Starting phenix.real_space_refine on Sat Jul 4 21:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx8_54361/07_2026/9rx8_54361.map" } resolution = 3.87 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= 0.003 sd= 0.025 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 2 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 14442 2.51 5 N 3920 2.21 5 O 4220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s 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: 22701 Number of models: 1 Model: "" Number of chains: 7 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16110 SG CYS C 18 42.275 134.476 39.383 1.00186.33 S ATOM 16136 SG CYS C 21 40.440 133.230 41.856 1.00195.76 S ATOM 16607 SG CYS C 137 38.946 137.020 40.960 1.00216.41 S ATOM 16631 SG CYS C 140 40.756 136.689 42.710 1.00236.92 S Time building chain proxies: 4.73, per 1000 atoms: 0.21 Number of scatterers: 22701 At special positions: 0 Unit cell: (104.39, 179.58, 245.28, 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 115 16.00 P 2 15.00 Mg 1 11.99 O 4220 8.00 N 3920 7.00 C 14442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.0 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 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 25 sheets defined 49.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.859A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.562A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY A 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 49 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 51 " --> pdb=" O GLY A 48 " (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: 3.938A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.623A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.849A pdb=" N HIS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.633A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.635A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.973A 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 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.526A pdb=" N LEU A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.684A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.527A 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 401 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.608A pdb=" N TYR A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.961A 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 500 removed outlier: 3.769A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.663A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.735A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.690A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 660 removed outlier: 4.259A 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: 3.509A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.664A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.993A pdb=" N MET A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 810 removed outlier: 3.642A pdb=" N ALA A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 810 " --> pdb=" O PHE A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.851A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.629A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.024A pdb=" N LYS A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 869 removed outlier: 3.553A 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 18 through 22 removed outlier: 3.868A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.795A pdb=" N LYS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.526A pdb=" N ILE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 121 through 141 removed outlier: 3.654A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.705A pdb=" N CYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.823A pdb=" N LEU B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.790A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.722A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 removed outlier: 3.517A pdb=" N ILE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.604A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.627A 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 415 Processing helix chain 'B' and resid 418 through 425 removed outlier: 3.756A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.685A pdb=" N LEU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.794A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 468 through 473' Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.740A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.754A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.911A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.083A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.656A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 567 " --> pdb=" O ARG B 563 " (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 removed outlier: 3.560A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 609 removed outlier: 4.252A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY B 603 " --> pdb=" O ASP B 599 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.544A 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: 3.818A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 removed outlier: 3.533A pdb=" N GLU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.800A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 666 " --> pdb=" O PHE B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.669A pdb=" N GLY B 674 " --> pdb=" O TRP B 670 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.652A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 725 through 733 removed outlier: 3.533A pdb=" N TYR B 731 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 780 through 790 removed outlier: 3.799A pdb=" N GLU B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 786 " --> pdb=" O GLU B 782 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 790 " --> pdb=" O LYS B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.547A pdb=" N MET B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.814A 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: 3.611A pdb=" N GLN B 945 " --> pdb=" O LYS B 941 " (cutoff:3.500A) removed outlier: 3.635A 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 1138 through 1142 removed outlier: 3.655A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.501A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.678A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.693A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.586A 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 170 removed outlier: 4.228A pdb=" N ASP C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 217 removed outlier: 3.889A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 267 removed outlier: 4.276A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 4.043A pdb=" N THR C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE C 274 " --> pdb=" O ASN C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.594A pdb=" N GLU C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE C 303 " --> pdb=" O TRP C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 303' Processing helix chain 'C' and resid 306 through 320 removed outlier: 3.965A pdb=" N GLN C 309 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 310 " --> pdb=" O TRP C 307 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL C 311 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU C 312 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 314 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 315 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 316 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 317 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 318 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 319 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.635A pdb=" N VAL C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 371 " --> pdb=" O HIS C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 372 through 375 removed outlier: 4.510A pdb=" N CYS C 375 " --> pdb=" O PHE C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.728A pdb=" N GLU C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.973A pdb=" N ALA C 428 " --> pdb=" O TRP C 425 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS C 430 " --> pdb=" O LYS C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 438 removed outlier: 3.795A pdb=" N ASN C 435 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.590A pdb=" N HIS D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 45' Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.602A pdb=" N LEU D 61 " --> pdb=" O GLY D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 192 through 224 Processing helix chain 'D' and resid 227 through 278 removed outlier: 3.992A pdb=" N LEU D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS D 243 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 324 removed outlier: 3.635A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 324 " --> pdb=" O GLN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.697A pdb=" N GLN D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 378 removed outlier: 3.669A pdb=" N HIS D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.518A pdb=" N LEU D 403 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 404 " --> pdb=" O ASP D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'D' and resid 419 through 422 removed outlier: 4.090A pdb=" N PHE D 422 " --> pdb=" O LYS D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 423 through 434 removed outlier: 4.739A pdb=" N ALA D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 440 removed outlier: 3.624A pdb=" N TYR D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 6.845A pdb=" N CYS A 223 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N LYS A 6 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N GLY A 232 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.574A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 114 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 12.344A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.546A pdb=" N GLY A 680 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 673 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.620A pdb=" N LEU A 750 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 758 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.301A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 176 removed outlier: 5.792A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 998 through 1001 removed outlier: 3.878A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1047 through 1050 removed outlier: 3.846A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B1060 " --> pdb=" O THR B1047 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1097 through 1103 removed outlier: 3.773A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 4.085A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B1159 " --> pdb=" O SER B1146 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 6.291A pdb=" N ALA B1203 " --> pdb=" O ARG B1188 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B1190 " --> pdb=" O ILE B1201 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B1201 " --> pdb=" O LEU B1190 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N MET B1192 " --> pdb=" O TRP B1199 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TRP B1199 " --> pdb=" O MET B1192 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1242 through 1247 removed outlier: 4.335A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B1256 " --> pdb=" O TRP B1268 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY B1260 " --> pdb=" O LYS B1264 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS B1264 " --> pdb=" O GLY B1260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1332 through 1339 Processing sheet with id=AB8, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 331 Processing sheet with id=AC2, first strand: chain 'C' and resid 394 through 397 Processing sheet with id=AC3, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=AC4, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.848A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.848A pdb=" N TYR D 81 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 113 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY D 119 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 127 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS D 121 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 5.280A 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: 3.948A 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 396 973 hydrogen bonds defined for protein. 2781 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: 4.67 Time building geometry restraints manager: 2.44 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: 7369 1.34 - 1.46: 3977 1.46 - 1.58: 11638 1.58 - 1.70: 3 1.70 - 1.81: 178 Bond restraints: 23165 Sorted by residual: bond pdb=" C ASP B 700 " pdb=" N PRO B 701 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.44e-02 4.82e+03 9.22e+00 bond pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.50e+00 bond pdb=" C GLU A 263 " pdb=" N ASN A 264 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.28e+00 bond pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" C HIS B1181 " pdb=" N PRO B1182 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.19e-02 7.06e+03 3.96e+00 ... (remaining 23160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 31020 2.78 - 5.56: 246 5.56 - 8.35: 31 8.35 - 11.13: 5 11.13 - 13.91: 6 Bond angle restraints: 31308 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 121.70 135.61 -13.91 1.80e+00 3.09e-01 5.97e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 134.86 -13.16 1.80e+00 3.09e-01 5.34e+01 angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 133.28 -11.58 1.80e+00 3.09e-01 4.14e+01 angle pdb=" C SER B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta sigma weight residual 121.70 132.55 -10.85 1.80e+00 3.09e-01 3.63e+01 angle pdb=" C LYS B 371 " pdb=" N GLU B 372 " pdb=" CA GLU B 372 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 ... (remaining 31303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 13604 28.13 - 56.27: 416 56.27 - 84.40: 71 84.40 - 112.54: 10 112.54 - 140.67: 1 Dihedral angle restraints: 14102 sinusoidal: 5864 harmonic: 8238 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 38.53 -38.53 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" O2B GDP B1401 " pdb=" O3A GDP B1401 " pdb=" PB GDP B1401 " pdb=" PA GDP B1401 " ideal model delta sinusoidal sigma weight residual 180.00 39.33 140.67 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta harmonic sigma weight residual 0.00 30.61 -30.61 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 14099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2731 0.049 - 0.097: 566 0.097 - 0.146: 161 0.146 - 0.194: 18 0.194 - 0.243: 1 Chirality restraints: 3477 Sorted by residual: chirality pdb=" CB VAL B 986 " pdb=" CA VAL B 986 " pdb=" CG1 VAL B 986 " pdb=" CG2 VAL B 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 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 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CB ILE B1176 " pdb=" CA ILE B1176 " pdb=" CG1 ILE B1176 " pdb=" CG2 ILE B1176 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 3474 not shown) Planarity restraints: 4015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 650 " 0.060 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 651 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 651 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 651 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 667 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 661 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO B 662 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 662 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 662 " 0.036 5.00e-02 4.00e+02 ... (remaining 4012 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 251 2.66 - 3.22: 19146 3.22 - 3.78: 32784 3.78 - 4.34: 43411 4.34 - 4.90: 71873 Nonbonded interactions: 167465 Sorted by model distance: nonbonded pdb=" O3A GDP B1401 " pdb="MG MG B1402 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1402 " model vdw 2.172 2.170 nonbonded pdb=" OE1 GLN B 292 " pdb=" OH TYR B 307 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 130 " pdb=" OE1 GLN D 203 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR B 157 " pdb=" O TRP B 159 " model vdw 2.312 3.040 ... (remaining 167460 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 23.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.099 23170 Z= 0.190 Angle : 0.820 43.811 31314 Z= 0.431 Chirality : 0.044 0.243 3477 Planarity : 0.006 0.090 4015 Dihedral : 14.267 140.670 8758 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.34 % 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: -1.53 (0.14), residues: 2781 helix: -1.05 (0.13), residues: 1187 sheet: -0.26 (0.29), residues: 311 loop : -1.04 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 81 TYR 0.041 0.002 TYR B 307 PHE 0.018 0.002 PHE A 703 TRP 0.019 0.001 TRP D 131 HIS 0.009 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.18 (23165) covalent geometry : angle 0.73347 / 0.43 (31308) hydrogen bonds : bond 0.20147 / 12.71 ( 966) hydrogen bonds : angle 6.36514 / 4.19 ( 2781) metal coordination : bond 0.04770 / 1.92 ( 4) metal coordination : angle 26.55587 / 15.71 ( 6) Misc. bond : bond 0.09922 / 5.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.976 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: A 203 MET cc_start: 0.9421 (mpt) cc_final: 0.8997 (mpt) REVERT: A 538 MET cc_start: 0.9415 (mtm) cc_final: 0.9129 (mmt) REVERT: A 787 MET cc_start: 0.9021 (ptp) cc_final: 0.8680 (ptp) REVERT: B 155 MET cc_start: 0.8602 (mmm) cc_final: 0.7859 (mmm) REVERT: B 1258 THR cc_start: 0.6979 (p) cc_final: 0.5910 (p) REVERT: C 172 MET cc_start: 0.7280 (pmm) cc_final: 0.6983 (pmm) REVERT: C 338 TYR cc_start: 0.7890 (p90) cc_final: 0.7610 (p90) REVERT: C 396 MET cc_start: -0.6168 (ptt) cc_final: -0.6389 (ttm) REVERT: C 432 MET cc_start: -0.7624 (tpt) cc_final: -0.7915 (mmt) REVERT: D 97 LEU cc_start: 0.8780 (mt) cc_final: 0.8441 (tt) REVERT: D 463 MET cc_start: 0.1911 (mmt) cc_final: 0.1023 (mmt) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.1710 time to fit residues: 40.5023 Evaluate side-chains 98 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 370 HIS B 58 GLN B 314 ASN B 457 ASN B 485 ASN B 506 ASN B1137 HIS C 181 GLN C 275 HIS C 446 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.054913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037085 restraints weight = 196343.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037509 restraints weight = 126667.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.037654 restraints weight = 86508.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037816 restraints weight = 75886.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.037874 restraints weight = 67112.034| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23170 Z= 0.230 Angle : 0.677 16.380 31314 Z= 0.342 Chirality : 0.042 0.225 3477 Planarity : 0.005 0.080 4015 Dihedral : 5.670 136.615 3069 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.42 % Favored : 96.44 % Rotamer: Outliers : 0.96 % Allowed : 7.69 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.03 (0.16), residues: 2781 helix: 0.93 (0.15), residues: 1209 sheet: -0.29 (0.29), residues: 293 loop : -0.73 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 952 TYR 0.030 0.002 TYR B 307 PHE 0.020 0.002 PHE B 331 TRP 0.019 0.002 TRP B1213 HIS 0.010 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (23165) covalent geometry : angle 0.66261 / 0.34 (31308) hydrogen bonds : bond 0.04388 / 2.86 ( 966) hydrogen bonds : angle 4.60921 / 3.09 ( 2781) metal coordination : bond 0.00431 / 0.20 ( 4) metal coordination : angle 10.22279 / 5.89 ( 6) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 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: A 152 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 172 MET cc_start: 0.5822 (mmt) cc_final: 0.5612 (mmt) REVERT: A 187 MET cc_start: 0.2724 (ttt) cc_final: 0.2294 (ttt) REVERT: A 218 MET cc_start: 0.8686 (mmm) cc_final: 0.8364 (tpt) REVERT: A 538 MET cc_start: 0.9647 (mtm) cc_final: 0.9354 (mmt) REVERT: A 787 MET cc_start: 0.8881 (ptp) cc_final: 0.8532 (ptp) REVERT: B 568 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 696 MET cc_start: 0.9112 (tpp) cc_final: 0.8757 (mpp) REVERT: B 990 HIS cc_start: 0.8128 (m90) cc_final: 0.7649 (t-90) REVERT: B 1170 MET cc_start: 0.8236 (mtp) cc_final: 0.7862 (mpp) REVERT: B 1263 MET cc_start: 0.7492 (mtt) cc_final: 0.6627 (mpp) REVERT: B 1339 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5546 (tt0) REVERT: C 172 MET cc_start: 0.7217 (pmm) cc_final: 0.6665 (pmm) REVERT: C 432 MET cc_start: -0.7092 (tpt) cc_final: -0.7476 (mmt) REVERT: D 97 LEU cc_start: 0.9003 (mt) cc_final: 0.8481 (tt) REVERT: D 458 MET cc_start: 0.2229 (mmt) cc_final: 0.1691 (mmt) REVERT: D 463 MET cc_start: 0.3589 (mmt) cc_final: 0.1715 (mmt) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.1628 time to fit residues: 30.8228 Evaluate side-chains 98 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 402 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 274 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 273 optimal weight: 2.9990 chunk 233 optimal weight: 40.0000 chunk 165 optimal weight: 0.0010 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 0.0020 chunk 139 optimal weight: 5.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS A 554 HIS D 59 HIS D 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.055831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036493 restraints weight = 192550.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.037486 restraints weight = 111767.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.038179 restraints weight = 77810.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.038611 restraints weight = 60887.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.038838 restraints weight = 51878.873| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23170 Z= 0.095 Angle : 0.528 15.289 31314 Z= 0.266 Chirality : 0.039 0.151 3477 Planarity : 0.004 0.069 4015 Dihedral : 5.205 121.693 3068 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.02 % Rotamer: Outliers : 0.88 % Allowed : 8.21 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.51 (0.16), residues: 2781 helix: 1.43 (0.15), residues: 1213 sheet: -0.06 (0.29), residues: 304 loop : -0.61 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 952 TYR 0.024 0.001 TYR A 803 PHE 0.013 0.001 PHE B 170 TRP 0.015 0.001 TRP C 438 HIS 0.004 0.000 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 (23165) covalent geometry : angle 0.51267 / 0.26 (31308) hydrogen bonds : bond 0.03627 / 2.35 ( 966) hydrogen bonds : angle 4.13509 / 2.78 ( 2781) metal coordination : bond 0.00599 / 0.31 ( 4) metal coordination : angle 9.03932 / 5.37 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7046 (p0) REVERT: A 187 MET cc_start: 0.2269 (ttt) cc_final: 0.1872 (ttt) REVERT: A 218 MET cc_start: 0.8728 (mmm) cc_final: 0.8516 (tpp) REVERT: A 538 MET cc_start: 0.9630 (mtm) cc_final: 0.9351 (mmt) REVERT: A 583 MET cc_start: 0.6480 (mmt) cc_final: 0.5807 (mmt) REVERT: A 783 MET cc_start: 0.8796 (tmm) cc_final: 0.8538 (tmm) REVERT: B 155 MET cc_start: 0.9000 (mmm) cc_final: 0.8157 (mmm) REVERT: B 166 ASP cc_start: 0.8049 (t0) cc_final: 0.7769 (t0) REVERT: B 568 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 1170 MET cc_start: 0.8239 (mtp) cc_final: 0.7930 (mtp) REVERT: B 1339 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5669 (tt0) REVERT: C 172 MET cc_start: 0.7163 (pmm) cc_final: 0.6845 (pmm) REVERT: C 432 MET cc_start: -0.7127 (tpt) cc_final: -0.7390 (mmt) REVERT: D 97 LEU cc_start: 0.8977 (mt) cc_final: 0.8398 (tt) REVERT: D 458 MET cc_start: 0.2043 (mmt) cc_final: 0.1555 (mmt) REVERT: D 463 MET cc_start: 0.3641 (mmt) cc_final: 0.1935 (mmt) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 0.1424 time to fit residues: 25.1671 Evaluate side-chains 99 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 402 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 254 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN B 387 GLN B1086 GLN ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.053475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.036466 restraints weight = 198414.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036115 restraints weight = 116838.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036284 restraints weight = 104519.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036308 restraints weight = 86742.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.036389 restraints weight = 77526.701| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23170 Z= 0.232 Angle : 0.663 12.306 31314 Z= 0.331 Chirality : 0.042 0.185 3477 Planarity : 0.004 0.068 4015 Dihedral : 5.361 121.455 3068 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 1.51 % Allowed : 8.61 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.63 (0.16), residues: 2781 helix: 1.65 (0.15), residues: 1209 sheet: -0.41 (0.27), residues: 308 loop : -0.53 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 672 TYR 0.031 0.002 TYR C 333 PHE 0.018 0.002 PHE B 331 TRP 0.016 0.001 TRP B1357 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (23165) covalent geometry : angle 0.65337 / 0.33 (31308) hydrogen bonds : bond 0.04031 / 2.64 ( 966) hydrogen bonds : angle 4.35453 / 2.94 ( 2781) metal coordination : bond 0.00456 / 0.20 ( 4) metal coordination : angle 8.10575 / 4.68 ( 6) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7603 (p0) REVERT: A 172 MET cc_start: 0.5394 (mmt) cc_final: 0.5124 (mmt) REVERT: A 215 MET cc_start: 0.8849 (mmm) cc_final: 0.8591 (mmp) REVERT: A 218 MET cc_start: 0.8759 (mmm) cc_final: 0.8546 (tpp) REVERT: A 262 MET cc_start: 0.8773 (mpp) cc_final: 0.8428 (mpp) REVERT: A 538 MET cc_start: 0.9645 (mtm) cc_final: 0.9377 (mmt) REVERT: A 722 MET cc_start: 0.9168 (ptp) cc_final: 0.8858 (ptp) REVERT: A 783 MET cc_start: 0.9069 (tmm) cc_final: 0.8780 (tmm) REVERT: B 568 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7796 (t80) REVERT: B 696 MET cc_start: 0.9235 (tpp) cc_final: 0.8936 (mpp) REVERT: B 1170 MET cc_start: 0.8157 (mtp) cc_final: 0.7858 (mtp) REVERT: B 1263 MET cc_start: 0.7652 (mtt) cc_final: 0.7022 (mmt) REVERT: B 1339 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: C 172 MET cc_start: 0.7139 (pmm) cc_final: 0.6708 (pmm) REVERT: C 254 MET cc_start: 0.9245 (mmm) cc_final: 0.9042 (mmm) REVERT: C 432 MET cc_start: -0.6723 (tpt) cc_final: -0.7029 (mmt) REVERT: D 42 LEU cc_start: 0.9790 (OUTLIER) cc_final: 0.9582 (tt) REVERT: D 458 MET cc_start: 0.2154 (mmt) cc_final: 0.1574 (mmt) REVERT: D 463 MET cc_start: 0.3997 (mmt) cc_final: 0.2121 (mmt) outliers start: 38 outliers final: 22 residues processed: 117 average time/residue: 0.1337 time to fit residues: 26.7243 Evaluate side-chains 102 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 236 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 273 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN A 794 GLN B 3 ASN B 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.052809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034181 restraints weight = 198559.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035020 restraints weight = 117761.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035585 restraints weight = 83489.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035996 restraints weight = 66206.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036249 restraints weight = 56925.058| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23170 Z= 0.207 Angle : 0.619 14.365 31314 Z= 0.312 Chirality : 0.041 0.187 3477 Planarity : 0.004 0.071 4015 Dihedral : 5.363 116.390 3068 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.33 % Rotamer: Outliers : 1.63 % Allowed : 9.37 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.69 (0.16), residues: 2781 helix: 1.75 (0.15), residues: 1217 sheet: -0.54 (0.27), residues: 305 loop : -0.53 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 561 TYR 0.044 0.002 TYR C 333 PHE 0.018 0.001 PHE A 612 TRP 0.015 0.001 TRP C 438 HIS 0.006 0.001 HIS B1193 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (23165) covalent geometry : angle 0.60918 / 0.31 (31308) hydrogen bonds : bond 0.03693 / 2.41 ( 966) hydrogen bonds : angle 4.29519 / 2.91 ( 2781) metal coordination : bond 0.00452 / 0.21 ( 4) metal coordination : angle 8.08266 / 4.73 ( 6) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9496 (tpt) cc_final: 0.9225 (tpt) REVERT: A 172 MET cc_start: 0.5483 (mmt) cc_final: 0.4623 (mmt) REVERT: A 187 MET cc_start: 0.2669 (ttt) cc_final: 0.2388 (ttt) REVERT: A 218 MET cc_start: 0.8779 (mmm) cc_final: 0.8543 (tpp) REVERT: A 538 MET cc_start: 0.9634 (mtm) cc_final: 0.9363 (mmt) REVERT: A 556 MET cc_start: 0.9613 (mmm) cc_final: 0.9301 (tpt) REVERT: A 787 MET cc_start: 0.8722 (ptp) cc_final: 0.7881 (ptp) REVERT: B 1263 MET cc_start: 0.7942 (mtt) cc_final: 0.7291 (mmt) REVERT: B 1339 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.6031 (tt0) REVERT: C 137 CYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5228 (p) REVERT: C 172 MET cc_start: 0.7153 (pmm) cc_final: 0.6657 (pmm) REVERT: D 458 MET cc_start: 0.1983 (mmt) cc_final: 0.1394 (mmt) REVERT: D 463 MET cc_start: 0.3994 (mmt) cc_final: 0.2470 (mmt) outliers start: 41 outliers final: 24 residues processed: 112 average time/residue: 0.1327 time to fit residues: 25.6794 Evaluate side-chains 99 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 59 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 196 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.053225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034558 restraints weight = 198360.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035485 restraints weight = 115539.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036098 restraints weight = 81335.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036479 restraints weight = 64347.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036660 restraints weight = 55287.788| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23170 Z= 0.122 Angle : 0.552 12.983 31314 Z= 0.276 Chirality : 0.040 0.155 3477 Planarity : 0.003 0.069 4015 Dihedral : 5.096 109.543 3068 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 1.39 % Allowed : 10.08 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.95 (0.17), residues: 2781 helix: 2.04 (0.16), residues: 1206 sheet: -0.46 (0.28), residues: 306 loop : -0.45 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 952 TYR 0.023 0.001 TYR A 803 PHE 0.011 0.001 PHE B 170 TRP 0.015 0.001 TRP C 438 HIS 0.004 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23165) covalent geometry : angle 0.54241 / 0.28 (31308) hydrogen bonds : bond 0.03309 / 2.15 ( 966) hydrogen bonds : angle 4.04474 / 2.73 ( 2781) metal coordination : bond 0.00376 / 0.20 ( 4) metal coordination : angle 7.25228 / 4.25 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9492 (tpt) cc_final: 0.9282 (tpt) REVERT: A 172 MET cc_start: 0.5090 (mmt) cc_final: 0.4582 (mmt) REVERT: A 218 MET cc_start: 0.8799 (mmm) cc_final: 0.8588 (tpp) REVERT: A 538 MET cc_start: 0.9620 (mtm) cc_final: 0.9351 (mmt) REVERT: A 556 MET cc_start: 0.9579 (mmm) cc_final: 0.9379 (mmm) REVERT: A 583 MET cc_start: 0.6427 (mmt) cc_final: 0.5673 (mtp) REVERT: A 722 MET cc_start: 0.9215 (ptp) cc_final: 0.8874 (ptp) REVERT: B 318 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8586 (tp30) REVERT: B 568 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 581 MET cc_start: 0.8981 (mmm) cc_final: 0.8665 (tpp) REVERT: B 1263 MET cc_start: 0.8028 (mtt) cc_final: 0.7385 (mmt) REVERT: B 1339 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6069 (tt0) REVERT: C 137 CYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5078 (p) REVERT: C 172 MET cc_start: 0.7026 (pmm) cc_final: 0.6530 (pmm) REVERT: D 373 MET cc_start: 0.6136 (ppp) cc_final: 0.5381 (pmm) REVERT: D 458 MET cc_start: 0.2212 (mmt) cc_final: 0.1582 (mmp) REVERT: D 463 MET cc_start: 0.4011 (mmt) cc_final: 0.2812 (mmt) outliers start: 35 outliers final: 20 residues processed: 104 average time/residue: 0.1337 time to fit residues: 24.2570 Evaluate side-chains 97 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 59 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 263 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 249 ASN D 453 ASN D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.052521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.033988 restraints weight = 201172.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034886 restraints weight = 117289.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035455 restraints weight = 82199.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035760 restraints weight = 65424.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036019 restraints weight = 56877.026| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23170 Z= 0.166 Angle : 0.584 12.899 31314 Z= 0.292 Chirality : 0.040 0.179 3477 Planarity : 0.003 0.068 4015 Dihedral : 5.127 110.069 3068 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 1.28 % Allowed : 10.44 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.37 % 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: 0.90 (0.17), residues: 2781 helix: 2.01 (0.16), residues: 1210 sheet: -0.50 (0.28), residues: 312 loop : -0.49 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 75 TYR 0.043 0.001 TYR A 58 PHE 0.016 0.001 PHE B 630 TRP 0.015 0.001 TRP C 438 HIS 0.004 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (23165) covalent geometry : angle 0.57565 / 0.29 (31308) hydrogen bonds : bond 0.03434 / 2.23 ( 966) hydrogen bonds : angle 4.14097 / 2.81 ( 2781) metal coordination : bond 0.00369 / 0.18 ( 4) metal coordination : angle 6.92400 / 4.06 ( 6) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.5237 (mmt) cc_final: 0.4706 (mmt) REVERT: A 218 MET cc_start: 0.8792 (mmm) cc_final: 0.8587 (tpp) REVERT: A 262 MET cc_start: 0.8742 (mpp) cc_final: 0.8265 (mpp) REVERT: A 538 MET cc_start: 0.9624 (mtm) cc_final: 0.9354 (mmt) REVERT: A 556 MET cc_start: 0.9628 (mmm) cc_final: 0.9409 (mmm) REVERT: A 583 MET cc_start: 0.6592 (mmt) cc_final: 0.5963 (mtp) REVERT: A 787 MET cc_start: 0.8723 (ptp) cc_final: 0.7722 (ptp) REVERT: B 318 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8525 (tp30) REVERT: B 568 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 1263 MET cc_start: 0.8139 (mtt) cc_final: 0.7440 (mmt) REVERT: B 1339 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.6053 (tt0) REVERT: C 137 CYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5133 (p) REVERT: C 172 MET cc_start: 0.6932 (pmm) cc_final: 0.6399 (pmm) REVERT: C 321 MET cc_start: -0.2492 (ttt) cc_final: -0.2971 (tpt) REVERT: D 42 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9561 (tt) REVERT: D 458 MET cc_start: 0.2297 (mmt) cc_final: 0.1686 (mmp) REVERT: D 463 MET cc_start: 0.4188 (mmt) cc_final: 0.3118 (mmt) outliers start: 32 outliers final: 23 residues processed: 102 average time/residue: 0.1360 time to fit residues: 23.8597 Evaluate side-chains 102 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 249 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 30.0000 chunk 278 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 223 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 chunk 232 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 546 GLN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1329 HIS ** D 283 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 = 0.3513 r_free = 0.3513 target = 0.050951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.033415 restraints weight = 204160.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034426 restraints weight = 128117.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034480 restraints weight = 79628.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034566 restraints weight = 65530.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.034644 restraints weight = 66944.129| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 23170 Z= 0.264 Angle : 0.720 12.236 31314 Z= 0.359 Chirality : 0.043 0.201 3477 Planarity : 0.004 0.064 4015 Dihedral : 5.647 118.934 3068 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 10.24 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.37 % Twisted Proline : 0.88 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2781 helix: 1.55 (0.15), residues: 1210 sheet: -0.55 (0.29), residues: 298 loop : -0.66 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 222 TYR 0.071 0.002 TYR A 58 PHE 0.028 0.002 PHE B 630 TRP 0.019 0.002 TRP C 438 HIS 0.007 0.002 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 (23165) covalent geometry : angle 0.71288 / 0.36 (31308) hydrogen bonds : bond 0.04130 / 2.70 ( 966) hydrogen bonds : angle 4.55551 / 3.12 ( 2781) metal coordination : bond 0.00450 / 0.20 ( 4) metal coordination : angle 7.29533 / 4.22 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 76 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9672 (tpt) cc_final: 0.9446 (tpp) REVERT: A 172 MET cc_start: 0.5339 (mmt) cc_final: 0.4874 (mmt) REVERT: A 538 MET cc_start: 0.9644 (mtm) cc_final: 0.9360 (mmt) REVERT: A 556 MET cc_start: 0.9673 (mmm) cc_final: 0.9463 (mmm) REVERT: A 583 MET cc_start: 0.7014 (mmt) cc_final: 0.6423 (mtp) REVERT: A 787 MET cc_start: 0.8592 (ptp) cc_final: 0.7973 (ptp) REVERT: B 318 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: B 568 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 1263 MET cc_start: 0.8236 (mtt) cc_final: 0.7489 (mmt) REVERT: B 1339 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6150 (mt0) REVERT: C 137 CYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5609 (p) REVERT: C 172 MET cc_start: 0.6648 (pmm) cc_final: 0.6010 (pmm) REVERT: D 42 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9540 (tt) REVERT: D 373 MET cc_start: 0.6671 (ppp) cc_final: 0.6131 (pmm) REVERT: D 458 MET cc_start: 0.2492 (mmt) cc_final: 0.1807 (mmp) REVERT: D 463 MET cc_start: 0.4739 (mmt) cc_final: 0.3439 (mmt) outliers start: 45 outliers final: 29 residues processed: 113 average time/residue: 0.1420 time to fit residues: 27.6590 Evaluate side-chains 109 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 272 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 275 optimal weight: 0.0370 chunk 174 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 794 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.051249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.034752 restraints weight = 203226.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034754 restraints weight = 118857.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.034914 restraints weight = 92429.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035002 restraints weight = 86833.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035043 restraints weight = 74877.134| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23170 Z= 0.181 Angle : 0.627 13.082 31314 Z= 0.312 Chirality : 0.041 0.171 3477 Planarity : 0.004 0.090 4015 Dihedral : 5.458 115.472 3068 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.83 % Rotamer: Outliers : 1.28 % Allowed : 10.88 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.37 % Twisted Proline : 0.88 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2781 helix: 1.75 (0.15), residues: 1209 sheet: -0.56 (0.29), residues: 298 loop : -0.62 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 75 TYR 0.071 0.001 TYR A 58 PHE 0.021 0.001 PHE B 630 TRP 0.015 0.001 TRP C 438 HIS 0.009 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (23165) covalent geometry : angle 0.61877 / 0.31 (31308) hydrogen bonds : bond 0.03621 / 2.36 ( 966) hydrogen bonds : angle 4.33845 / 2.96 ( 2781) metal coordination : bond 0.00356 / 0.17 ( 4) metal coordination : angle 7.22333 / 4.21 ( 6) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.5461 (mmt) cc_final: 0.4997 (mmt) REVERT: A 187 MET cc_start: 0.4018 (ttt) cc_final: 0.3669 (ttt) REVERT: A 538 MET cc_start: 0.9636 (mtm) cc_final: 0.9361 (mmt) REVERT: A 556 MET cc_start: 0.9653 (mmm) cc_final: 0.9421 (mmm) REVERT: A 583 MET cc_start: 0.7086 (mmt) cc_final: 0.6539 (mtp) REVERT: A 722 MET cc_start: 0.9214 (ptp) cc_final: 0.8968 (ptp) REVERT: A 787 MET cc_start: 0.8651 (ptp) cc_final: 0.7977 (ptp) REVERT: B 318 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: B 1165 MET cc_start: 0.7984 (ppp) cc_final: 0.7677 (ppp) REVERT: B 1263 MET cc_start: 0.8394 (mtt) cc_final: 0.7670 (mmt) REVERT: B 1339 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6198 (mt0) REVERT: C 126 MET cc_start: 0.9764 (mtm) cc_final: 0.9492 (ptt) REVERT: C 137 CYS cc_start: 0.6584 (OUTLIER) cc_final: 0.5964 (p) REVERT: C 172 MET cc_start: 0.6708 (pmm) cc_final: 0.6041 (pmm) REVERT: D 458 MET cc_start: 0.2742 (mmt) cc_final: 0.2096 (mmp) REVERT: D 463 MET cc_start: 0.4763 (mmt) cc_final: 0.3418 (mmt) outliers start: 32 outliers final: 25 residues processed: 104 average time/residue: 0.1323 time to fit residues: 23.9281 Evaluate side-chains 101 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.0060 chunk 200 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 0.0570 chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.052243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035910 restraints weight = 198855.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035669 restraints weight = 115916.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.035721 restraints weight = 95254.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035846 restraints weight = 77920.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.035859 restraints weight = 69079.925| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23170 Z= 0.099 Angle : 0.562 12.283 31314 Z= 0.279 Chirality : 0.040 0.162 3477 Planarity : 0.003 0.069 4015 Dihedral : 5.093 105.745 3068 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 1.08 % Allowed : 11.08 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.37 % Twisted Proline : 0.88 % 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: 1.00 (0.17), residues: 2781 helix: 2.13 (0.16), residues: 1200 sheet: -0.47 (0.29), residues: 300 loop : -0.45 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 75 TYR 0.049 0.001 TYR A 58 PHE 0.019 0.001 PHE B 167 TRP 0.019 0.001 TRP C 438 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (23165) covalent geometry : angle 0.55437 / 0.28 (31308) hydrogen bonds : bond 0.03128 / 2.03 ( 966) hydrogen bonds : angle 3.97806 / 2.71 ( 2781) metal coordination : bond 0.00474 / 0.25 ( 4) metal coordination : angle 6.63455 / 3.91 ( 6) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.5345 (mmt) cc_final: 0.4968 (mmt) REVERT: A 187 MET cc_start: 0.3697 (ttt) cc_final: 0.3376 (ttt) REVERT: A 262 MET cc_start: 0.8648 (mpp) cc_final: 0.8188 (mpp) REVERT: A 516 MET cc_start: 0.9217 (tmm) cc_final: 0.8928 (ppp) REVERT: A 538 MET cc_start: 0.9625 (mtm) cc_final: 0.9355 (mmt) REVERT: A 556 MET cc_start: 0.9655 (mmm) cc_final: 0.9417 (mmm) REVERT: A 583 MET cc_start: 0.7204 (mmt) cc_final: 0.6915 (ptm) REVERT: A 617 MET cc_start: 0.8185 (ppp) cc_final: 0.7895 (ppp) REVERT: A 722 MET cc_start: 0.9203 (ptp) cc_final: 0.8926 (ptp) REVERT: A 748 ASN cc_start: 0.9554 (OUTLIER) cc_final: 0.8999 (p0) REVERT: A 787 MET cc_start: 0.8613 (ptp) cc_final: 0.8028 (ptp) REVERT: B 100 MET cc_start: 0.9157 (mtt) cc_final: 0.8918 (ptp) REVERT: B 155 MET cc_start: 0.8977 (mmm) cc_final: 0.8182 (mmm) REVERT: B 318 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: B 1165 MET cc_start: 0.7930 (ppp) cc_final: 0.7589 (ppp) REVERT: B 1263 MET cc_start: 0.8427 (mtt) cc_final: 0.7795 (mmt) REVERT: B 1339 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6074 (mt0) REVERT: C 126 MET cc_start: 0.9721 (mtm) cc_final: 0.9482 (ptt) REVERT: C 137 CYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5685 (p) REVERT: C 172 MET cc_start: 0.6852 (pmm) cc_final: 0.6244 (pmm) REVERT: D 42 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9556 (tt) REVERT: D 458 MET cc_start: 0.2808 (mmt) cc_final: 0.2169 (mmp) REVERT: D 463 MET cc_start: 0.4838 (mmt) cc_final: 0.3503 (mmt) outliers start: 27 outliers final: 18 residues processed: 101 average time/residue: 0.1202 time to fit residues: 20.8144 Evaluate side-chains 97 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1339 GLN Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 83 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 277 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.050683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032531 restraints weight = 206254.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033403 restraints weight = 117078.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033943 restraints weight = 81731.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034337 restraints weight = 64694.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.034541 restraints weight = 55384.028| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23170 Z= 0.253 Angle : 0.704 12.508 31314 Z= 0.350 Chirality : 0.042 0.164 3477 Planarity : 0.004 0.104 4015 Dihedral : 5.507 116.277 3068 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 1.12 % Allowed : 11.12 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.37 % Twisted Proline : 0.88 % Twisted General : 0.11 % 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: 0.60 (0.17), residues: 2781 helix: 1.73 (0.15), residues: 1217 sheet: -0.63 (0.28), residues: 312 loop : -0.63 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 75 TYR 0.025 0.002 TYR A 58 PHE 0.021 0.002 PHE D 307 TRP 0.015 0.002 TRP C 438 HIS 0.007 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (23165) covalent geometry : angle 0.69872 / 0.35 (31308) hydrogen bonds : bond 0.03888 / 2.55 ( 966) hydrogen bonds : angle 4.40872 / 3.02 ( 2781) metal coordination : bond 0.00394 / 0.18 ( 4) metal coordination : angle 6.38727 / 3.70 ( 6) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4315.40 seconds wall clock time: 75 minutes 16.62 seconds (4516.62 seconds total)