0.36 (33192) hydrogen bonds : bond 0.03961 / 2.57 ( 1031) hydrogen bonds : angle 4.22172 / 2.91 ( 2946) metal coordination : bond 0.00544 / 0.27 ( 4) metal coordination : angle 6.23634 / 3.73 ( 6) Misc. bond : bond 0.00455 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 0.916 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 16 ASP cc_start: 0.8707 (t0) cc_final: 0.8332 (t0) REVERT: A 92 LYS cc_start: 0.8629 (tttt) cc_final: 0.8395 (tttp) REVERT: A 171 GLN cc_start: 0.8431 (tp40) cc_final: 0.8188 (tp40) REVERT: A 296 LEU cc_start: 0.9293 (mt) cc_final: 0.8797 (pp) REVERT: A 312 GLU cc_start: 0.8814 (mp0) cc_final: 0.8476 (mp0) REVERT: A 338 ASN cc_start: 0.9028 (t0) cc_final: 0.8376 (t0) REVERT: A 344 GLU cc_start: 0.8058 (tt0) cc_final: 0.7537 (tt0) REVERT: A 361 GLU cc_start: 0.8898 (mp0) cc_final: 0.8690 (mp0) REVERT: A 492 TYR cc_start: 0.8987 (m-10) cc_final: 0.8775 (m-10) REVERT: A 494 TYR cc_start: 0.8899 (t80) cc_final: 0.8530 (t80) REVERT: A 548 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8866 (m-10) REVERT: A 556 MET cc_start: 0.8496 (tpp) cc_final: 0.7897 (tmm) REVERT: A 646 LEU cc_start: 0.9499 (mm) cc_final: 0.9270 (pp) REVERT: A 722 MET cc_start: 0.7659 (mtp) cc_final: 0.7430 (mpp) REVERT: A 795 TYR cc_start: 0.8796 (t80) cc_final: 0.8475 (t80) REVERT: A 803 TYR cc_start: 0.8710 (p90) cc_final: 0.8248 (p90) REVERT: A 823 MET cc_start: 0.8338 (mmm) cc_final: 0.8029 (mmm) REVERT: A 833 LEU cc_start: 0.8813 (mt) cc_final: 0.8430 (pt) REVERT: A 845 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8899 (mmtm) REVERT: A 846 PHE cc_start: 0.9010 (m-80) cc_final: 0.8564 (m-80) REVERT: B 78 LEU cc_start: 0.9205 (mt) cc_final: 0.8886 (mm) REVERT: B 89 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7800 (tptp) REVERT: B 108 ASP cc_start: 0.8216 (t0) cc_final: 0.7674 (t0) REVERT: B 155 MET cc_start: 0.7925 (mmm) cc_final: 0.7580 (mmm) REVERT: B 159 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8274 (p-90) REVERT: B 193 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8665 (mmm-85) REVERT: B 196 TYR cc_start: 0.8363 (m-80) cc_final: 0.7612 (m-80) REVERT: B 272 PHE cc_start: 0.8274 (t80) cc_final: 0.7982 (t80) REVERT: B 273 PHE cc_start: 0.8432 (t80) cc_final: 0.8009 (t80) REVERT: B 293 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (mmm) REVERT: B 305 GLU cc_start: 0.8678 (tt0) cc_final: 0.8340 (tt0) REVERT: B 309 LYS cc_start: 0.8927 (mttm) cc_final: 0.8653 (mmtp) REVERT: B 340 ASP cc_start: 0.8836 (m-30) cc_final: 0.8199 (p0) REVERT: B 436 GLU cc_start: 0.8778 (tp30) cc_final: 0.8525 (tp30) REVERT: B 581 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: B 587 ASP cc_start: 0.9025 (t0) cc_final: 0.8684 (t0) REVERT: B 730 ASP cc_start: 0.8816 (m-30) cc_final: 0.8514 (p0) REVERT: B 747 MET cc_start: 0.8655 (ptp) cc_final: 0.8343 (ptp) REVERT: B 783 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 792 ASP cc_start: 0.8987 (p0) cc_final: 0.8647 (p0) REVERT: B 797 SER cc_start: 0.9510 (t) cc_final: 0.9108 (p) REVERT: B 941 LYS cc_start: 0.8728 (ptpt) cc_final: 0.8311 (ptpt) REVERT: B 964 MET cc_start: 0.8423 (mmm) cc_final: 0.8145 (mpp) REVERT: B 1192 MET cc_start: 0.8663 (mmm) cc_final: 0.8292 (mmm) REVERT: B 1216 GLU cc_start: 0.8070 (tp30) cc_final: 0.7782 (tp30) REVERT: C 162 TYR cc_start: 0.8704 (m-10) cc_final: 0.8291 (m-80) REVERT: C 165 CYS cc_start: 0.8965 (m) cc_final: 0.8706 (m) REVERT: C 271 ASN cc_start: 0.9090 (m110) cc_final: 0.8667 (p0) REVERT: C 369 MET cc_start: 0.2039 (mtt) cc_final: 0.1467 (ppp) REVERT: C 396 MET cc_start: 0.4324 (ptt) cc_final: 0.2985 (tpt) REVERT: D 191 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7737 (t80) REVERT: D 204 CYS cc_start: 0.9326 (m) cc_final: 0.8961 (m) REVERT: D 327 TYR cc_start: 0.8120 (m-10) cc_final: 0.7841 (m-10) REVERT: D 329 TYR cc_start: 0.8710 (m-80) cc_final: 0.7673 (m-80) REVERT: D 380 VAL cc_start: 0.9000 (t) cc_final: 0.8767 (m) REVERT: D 427 TYR cc_start: 0.9082 (m-10) cc_final: 0.8554 (m-80) REVERT: D 428 LEU cc_start: 0.9496 (mt) cc_final: 0.9224 (mt) REVERT: D 431 LYS cc_start: 0.9341 (tttt) cc_final: 0.9034 (mttt) REVERT: E 28 GLU cc_start: 0.8314 (tp30) cc_final: 0.7844 (tm-30) REVERT: E 44 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8403 (tm-30) REVERT: E 159 PHE cc_start: 0.7832 (t80) cc_final: 0.7538 (t80) REVERT: E 179 LYS cc_start: 0.9273 (mtmm) cc_final: 0.9028 (mmtm) outliers start: 51 outliers final: 36 residues processed: 388 average time/residue: 0.1839 time to fit residues: 108.9978 Evaluate side-chains 382 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 340 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 61 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 440 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.061623 restraints weight = 115164.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.063471 restraints weight = 61808.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064667 restraints weight = 40769.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065415 restraints weight = 30791.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065785 restraints weight = 25713.913| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24562 Z= 0.143 Angle : 0.774 16.436 33198 Z= 0.374 Chirality : 0.044 0.385 3688 Planarity : 0.004 0.090 4251 Dihedral : 6.933 176.795 3262 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.19 % Allowed : 19.12 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.16), residues: 2949 helix: 1.44 (0.15), residues: 1286 sheet: 0.20 (0.27), residues: 350 loop : -0.79 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 95 TYR 0.022 0.001 TYR A 803 PHE 0.053 0.002 PHE E 108 TRP 0.018 0.001 TRP B1213 HIS 0.010 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (24555) covalent geometry : angle 0.76999 / 0.37 (33192) hydrogen bonds : bond 0.03967 / 2.60 ( 1031) hydrogen bonds : angle 4.28000 / 2.96 ( 2946) metal coordination : bond 0.00401 / 0.19 ( 4) metal coordination : angle 5.54674 / 3.30 ( 6) Misc. bond : bond 0.00859 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 357 time to evaluate : 0.983 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 16 ASP cc_start: 0.8700 (t0) cc_final: 0.8333 (t0) REVERT: A 79 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: A 92 LYS cc_start: 0.8643 (tttt) cc_final: 0.8394 (tttp) REVERT: A 171 GLN cc_start: 0.8475 (tp40) cc_final: 0.8222 (tp40) REVERT: A 296 LEU cc_start: 0.9299 (mt) cc_final: 0.8801 (pp) REVERT: A 338 ASN cc_start: 0.9027 (t0) cc_final: 0.8357 (t0) REVERT: A 344 GLU cc_start: 0.8098 (tt0) cc_final: 0.7543 (tt0) REVERT: A 494 TYR cc_start: 0.8906 (t80) cc_final: 0.8504 (t80) REVERT: A 548 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8880 (m-10) REVERT: A 556 MET cc_start: 0.8526 (tpp) cc_final: 0.7936 (tmm) REVERT: A 646 LEU cc_start: 0.9500 (mm) cc_final: 0.9280 (pp) REVERT: A 722 MET cc_start: 0.7582 (mtp) cc_final: 0.7301 (mpp) REVERT: A 729 CYS cc_start: 0.8298 (m) cc_final: 0.8089 (m) REVERT: A 795 TYR cc_start: 0.8807 (t80) cc_final: 0.8541 (t80) REVERT: A 803 TYR cc_start: 0.8716 (p90) cc_final: 0.8275 (p90) REVERT: A 823 MET cc_start: 0.8396 (mmm) cc_final: 0.8024 (mmm) REVERT: A 833 LEU cc_start: 0.8874 (mt) cc_final: 0.8478 (pt) REVERT: A 845 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8934 (mmtm) REVERT: A 846 PHE cc_start: 0.9063 (m-80) cc_final: 0.8605 (m-80) REVERT: B 30 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8496 (tmtt) REVERT: B 78 LEU cc_start: 0.9263 (mt) cc_final: 0.8960 (mm) REVERT: B 89 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8340 (ttpp) REVERT: B 108 ASP cc_start: 0.8208 (t0) cc_final: 0.7658 (t0) REVERT: B 155 MET cc_start: 0.7932 (mmm) cc_final: 0.7545 (mmm) REVERT: B 159 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.8257 (p-90) REVERT: B 193 ARG cc_start: 0.8950 (mmm-85) cc_final: 0.8686 (mmm-85) REVERT: B 196 TYR cc_start: 0.8374 (m-80) cc_final: 0.7591 (m-80) REVERT: B 272 PHE cc_start: 0.8323 (t80) cc_final: 0.8058 (t80) REVERT: B 273 PHE cc_start: 0.8499 (t80) cc_final: 0.8053 (t80) REVERT: B 293 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (mmm) REVERT: B 305 GLU cc_start: 0.8703 (tt0) cc_final: 0.8342 (tt0) REVERT: B 309 LYS cc_start: 0.8924 (mttm) cc_final: 0.8650 (mmtp) REVERT: B 340 ASP cc_start: 0.8851 (m-30) cc_final: 0.8177 (p0) REVERT: B 436 GLU cc_start: 0.8776 (tp30) cc_final: 0.8520 (tp30) REVERT: B 531 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8193 (mp10) REVERT: B 587 ASP cc_start: 0.9056 (t0) cc_final: 0.8697 (t0) REVERT: B 730 ASP cc_start: 0.8812 (m-30) cc_final: 0.8520 (p0) REVERT: B 783 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8586 (mt-10) REVERT: B 792 ASP cc_start: 0.8996 (p0) cc_final: 0.8655 (p0) REVERT: B 797 SER cc_start: 0.9518 (t) cc_final: 0.9127 (p) REVERT: B 941 LYS cc_start: 0.8724 (ptpt) cc_final: 0.8414 (ptpt) REVERT: B 964 MET cc_start: 0.8444 (mmm) cc_final: 0.8179 (mpp) REVERT: B 1192 MET cc_start: 0.8669 (mmm) cc_final: 0.8292 (mmm) REVERT: B 1216 GLU cc_start: 0.8128 (tp30) cc_final: 0.7702 (tp30) REVERT: C 144 LEU cc_start: 0.9489 (mp) cc_final: 0.9246 (pp) REVERT: C 162 TYR cc_start: 0.8749 (m-10) cc_final: 0.8340 (m-80) REVERT: C 165 CYS cc_start: 0.8923 (m) cc_final: 0.8588 (m) REVERT: C 271 ASN cc_start: 0.9102 (m110) cc_final: 0.8678 (p0) REVERT: C 369 MET cc_start: 0.2097 (mtt) cc_final: 0.1530 (ppp) REVERT: C 396 MET cc_start: 0.4395 (ptt) cc_final: 0.3042 (tpt) REVERT: D 191 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7759 (t80) REVERT: D 204 CYS cc_start: 0.9305 (m) cc_final: 0.8949 (m) REVERT: D 317 ARG cc_start: 0.9068 (tpt170) cc_final: 0.8706 (tpt-90) REVERT: D 327 TYR cc_start: 0.8115 (m-10) cc_final: 0.7838 (m-10) REVERT: D 329 TYR cc_start: 0.8732 (m-80) cc_final: 0.7708 (m-80) REVERT: D 427 TYR cc_start: 0.9088 (m-10) cc_final: 0.8556 (m-80) REVERT: D 428 LEU cc_start: 0.9497 (mt) cc_final: 0.9214 (mt) REVERT: D 431 LYS cc_start: 0.9357 (tttt) cc_final: 0.9039 (mttt) REVERT: E 44 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8407 (tm-30) REVERT: E 159 PHE cc_start: 0.7790 (t80) cc_final: 0.7510 (t80) REVERT: E 179 LYS cc_start: 0.9279 (mtmm) cc_final: 0.9014 (mmtm) outliers start: 58 outliers final: 44 residues processed: 395 average time/residue: 0.1790 time to fit residues: 108.8957 Evaluate side-chains 390 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 280 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 HIS A 264 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061695 restraints weight = 114627.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063504 restraints weight = 61368.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064675 restraints weight = 40472.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065468 restraints weight = 30536.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065834 restraints weight = 25274.668| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24562 Z= 0.146 Angle : 0.783 15.600 33198 Z= 0.380 Chirality : 0.045 0.479 3688 Planarity : 0.004 0.090 4251 Dihedral : 6.944 178.037 3262 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 2.04 % Allowed : 19.35 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.16), residues: 2949 helix: 1.40 (0.15), residues: 1282 sheet: 0.24 (0.28), residues: 350 loop : -0.80 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 95 TYR 0.027 0.001 TYR E 90 PHE 0.063 0.002 PHE E 108 TRP 0.018 0.001 TRP B1213 HIS 0.009 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (24555) covalent geometry : angle 0.77943 / 0.38 (33192) hydrogen bonds : bond 0.04001 / 2.62 ( 1031) hydrogen bonds : angle 4.30594 / 2.99 ( 2946) metal coordination : bond 0.00394 / 0.20 ( 4) metal coordination : angle 5.39397 / 3.21 ( 6) Misc. bond : bond 0.00675 / 0.26 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 0.981 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 16 ASP cc_start: 0.8700 (t0) cc_final: 0.8338 (t0) REVERT: A 92 LYS cc_start: 0.8659 (tttt) cc_final: 0.8425 (tttp) REVERT: A 171 GLN cc_start: 0.8484 (tp40) cc_final: 0.8255 (tp40) REVERT: A 218 MET cc_start: 0.8169 (tpp) cc_final: 0.7925 (tpp) REVERT: A 296 LEU cc_start: 0.9303 (mt) cc_final: 0.8803 (pp) REVERT: A 338 ASN cc_start: 0.9034 (t0) cc_final: 0.8353 (t0) REVERT: A 344 GLU cc_start: 0.8144 (tt0) cc_final: 0.7571 (tt0) REVERT: A 492 TYR cc_start: 0.8852 (m-10) cc_final: 0.8651 (m-10) REVERT: A 494 TYR cc_start: 0.8931 (t80) cc_final: 0.8500 (t80) REVERT: A 548 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8885 (m-10) REVERT: A 556 MET cc_start: 0.8566 (tpp) cc_final: 0.7979 (tmm) REVERT: A 646 LEU cc_start: 0.9509 (mm) cc_final: 0.9297 (pp) REVERT: A 722 MET cc_start: 0.7560 (mtp) cc_final: 0.7339 (mtp) REVERT: A 729 CYS cc_start: 0.8278 (m) cc_final: 0.8076 (m) REVERT: A 795 TYR cc_start: 0.8816 (t80) cc_final: 0.8498 (t80) REVERT: A 803 TYR cc_start: 0.8717 (p90) cc_final: 0.8284 (p90) REVERT: A 823 MET cc_start: 0.8457 (mmm) cc_final: 0.8087 (mmm) REVERT: A 833 LEU cc_start: 0.8911 (mt) cc_final: 0.8524 (pt) REVERT: A 845 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8910 (mmtm) REVERT: A 846 PHE cc_start: 0.9095 (m-80) cc_final: 0.8668 (m-80) REVERT: B 36 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7783 (ttp80) REVERT: B 78 LEU cc_start: 0.9295 (mt) cc_final: 0.9019 (mm) REVERT: B 89 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8322 (ttpp) REVERT: B 108 ASP cc_start: 0.8228 (t0) cc_final: 0.7665 (t0) REVERT: B 155 MET cc_start: 0.7943 (mmm) cc_final: 0.7497 (mmm) REVERT: B 159 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (p-90) REVERT: B 165 THR cc_start: 0.7593 (p) cc_final: 0.7165 (t) REVERT: B 178 ASP cc_start: 0.8530 (t0) cc_final: 0.8320 (t0) REVERT: B 196 TYR cc_start: 0.8351 (m-80) cc_final: 0.7590 (m-80) REVERT: B 272 PHE cc_start: 0.8282 (t80) cc_final: 0.8072 (t80) REVERT: B 273 PHE cc_start: 0.8506 (t80) cc_final: 0.8065 (t80) REVERT: B 305 GLU cc_start: 0.8701 (tt0) cc_final: 0.8115 (tt0) REVERT: B 309 LYS cc_start: 0.8932 (mttm) cc_final: 0.8566 (mmtp) REVERT: B 340 ASP cc_start: 0.8861 (m-30) cc_final: 0.8185 (p0) REVERT: B 436 GLU cc_start: 0.8775 (tp30) cc_final: 0.8518 (tp30) REVERT: B 587 ASP cc_start: 0.9070 (t0) cc_final: 0.8700 (t0) REVERT: B 730 ASP cc_start: 0.8813 (m-30) cc_final: 0.8525 (p0) REVERT: B 747 MET cc_start: 0.8771 (ptp) cc_final: 0.8527 (mpp) REVERT: B 783 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8588 (mt-10) REVERT: B 792 ASP cc_start: 0.8993 (p0) cc_final: 0.8655 (p0) REVERT: B 794 MET cc_start: 0.8682 (mmm) cc_final: 0.8413 (mmm) REVERT: B 797 SER cc_start: 0.9523 (t) cc_final: 0.9143 (p) REVERT: B 941 LYS cc_start: 0.8711 (ptpt) cc_final: 0.8326 (ptpt) REVERT: B 964 MET cc_start: 0.8438 (mmm) cc_final: 0.8206 (mpp) REVERT: B 1192 MET cc_start: 0.8672 (mmm) cc_final: 0.8300 (mmm) REVERT: B 1216 GLU cc_start: 0.8140 (tp30) cc_final: 0.7701 (tp30) REVERT: C 144 LEU cc_start: 0.9481 (mp) cc_final: 0.9239 (pp) REVERT: C 162 TYR cc_start: 0.8784 (m-10) cc_final: 0.8262 (m-80) REVERT: C 271 ASN cc_start: 0.9165 (m110) cc_final: 0.8754 (p0) REVERT: C 369 MET cc_start: 0.2096 (mtt) cc_final: 0.1577 (ppp) REVERT: C 396 MET cc_start: 0.4275 (ptt) cc_final: 0.2901 (tpt) REVERT: D 191 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7692 (t80) REVERT: D 204 CYS cc_start: 0.9310 (m) cc_final: 0.8966 (m) REVERT: D 321 LEU cc_start: 0.9119 (tp) cc_final: 0.8883 (pp) REVERT: D 323 SER cc_start: 0.8762 (t) cc_final: 0.8375 (m) REVERT: D 327 TYR cc_start: 0.8086 (m-10) cc_final: 0.7800 (m-10) REVERT: D 329 TYR cc_start: 0.8718 (m-80) cc_final: 0.7706 (m-80) REVERT: D 427 TYR cc_start: 0.9088 (m-10) cc_final: 0.8547 (m-80) REVERT: D 428 LEU cc_start: 0.9496 (mt) cc_final: 0.9213 (mt) REVERT: D 431 LYS cc_start: 0.9368 (tttt) cc_final: 0.9060 (mttt) REVERT: E 44 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 112 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8828 (mmtm) REVERT: E 116 LYS cc_start: 0.9283 (ptpp) cc_final: 0.8995 (ptpp) REVERT: E 119 GLN cc_start: 0.8821 (mt0) cc_final: 0.8535 (mp10) REVERT: E 159 PHE cc_start: 0.7795 (t80) cc_final: 0.7556 (t80) REVERT: E 160 MET cc_start: 0.8982 (tpp) cc_final: 0.8540 (tmm) outliers start: 54 outliers final: 46 residues processed: 394 average time/residue: 0.1817 time to fit residues: 110.0264 Evaluate side-chains 395 residues out of total 2651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 820 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 159 TRP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1213 TRP Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 239 optimal weight: 0.0470 chunk 187 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 GLN B1083 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062177 restraints weight = 113756.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064002 restraints weight = 61024.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065179 restraints weight = 40396.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066009 restraints weight = 30518.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066330 restraints weight = 25233.421| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24562 Z= 0.129 Angle : 0.788 15.084 33198 Z= 0.378 Chirality : 0.045 0.464 3688 Planarity : 0.004 0.090 4251 Dihedral : 6.905 178.936 3262 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 1.74 % Allowed : 20.03 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.50 (0.16), residues: 2949 helix: 1.43 (0.15), residues: 1276 sheet: 0.30 (0.27), residues: 360 loop : -0.74 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 95 TYR 0.027 0.001 TYR A 492 PHE 0.058 0.001 PHE E 108 TRP 0.017 0.001 TRP B1213 HIS 0.006 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24555) covalent geometry : angle 0.78569 / 0.38 (33192) hydrogen bonds : bond 0.03784 / 2.46 ( 1031) hydrogen bonds : angle 4.24794 / 2.96 ( 2946) metal coordination : bond 0.00405 / 0.21 ( 4) metal coordination : angle 4.89558 / 2.95 ( 6) Misc. bond : bond 0.00556 / 0.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4919.32 seconds wall clock time: 85 minutes 45.82 seconds (5145.82 seconds total)