Starting phenix.real_space_refine on Sun Jun 22 10:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygk_39254/06_2025/8ygk_39254.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.037 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 9212 2.51 5 N 2292 2.21 5 O 2714 1.98 5 H 11642 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25916 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "C" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 1 Chain: "A" Number of atoms: 11760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11760 Classifications: {'peptide': 708} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 698} Chain: "B" Number of atoms: 11760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11760 Classifications: {'peptide': 708} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 698} Time building chain proxies: 13.62, per 1000 atoms: 0.53 Number of scatterers: 25916 At special positions: 0 Unit cell: (117.03, 112.88, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2714 8.00 N 2292 7.00 C 9212 6.00 H 11642 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 2.2 seconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 5 sheets defined 61.6% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.450A pdb=" N ARG D 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.649A pdb=" N GLY D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.649A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.741A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.355A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.794A pdb=" N SER A 371 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 374 through 392 removed outlier: 3.562A pdb=" N PHE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.513A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.666A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.760A pdb=" N PHE A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.656A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 459 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 495 removed outlier: 4.578A pdb=" N TYR A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.632A pdb=" N PHE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.553A pdb=" N ASP A 526 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 531 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 542 through 547 removed outlier: 4.266A pdb=" N ASP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 571 removed outlier: 3.599A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 599 removed outlier: 3.553A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.684A pdb=" N TYR A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 651 through 659 removed outlier: 3.699A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.721A pdb=" N LYS A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.633A pdb=" N ILE A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 685 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.759A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.690A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 738 " --> pdb=" O GLY A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 4.108A pdb=" N TYR A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 761 " --> pdb=" O TRP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.561A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 810 removed outlier: 4.099A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.536A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.934A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 903 removed outlier: 3.576A pdb=" N GLU A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 removed outlier: 3.555A pdb=" N ILE A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 4.125A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 944 removed outlier: 3.878A pdb=" N PHE A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 957 through 961 Processing helix chain 'A' and resid 963 through 970 removed outlier: 3.518A pdb=" N LYS A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 977 Processing helix chain 'A' and resid 979 through 991 Processing helix chain 'A' and resid 993 through 1003 removed outlier: 3.788A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.682A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.908A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.219A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.571A pdb=" N PHE B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.556A pdb=" N SER B 371 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 Processing helix chain 'B' and resid 417 through 427 removed outlier: 3.512A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.926A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.718A pdb=" N TYR B 452 " --> pdb=" O TRP B 448 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 468 through 495 removed outlier: 3.803A pdb=" N ASN B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 495 " --> pdb=" O GLN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.551A pdb=" N GLY B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.501A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.725A pdb=" N MET B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 3.652A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 removed outlier: 4.002A pdb=" N PHE B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 551 through 569 removed outlier: 3.581A pdb=" N VAL B 556 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.981A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG B 593 " --> pdb=" O TYR B 589 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 595 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 626 removed outlier: 3.513A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.533A pdb=" N VAL B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.804A pdb=" N LYS B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 670 " --> pdb=" O ASN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 682 through 701 removed outlier: 3.634A pdb=" N GLU B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.783A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 713 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.688A pdb=" N VAL B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 removed outlier: 4.042A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 763 removed outlier: 3.611A pdb=" N LYS B 763 " --> pdb=" O ARG B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 760 through 763' Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.675A pdb=" N LEU B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.835A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 removed outlier: 3.709A pdb=" N CYS B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 841 removed outlier: 4.289A pdb=" N ASP B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE B 837 " --> pdb=" O LYS B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.719A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.553A pdb=" N ILE B 871 " --> pdb=" O ASN B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 902 removed outlier: 3.657A pdb=" N THR B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.600A pdb=" N TYR B 920 " --> pdb=" O PHE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.678A pdb=" N MET B 930 " --> pdb=" O ASN B 927 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.739A pdb=" N PHE B 942 " --> pdb=" O ASP B 938 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 945 " --> pdb=" O ASP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.836A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 removed outlier: 3.545A pdb=" N GLY B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.743A pdb=" N VAL B 983 " --> pdb=" O HIS B 979 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.583A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.608A pdb=" N ALA D 232 " --> pdb=" O PHE A 907 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 32 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 24 removed outlier: 3.655A pdb=" N LYS C 20 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 233 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 596 hydrogen bonds defined for protein. 1683 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: 9.87 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11626 1.03 - 1.23: 199 1.23 - 1.43: 6216 1.43 - 1.63: 8091 1.63 - 1.82: 96 Bond restraints: 26228 Sorted by residual: bond pdb=" N GLU A 298 " pdb=" H1 GLU A 298 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU B 298 " pdb=" H1 GLU B 298 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ILE B 862 " pdb=" CA ILE B 862 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.32e-02 5.74e+03 1.49e+01 bond pdb=" N GLU B 860 " pdb=" CA GLU B 860 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.24e+01 bond pdb=" N ASN B 861 " pdb=" CA ASN B 861 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.42e-02 4.96e+03 1.12e+01 ... (remaining 26223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 46108 10.92 - 21.83: 3 21.83 - 32.75: 1 32.75 - 43.67: 2 43.67 - 54.59: 6 Bond angle restraints: 46120 Sorted by residual: angle pdb=" C SER A 851 " pdb=" N HIS A 852 " pdb=" H HIS A 852 " ideal model delta sigma weight residual 125.01 70.42 54.59 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CA HIS A 852 " pdb=" N HIS A 852 " pdb=" H HIS A 852 " ideal model delta sigma weight residual 114.71 60.33 54.38 3.00e+00 1.11e-01 3.29e+02 angle pdb=" C VAL A 859 " pdb=" N GLU A 860 " pdb=" H GLU A 860 " ideal model delta sigma weight residual 125.48 73.97 51.50 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C SER A 858 " pdb=" N VAL A 859 " pdb=" H VAL A 859 " ideal model delta sigma weight residual 124.17 73.33 50.83 3.00e+00 1.11e-01 2.87e+02 angle pdb=" CA VAL A 859 " pdb=" N VAL A 859 " pdb=" H VAL A 859 " ideal model delta sigma weight residual 113.87 63.89 49.97 3.00e+00 1.11e-01 2.77e+02 ... (remaining 46115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10814 17.83 - 35.67: 1321 35.67 - 53.50: 395 53.50 - 71.34: 87 71.34 - 89.17: 33 Dihedral angle restraints: 12650 sinusoidal: 6468 harmonic: 6182 Sorted by residual: dihedral pdb=" CA SER A 858 " pdb=" C SER A 858 " pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta harmonic sigma weight residual -180.00 -148.97 -31.03 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA LYS D 64 " pdb=" C LYS D 64 " pdb=" N ASN D 65 " pdb=" CA ASN D 65 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN A 861 " pdb=" C ASN A 861 " pdb=" N ILE A 862 " pdb=" CA ILE A 862 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1852 0.065 - 0.129: 202 0.129 - 0.193: 22 0.193 - 0.258: 1 0.258 - 0.322: 1 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CA ILE A 302 " pdb=" N ILE A 302 " pdb=" C ILE A 302 " pdb=" CB ILE A 302 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL D 173 " pdb=" CA VAL D 173 " pdb=" CG1 VAL D 173 " pdb=" CG2 VAL D 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE B 862 " pdb=" N ILE B 862 " pdb=" C ILE B 862 " pdb=" CB ILE B 862 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 2075 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 861 " 0.144 2.00e-02 2.50e+03 1.56e-01 3.65e+02 pdb=" CG ASN B 861 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 861 " -0.139 2.00e-02 2.50e+03 pdb=" ND2 ASN B 861 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 861 " -0.227 2.00e-02 2.50e+03 pdb="HD22 ASN B 861 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 859 " -0.023 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C VAL B 859 " 0.081 2.00e-02 2.50e+03 pdb=" O VAL B 859 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU B 860 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 862 " -0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" N ASN B 863 " 0.063 2.00e-02 2.50e+03 pdb=" CA ASN B 863 " -0.017 2.00e-02 2.50e+03 pdb=" H ASN B 863 " -0.027 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 752 2.15 - 2.76: 44437 2.76 - 3.37: 68486 3.37 - 3.99: 83567 3.99 - 4.60: 131140 Nonbonded interactions: 328382 Sorted by model distance: nonbonded pdb=" H GLU A 860 " pdb=" HA GLU A 860 " model vdw 1.533 1.816 nonbonded pdb=" H HIS A 852 " pdb=" HA HIS A 852 " model vdw 1.596 1.816 nonbonded pdb=" HH TYR A 414 " pdb=" OD1 ASN A 654 " model vdw 1.601 2.450 nonbonded pdb=" O ILE A 808 " pdb=" H GLU A 812 " model vdw 1.630 2.450 nonbonded pdb=" H TYR B 800 " pdb=" OD2 ASP B 803 " model vdw 1.647 2.450 ... (remaining 328377 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: 0.28 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.520 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 56.690 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4405 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 : 0.004 0.082 14586 Z= 0.184 Angle : 0.782 19.987 19618 Z= 0.446 Chirality : 0.041 0.322 2078 Planarity : 0.005 0.069 2516 Dihedral : 18.514 89.174 5450 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.85 % Favored : 91.21 % Rotamer: Outliers : 0.32 % Allowed : 26.28 % Favored : 73.41 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.19), residues: 1706 helix: -1.53 (0.16), residues: 827 sheet: -1.82 (0.47), residues: 120 loop : -1.88 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 72 HIS 0.011 0.001 HIS A 978 PHE 0.040 0.002 PHE D 13 TYR 0.021 0.002 TYR A 625 ARG 0.005 0.001 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.31246 ( 596) hydrogen bonds : angle 9.19093 ( 1683) covalent geometry : bond 0.00395 (14586) covalent geometry : angle 0.78172 (19618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 LYS cc_start: 0.4731 (mtpt) cc_final: 0.4134 (mtpt) REVERT: A 746 GLU cc_start: 0.6493 (mm-30) cc_final: 0.5971 (tp30) REVERT: A 793 GLU cc_start: 0.7465 (pm20) cc_final: 0.7252 (pm20) outliers start: 5 outliers final: 3 residues processed: 199 average time/residue: 0.4943 time to fit residues: 146.8936 Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain B residue 722 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 491 GLN A 563 ASN A 598 ASN A 609 HIS A 610 GLN A 614 ASN ** A 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN A 975 HIS A 979 HIS B 461 ASN B 491 GLN B 548 ASN B 563 ASN B 852 HIS B 861 ASN B 990 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.260357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.232401 restraints weight = 59378.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.240082 restraints weight = 28280.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.244938 restraints weight = 16315.014| |-----------------------------------------------------------------------------| r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4459 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14586 Z= 0.199 Angle : 0.655 15.823 19618 Z= 0.375 Chirality : 0.042 0.242 2078 Planarity : 0.004 0.054 2516 Dihedral : 6.017 58.353 1891 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.56 % Favored : 90.50 % Rotamer: Outliers : 3.25 % Allowed : 22.64 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.19), residues: 1706 helix: -1.04 (0.16), residues: 864 sheet: -1.53 (0.51), residues: 121 loop : -2.02 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 757 HIS 0.012 0.002 HIS A 978 PHE 0.020 0.002 PHE D 220 TYR 0.026 0.002 TYR A 324 ARG 0.007 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.07052 ( 596) hydrogen bonds : angle 6.22638 ( 1683) covalent geometry : bond 0.00421 (14586) covalent geometry : angle 0.65527 (19618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.0638 (pp-130) cc_final: 0.0270 (pp-130) REVERT: D 2 LYS cc_start: -0.0541 (OUTLIER) cc_final: -0.1024 (tptm) REVERT: C 16 LYS cc_start: 0.4736 (mtpt) cc_final: 0.4421 (mtpt) REVERT: C 180 TYR cc_start: 0.3508 (OUTLIER) cc_final: 0.3259 (m-10) REVERT: A 507 PHE cc_start: 0.1971 (m-10) cc_final: 0.0349 (m-80) REVERT: A 551 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6321 (mt) REVERT: A 566 ARG cc_start: 0.7598 (mtm180) cc_final: 0.7370 (mtm180) REVERT: A 814 ASN cc_start: 0.5908 (t0) cc_final: 0.5684 (t0) REVERT: A 954 PHE cc_start: 0.4827 (t80) cc_final: 0.4247 (t80) REVERT: B 961 ASN cc_start: 0.2584 (OUTLIER) cc_final: 0.2196 (m110) outliers start: 51 outliers final: 31 residues processed: 238 average time/residue: 0.5013 time to fit residues: 178.2422 Evaluate side-chains 228 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 461 ASN B 614 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.259730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.231790 restraints weight = 60075.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.239563 restraints weight = 28849.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.244439 restraints weight = 16781.307| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4466 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14586 Z= 0.159 Angle : 0.596 15.313 19618 Z= 0.336 Chirality : 0.039 0.231 2078 Planarity : 0.004 0.055 2516 Dihedral : 5.821 59.615 1891 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.79 % Favored : 90.33 % Rotamer: Outliers : 3.12 % Allowed : 23.34 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1706 helix: -0.78 (0.16), residues: 882 sheet: -1.44 (0.52), residues: 121 loop : -2.08 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 757 HIS 0.009 0.001 HIS A 978 PHE 0.017 0.001 PHE A 856 TYR 0.020 0.001 TYR A 324 ARG 0.004 0.000 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 596) hydrogen bonds : angle 5.64397 ( 1683) covalent geometry : bond 0.00336 (14586) covalent geometry : angle 0.59627 (19618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.0649 (pp-130) cc_final: 0.0429 (pp-130) REVERT: D 2 LYS cc_start: -0.0569 (OUTLIER) cc_final: -0.1119 (tptm) REVERT: D 51 TYR cc_start: -0.1501 (OUTLIER) cc_final: -0.3023 (m-80) REVERT: D 54 LYS cc_start: -0.1503 (OUTLIER) cc_final: -0.3290 (ttpt) REVERT: D 180 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5258 (m-10) REVERT: D 239 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4896 (ptm-80) REVERT: C 16 LYS cc_start: 0.4753 (mtpt) cc_final: 0.4516 (mtpt) REVERT: C 180 TYR cc_start: 0.3544 (OUTLIER) cc_final: 0.3305 (m-10) REVERT: C 193 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.6003 (mt) REVERT: A 551 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6427 (mt) REVERT: A 954 PHE cc_start: 0.4749 (t80) cc_final: 0.4141 (t80) REVERT: B 648 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5832 (mm-30) REVERT: B 680 GLU cc_start: 0.7970 (mt-10) cc_final: 0.6649 (mt-10) REVERT: B 899 GLU cc_start: 0.1542 (OUTLIER) cc_final: 0.0679 (mm-30) REVERT: B 961 ASN cc_start: 0.2285 (OUTLIER) cc_final: 0.1977 (m110) outliers start: 49 outliers final: 30 residues processed: 236 average time/residue: 0.4880 time to fit residues: 172.9991 Evaluate side-chains 239 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 829 GLN A 979 HIS B 461 ASN B 614 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.259368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.231446 restraints weight = 60641.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.239200 restraints weight = 29177.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.244024 restraints weight = 16988.108| |-----------------------------------------------------------------------------| r_work (final): 0.4861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4474 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14586 Z= 0.145 Angle : 0.562 15.177 19618 Z= 0.317 Chirality : 0.039 0.229 2078 Planarity : 0.003 0.052 2516 Dihedral : 5.682 58.526 1891 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.85 % Favored : 90.27 % Rotamer: Outliers : 3.19 % Allowed : 23.15 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1706 helix: -0.53 (0.16), residues: 887 sheet: -1.36 (0.51), residues: 121 loop : -2.08 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 757 HIS 0.008 0.001 HIS A 978 PHE 0.020 0.001 PHE C 68 TYR 0.020 0.001 TYR A 324 ARG 0.004 0.001 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 596) hydrogen bonds : angle 5.26544 ( 1683) covalent geometry : bond 0.00318 (14586) covalent geometry : angle 0.56187 (19618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0504 (OUTLIER) cc_final: -0.1162 (tptm) REVERT: D 51 TYR cc_start: -0.1582 (OUTLIER) cc_final: -0.3067 (m-80) REVERT: D 54 LYS cc_start: -0.1263 (OUTLIER) cc_final: -0.3124 (ttpt) REVERT: D 180 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.5325 (m-10) REVERT: D 239 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.4827 (ptm-80) REVERT: C 16 LYS cc_start: 0.4807 (mtpt) cc_final: 0.4607 (mtpt) REVERT: C 193 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5812 (mt) REVERT: A 329 ASP cc_start: 0.3869 (m-30) cc_final: 0.3649 (m-30) REVERT: A 551 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6212 (mt) REVERT: A 645 PHE cc_start: 0.6111 (t80) cc_final: 0.5752 (t80) REVERT: A 866 MET cc_start: 0.3215 (ptm) cc_final: 0.2798 (ptm) REVERT: A 954 PHE cc_start: 0.4699 (t80) cc_final: 0.4132 (t80) REVERT: B 648 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5985 (mm-30) REVERT: B 899 GLU cc_start: 0.1633 (OUTLIER) cc_final: 0.0602 (mm-30) outliers start: 50 outliers final: 31 residues processed: 227 average time/residue: 0.5247 time to fit residues: 179.9956 Evaluate side-chains 228 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 54 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.254991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.226474 restraints weight = 59686.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.234262 restraints weight = 28779.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.239090 restraints weight = 16727.819| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4651 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14586 Z= 0.260 Angle : 0.672 14.992 19618 Z= 0.381 Chirality : 0.042 0.229 2078 Planarity : 0.004 0.049 2516 Dihedral : 6.092 58.326 1891 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.14 % Favored : 87.92 % Rotamer: Outliers : 3.25 % Allowed : 24.36 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1706 helix: -0.69 (0.16), residues: 868 sheet: -1.36 (0.57), residues: 104 loop : -2.39 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 757 HIS 0.012 0.002 HIS A 332 PHE 0.020 0.002 PHE A 652 TYR 0.044 0.002 TYR C 180 ARG 0.007 0.001 ARG A 819 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 596) hydrogen bonds : angle 5.65892 ( 1683) covalent geometry : bond 0.00567 (14586) covalent geometry : angle 0.67220 (19618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0638 (OUTLIER) cc_final: -0.1600 (tptm) REVERT: D 51 TYR cc_start: -0.1100 (OUTLIER) cc_final: -0.2733 (m-80) REVERT: D 54 LYS cc_start: -0.0972 (OUTLIER) cc_final: -0.3237 (ttpt) REVERT: D 180 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.5239 (m-10) REVERT: D 239 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.4732 (ptm-80) REVERT: C 68 PHE cc_start: 0.4862 (t80) cc_final: 0.4648 (t80) REVERT: C 193 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5944 (mt) REVERT: A 563 ASN cc_start: 0.7353 (t0) cc_final: 0.7141 (t0) REVERT: A 746 GLU cc_start: 0.5866 (tp30) cc_final: 0.5399 (tp30) REVERT: A 866 MET cc_start: 0.3056 (ptm) cc_final: 0.2626 (ptm) REVERT: A 938 ASP cc_start: 0.1164 (OUTLIER) cc_final: 0.0142 (m-30) REVERT: B 648 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6148 (mm-30) REVERT: B 866 MET cc_start: -0.2203 (mmp) cc_final: -0.3217 (mmp) REVERT: B 916 PHE cc_start: 0.6728 (m-10) cc_final: 0.6482 (m-80) REVERT: B 961 ASN cc_start: 0.2523 (OUTLIER) cc_final: 0.1695 (m-40) outliers start: 51 outliers final: 34 residues processed: 237 average time/residue: 0.5211 time to fit residues: 185.2525 Evaluate side-chains 237 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 461 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.256084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.226997 restraints weight = 60648.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.234906 restraints weight = 29330.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.239843 restraints weight = 17227.307| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4635 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14586 Z= 0.179 Angle : 0.600 14.928 19618 Z= 0.337 Chirality : 0.040 0.226 2078 Planarity : 0.004 0.045 2516 Dihedral : 5.924 56.869 1891 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.26 % Favored : 89.80 % Rotamer: Outliers : 3.57 % Allowed : 24.11 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1706 helix: -0.56 (0.17), residues: 875 sheet: -1.42 (0.56), residues: 104 loop : -2.40 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 757 HIS 0.007 0.001 HIS A 332 PHE 0.017 0.002 PHE B 387 TYR 0.026 0.002 TYR A 324 ARG 0.004 0.001 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 596) hydrogen bonds : angle 5.29759 ( 1683) covalent geometry : bond 0.00397 (14586) covalent geometry : angle 0.60047 (19618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.0319 (pp-130) cc_final: -0.0124 (pp-130) REVERT: D 2 LYS cc_start: -0.0514 (OUTLIER) cc_final: -0.1440 (tptm) REVERT: D 51 TYR cc_start: -0.1312 (OUTLIER) cc_final: -0.2849 (m-80) REVERT: D 54 LYS cc_start: -0.1104 (OUTLIER) cc_final: -0.3367 (ttpt) REVERT: D 180 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: D 239 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.4782 (ptm-80) REVERT: C 68 PHE cc_start: 0.4899 (t80) cc_final: 0.4636 (t80) REVERT: C 193 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5923 (mp) REVERT: A 498 LEU cc_start: 0.6679 (pp) cc_final: 0.6402 (pp) REVERT: A 622 LYS cc_start: 0.7320 (tptt) cc_final: 0.7041 (tptt) REVERT: A 746 GLU cc_start: 0.5760 (tp30) cc_final: 0.5189 (tp30) REVERT: B 648 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6054 (mm-30) REVERT: B 866 MET cc_start: -0.2329 (mmp) cc_final: -0.3271 (mmp) REVERT: B 961 ASN cc_start: 0.2284 (OUTLIER) cc_final: 0.1606 (m-40) outliers start: 56 outliers final: 42 residues processed: 249 average time/residue: 0.6021 time to fit residues: 226.6112 Evaluate side-chains 247 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 810 HIS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN A 979 HIS ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.254238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.224635 restraints weight = 60200.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.232658 restraints weight = 29380.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.237645 restraints weight = 17239.476| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4710 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14586 Z= 0.231 Angle : 0.642 14.871 19618 Z= 0.362 Chirality : 0.041 0.224 2078 Planarity : 0.004 0.044 2516 Dihedral : 6.084 56.501 1891 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.37 % Favored : 87.75 % Rotamer: Outliers : 4.02 % Allowed : 23.85 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1706 helix: -0.61 (0.17), residues: 863 sheet: -1.46 (0.55), residues: 113 loop : -2.43 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 757 HIS 0.037 0.002 HIS B 810 PHE 0.030 0.002 PHE B 678 TYR 0.033 0.002 TYR A 324 ARG 0.005 0.001 ARG A 819 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 596) hydrogen bonds : angle 5.42432 ( 1683) covalent geometry : bond 0.00507 (14586) covalent geometry : angle 0.64220 (19618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0629 (OUTLIER) cc_final: -0.1653 (tptm) REVERT: D 51 TYR cc_start: -0.1075 (OUTLIER) cc_final: -0.2693 (m-80) REVERT: D 54 LYS cc_start: -0.0996 (OUTLIER) cc_final: -0.3260 (ttpt) REVERT: D 180 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.5130 (m-10) REVERT: D 218 ILE cc_start: 0.6602 (mt) cc_final: 0.6287 (tt) REVERT: D 239 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.5199 (ptm-80) REVERT: C 16 LYS cc_start: 0.4764 (mtpt) cc_final: 0.4541 (mtpt) REVERT: C 24 THR cc_start: 0.4647 (OUTLIER) cc_final: 0.4430 (t) REVERT: C 68 PHE cc_start: 0.4947 (t80) cc_final: 0.4696 (t80) REVERT: A 498 LEU cc_start: 0.6514 (pp) cc_final: 0.6243 (pp) REVERT: A 746 GLU cc_start: 0.5853 (tp30) cc_final: 0.5316 (tp30) REVERT: A 938 ASP cc_start: 0.1258 (OUTLIER) cc_final: 0.0179 (m-30) REVERT: B 648 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6129 (mm-30) REVERT: B 677 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.4170 (ptt180) REVERT: B 866 MET cc_start: -0.2136 (mmp) cc_final: -0.2983 (mmp) REVERT: B 961 ASN cc_start: 0.2438 (OUTLIER) cc_final: 0.1796 (m-40) outliers start: 63 outliers final: 46 residues processed: 250 average time/residue: 0.5857 time to fit residues: 216.9820 Evaluate side-chains 251 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 979 HIS B 461 ASN B 609 HIS B 614 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.256485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.227360 restraints weight = 60992.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.235363 restraints weight = 29475.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.240283 restraints weight = 17279.340| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4628 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14586 Z= 0.131 Angle : 0.569 15.241 19618 Z= 0.317 Chirality : 0.039 0.222 2078 Planarity : 0.003 0.042 2516 Dihedral : 5.791 58.362 1891 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.56 % Favored : 90.56 % Rotamer: Outliers : 3.38 % Allowed : 24.62 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.20), residues: 1706 helix: -0.33 (0.17), residues: 877 sheet: -1.36 (0.53), residues: 119 loop : -2.32 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 72 HIS 0.005 0.001 HIS B 810 PHE 0.024 0.001 PHE B 507 TYR 0.015 0.001 TYR A 324 ARG 0.003 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 596) hydrogen bonds : angle 5.03642 ( 1683) covalent geometry : bond 0.00289 (14586) covalent geometry : angle 0.56895 (19618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0803 (OUTLIER) cc_final: -0.1624 (tptm) REVERT: D 51 TYR cc_start: -0.1159 (OUTLIER) cc_final: -0.2765 (m-80) REVERT: D 54 LYS cc_start: -0.1045 (OUTLIER) cc_final: -0.3100 (ttpt) REVERT: D 180 TYR cc_start: 0.4579 (OUTLIER) cc_final: 0.4232 (m-10) REVERT: D 239 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5123 (ptm-80) REVERT: C 16 LYS cc_start: 0.4682 (mtpt) cc_final: 0.4385 (mtpt) REVERT: C 68 PHE cc_start: 0.5040 (t80) cc_final: 0.4718 (t80) REVERT: A 746 GLU cc_start: 0.5822 (tp30) cc_final: 0.5268 (tp30) REVERT: A 831 LYS cc_start: 0.5991 (mtmm) cc_final: 0.5570 (ptpp) REVERT: A 938 ASP cc_start: 0.1033 (OUTLIER) cc_final: 0.0776 (t0) REVERT: B 866 MET cc_start: -0.2331 (mmp) cc_final: -0.3104 (mmp) REVERT: B 961 ASN cc_start: 0.2254 (OUTLIER) cc_final: 0.1583 (m-40) outliers start: 53 outliers final: 40 residues processed: 245 average time/residue: 0.6240 time to fit residues: 229.5139 Evaluate side-chains 249 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.253272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.224117 restraints weight = 60581.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.232137 restraints weight = 29473.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.237046 restraints weight = 17300.324| |-----------------------------------------------------------------------------| r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4727 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14586 Z= 0.209 Angle : 0.640 14.857 19618 Z= 0.358 Chirality : 0.041 0.224 2078 Planarity : 0.004 0.041 2516 Dihedral : 6.014 58.178 1891 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.08 % Favored : 88.04 % Rotamer: Outliers : 3.64 % Allowed : 24.17 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1706 helix: -0.44 (0.17), residues: 863 sheet: -1.55 (0.53), residues: 119 loop : -2.42 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP C 72 HIS 0.013 0.002 HIS A 332 PHE 0.022 0.002 PHE D 220 TYR 0.031 0.002 TYR A 324 ARG 0.006 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 596) hydrogen bonds : angle 5.32476 ( 1683) covalent geometry : bond 0.00460 (14586) covalent geometry : angle 0.63974 (19618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0727 (OUTLIER) cc_final: -0.1575 (tptm) REVERT: D 51 TYR cc_start: -0.0983 (OUTLIER) cc_final: -0.2614 (m-80) REVERT: D 54 LYS cc_start: -0.0581 (OUTLIER) cc_final: -0.2970 (ttpt) REVERT: D 180 TYR cc_start: 0.4558 (OUTLIER) cc_final: 0.4204 (m-10) REVERT: D 239 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5158 (ptm-80) REVERT: C 16 LYS cc_start: 0.4773 (mtpt) cc_final: 0.4491 (mtpt) REVERT: C 68 PHE cc_start: 0.5217 (t80) cc_final: 0.4913 (t80) REVERT: A 391 ASN cc_start: 0.1348 (OUTLIER) cc_final: 0.0534 (t0) REVERT: A 746 GLU cc_start: 0.5827 (tp30) cc_final: 0.5303 (tp30) REVERT: A 831 LYS cc_start: 0.5960 (mtmm) cc_final: 0.5630 (ptpp) REVERT: B 485 ILE cc_start: 0.4428 (tp) cc_final: 0.4020 (tt) REVERT: B 592 LEU cc_start: 0.7222 (mt) cc_final: 0.7007 (mp) REVERT: B 677 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4156 (ptt180) REVERT: B 866 MET cc_start: -0.2068 (mmp) cc_final: -0.2931 (mmp) REVERT: B 960 LYS cc_start: 0.2328 (OUTLIER) cc_final: 0.1901 (mtmt) REVERT: B 961 ASN cc_start: 0.2450 (OUTLIER) cc_final: 0.1920 (m-40) REVERT: B 962 TYR cc_start: 0.1462 (OUTLIER) cc_final: 0.0927 (m-10) outliers start: 57 outliers final: 41 residues processed: 243 average time/residue: 0.5391 time to fit residues: 192.9056 Evaluate side-chains 244 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 962 TYR Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 461 ASN ** B 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.253896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.224350 restraints weight = 60912.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.232431 restraints weight = 29080.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.237598 restraints weight = 16985.810| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14586 Z= 0.170 Angle : 0.603 15.041 19618 Z= 0.337 Chirality : 0.040 0.223 2078 Planarity : 0.003 0.042 2516 Dihedral : 5.922 59.001 1891 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.73 % Favored : 89.45 % Rotamer: Outliers : 3.32 % Allowed : 24.94 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1706 helix: -0.43 (0.17), residues: 878 sheet: -1.49 (0.53), residues: 119 loop : -2.42 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP C 72 HIS 0.008 0.001 HIS A 332 PHE 0.021 0.002 PHE D 220 TYR 0.028 0.002 TYR A 324 ARG 0.004 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 596) hydrogen bonds : angle 5.18799 ( 1683) covalent geometry : bond 0.00374 (14586) covalent geometry : angle 0.60324 (19618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 LYS cc_start: -0.0908 (OUTLIER) cc_final: -0.1545 (tptm) REVERT: D 51 TYR cc_start: -0.0981 (OUTLIER) cc_final: -0.2591 (m-80) REVERT: D 54 LYS cc_start: -0.0716 (OUTLIER) cc_final: -0.2959 (ttpt) REVERT: D 180 TYR cc_start: 0.4575 (OUTLIER) cc_final: 0.4189 (m-10) REVERT: D 203 GLU cc_start: 0.7419 (mp0) cc_final: 0.7216 (mp0) REVERT: D 239 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.5189 (ptm-80) REVERT: C 16 LYS cc_start: 0.4659 (mtpt) cc_final: 0.4375 (mtpt) REVERT: A 388 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5178 (m-80) REVERT: A 746 GLU cc_start: 0.5770 (tp30) cc_final: 0.5250 (tp30) REVERT: B 592 LEU cc_start: 0.7178 (mt) cc_final: 0.6950 (mp) REVERT: B 677 ARG cc_start: 0.5550 (OUTLIER) cc_final: 0.4134 (ptt180) REVERT: B 866 MET cc_start: -0.2202 (mmp) cc_final: -0.2899 (mmp) REVERT: B 960 LYS cc_start: 0.2201 (OUTLIER) cc_final: 0.1806 (mtmt) REVERT: B 961 ASN cc_start: 0.2457 (OUTLIER) cc_final: 0.1979 (m-40) REVERT: B 962 TYR cc_start: 0.1349 (OUTLIER) cc_final: 0.0798 (m-10) outliers start: 52 outliers final: 39 residues processed: 244 average time/residue: 0.5212 time to fit residues: 187.8212 Evaluate side-chains 250 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 677 ARG Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 797 ASN Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 861 ASN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 937 ASP Chi-restraints excluded: chain B residue 960 LYS Chi-restraints excluded: chain B residue 961 ASN Chi-restraints excluded: chain B residue 962 TYR Chi-restraints excluded: chain B residue 987 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 614 ASN ** B 961 ASN ** 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 = 0.4955 r_free = 0.4955 target = 0.252915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.223734 restraints weight = 60761.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.231716 restraints weight = 29355.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.236817 restraints weight = 17206.995| |-----------------------------------------------------------------------------| r_work (final): 0.4801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14586 Z= 0.190 Angle : 0.622 15.132 19618 Z= 0.348 Chirality : 0.041 0.224 2078 Planarity : 0.004 0.042 2516 Dihedral : 5.961 59.761 1891 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.61 % Favored : 88.51 % Rotamer: Outliers : 3.51 % Allowed : 24.81 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1706 helix: -0.41 (0.17), residues: 871 sheet: -1.27 (0.55), residues: 113 loop : -2.48 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP C 72 HIS 0.009 0.002 HIS A 332 PHE 0.024 0.002 PHE A 544 TYR 0.029 0.002 TYR A 324 ARG 0.008 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 596) hydrogen bonds : angle 5.22733 ( 1683) covalent geometry : bond 0.00416 (14586) covalent geometry : angle 0.62201 (19618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8249.67 seconds wall clock time: 145 minutes 4.14 seconds (8704.14 seconds total)