Starting phenix.real_space_refine on Fri Sep 19 12:16:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygk_39254/09_2025/8ygk_39254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygk_39254/09_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_39254/09_2025/8ygk_39254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygk_39254/09_2025/8ygk_39254.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygk_39254/09_2025/8ygk_39254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygk_39254/09_2025/8ygk_39254.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.05, per 1000 atoms: 0.16 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: 2.24 Conformation dependent library (CDL) restraints added in 636.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.69 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: 4.85 Time building geometry restraints manager: 3.14 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: 0.01 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.170 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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 : 16.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 566 TYR 0.021 0.002 TYR A 625 PHE 0.040 0.002 PHE D 13 TRP 0.017 0.002 TRP C 72 HIS 0.011 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00395 (14586) covalent geometry : angle 0.78172 (19618) hydrogen bonds : bond 0.31246 ( 596) hydrogen bonds : angle 9.19093 ( 1683) *********************** 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 : 0.677 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: 0.2177 time to fit residues: 64.7671 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 : 0.485 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 861 ASN B 990 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.261798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.234015 restraints weight = 59580.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.241680 restraints weight = 28217.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.246598 restraints weight = 16204.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.249894 restraints weight = 10747.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.251939 restraints weight = 7802.868| |-----------------------------------------------------------------------------| r_work (final): 0.4941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4273 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14586 Z= 0.167 Angle : 0.629 15.827 19618 Z= 0.361 Chirality : 0.041 0.241 2078 Planarity : 0.004 0.055 2516 Dihedral : 5.906 58.756 1891 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.21 % Favored : 90.86 % Rotamer: Outliers : 2.87 % Allowed : 22.64 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.19), residues: 1706 helix: -0.96 (0.16), residues: 866 sheet: -1.50 (0.51), residues: 121 loop : -1.96 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 593 TYR 0.020 0.001 TYR A 324 PHE 0.016 0.002 PHE D 67 TRP 0.009 0.001 TRP A 757 HIS 0.011 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00345 (14586) covalent geometry : angle 0.62942 (19618) hydrogen bonds : bond 0.07329 ( 596) hydrogen bonds : angle 6.19568 ( 1683) *********************** 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: 45 poor density : 208 time to evaluate : 0.467 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: D 1 MET cc_start: 0.0542 (pp-130) cc_final: 0.0214 (pp-130) REVERT: D 2 LYS cc_start: -0.0563 (OUTLIER) cc_final: -0.0867 (tptm) REVERT: C 13 PHE cc_start: 0.2982 (OUTLIER) cc_final: 0.2243 (m-10) REVERT: C 16 LYS cc_start: 0.4731 (mtpt) cc_final: 0.4426 (mtpt) REVERT: C 68 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4838 (t80) REVERT: A 507 PHE cc_start: 0.1737 (m-10) cc_final: 0.0195 (m-80) REVERT: A 551 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6097 (mt) REVERT: A 954 PHE cc_start: 0.4700 (t80) cc_final: 0.4140 (t80) REVERT: B 660 LYS cc_start: 0.7425 (mmtp) cc_final: 0.7146 (mptt) REVERT: B 687 TYR cc_start: 0.5596 (t80) cc_final: 0.5241 (t80) REVERT: B 961 ASN cc_start: 0.2377 (OUTLIER) cc_final: 0.2031 (m110) outliers start: 45 outliers final: 26 residues processed: 239 average time/residue: 0.2284 time to fit residues: 80.0487 Evaluate side-chains 231 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 D residue 206 MET Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 68 PHE 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 634 LEU 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 829 GLN 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 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 17 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 = 0.5013 r_free = 0.5013 target = 0.260251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.232252 restraints weight = 60511.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.240076 restraints weight = 28891.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.245043 restraints weight = 16717.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.248365 restraints weight = 11085.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.250138 restraints weight = 8016.235| |-----------------------------------------------------------------------------| r_work (final): 0.4914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4322 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14586 Z= 0.158 Angle : 0.600 15.437 19618 Z= 0.340 Chirality : 0.039 0.232 2078 Planarity : 0.004 0.054 2516 Dihedral : 5.785 59.978 1891 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.79 % Favored : 90.33 % Rotamer: Outliers : 3.44 % Allowed : 22.51 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.19), residues: 1706 helix: -0.74 (0.16), residues: 882 sheet: -1.47 (0.51), residues: 121 loop : -2.01 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.019 0.001 TYR A 324 PHE 0.019 0.001 PHE D 67 TRP 0.017 0.002 TRP D 72 HIS 0.010 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00333 (14586) covalent geometry : angle 0.59961 (19618) hydrogen bonds : bond 0.05983 ( 596) hydrogen bonds : angle 5.71727 ( 1683) *********************** 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 248 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.651 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 1 MET cc_start: 0.0579 (pp-130) cc_final: 0.0359 (pp-130) REVERT: D 2 LYS cc_start: -0.0567 (OUTLIER) cc_final: -0.0952 (tptm) REVERT: D 51 TYR cc_start: -0.1519 (OUTLIER) cc_final: -0.3068 (m-80) REVERT: D 54 LYS cc_start: -0.1498 (OUTLIER) cc_final: -0.3268 (ttpt) REVERT: D 71 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5941 (pp20) REVERT: C 16 LYS cc_start: 0.4745 (mtpt) cc_final: 0.4480 (mtpt) REVERT: C 193 ILE cc_start: 0.6395 (OUTLIER) cc_final: 0.6088 (mt) REVERT: A 507 PHE cc_start: 0.1843 (m-10) cc_final: 0.0202 (m-80) REVERT: A 551 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6189 (mt) REVERT: A 954 PHE cc_start: 0.4725 (t80) cc_final: 0.4154 (t80) REVERT: B 648 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5915 (mm-30) REVERT: B 961 ASN cc_start: 0.2223 (OUTLIER) cc_final: 0.1897 (m110) outliers start: 54 outliers final: 36 residues processed: 231 average time/residue: 0.1947 time to fit residues: 68.5561 Evaluate side-chains 234 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 71 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 206 MET 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 634 LEU Chi-restraints excluded: chain A residue 671 CYS 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 A residue 941 ASP 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 41 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.256284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.227560 restraints weight = 60017.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.235363 restraints weight = 29110.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.240211 restraints weight = 17029.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.243415 restraints weight = 11511.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.245418 restraints weight = 8494.737| |-----------------------------------------------------------------------------| r_work (final): 0.4870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4468 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 14586 Z= 0.222 Angle : 0.649 15.041 19618 Z= 0.366 Chirality : 0.041 0.232 2078 Planarity : 0.004 0.049 2516 Dihedral : 6.017 58.918 1891 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.61 % Favored : 88.51 % Rotamer: Outliers : 4.08 % Allowed : 22.83 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.19), residues: 1706 helix: -0.62 (0.16), residues: 869 sheet: -1.26 (0.57), residues: 104 loop : -2.32 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 593 TYR 0.033 0.002 TYR A 324 PHE 0.020 0.002 PHE A 638 TRP 0.010 0.002 TRP A 757 HIS 0.009 0.002 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00492 (14586) covalent geometry : angle 0.64931 (19618) hydrogen bonds : bond 0.05237 ( 596) hydrogen bonds : angle 5.58871 ( 1683) *********************** 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 263 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.522 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: -0.0513 (OUTLIER) cc_final: -0.1696 (tptm) REVERT: D 51 TYR cc_start: -0.1234 (OUTLIER) cc_final: -0.2860 (m-80) REVERT: D 54 LYS cc_start: -0.1036 (OUTLIER) cc_final: -0.3391 (ttpt) REVERT: D 71 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5881 (pm20) REVERT: D 180 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.5296 (m-10) REVERT: D 239 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.4796 (ptm-80) REVERT: C 16 LYS cc_start: 0.4874 (mtpt) cc_final: 0.4610 (mtpt) REVERT: C 68 PHE cc_start: 0.5122 (t80) cc_final: 0.4909 (t80) REVERT: C 193 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5910 (mt) REVERT: A 866 MET cc_start: 0.3477 (ptm) cc_final: 0.3061 (ptm) REVERT: B 421 MET cc_start: 0.3189 (ttp) cc_final: 0.2914 (ttm) REVERT: B 648 GLU cc_start: 0.6386 (mm-30) cc_final: 0.5977 (mm-30) REVERT: B 916 PHE cc_start: 0.6535 (m-10) cc_final: 0.6306 (m-10) REVERT: B 961 ASN cc_start: 0.2441 (OUTLIER) cc_final: 0.0881 (m110) outliers start: 64 outliers final: 39 residues processed: 242 average time/residue: 0.2248 time to fit residues: 81.3199 Evaluate side-chains 240 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 71 GLU 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 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 357 MET 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 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 860 GLU Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 741 LEU 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 841 LEU Chi-restraints excluded: chain B residue 854 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 164 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 461 ASN B 810 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.256742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.228664 restraints weight = 59481.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.236400 restraints weight = 28559.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.241248 restraints weight = 16584.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.244568 restraints weight = 11093.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.246539 restraints weight = 8048.844| |-----------------------------------------------------------------------------| r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4447 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14586 Z= 0.180 Angle : 0.596 14.938 19618 Z= 0.337 Chirality : 0.040 0.228 2078 Planarity : 0.004 0.046 2516 Dihedral : 5.908 57.295 1891 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.55 % Favored : 89.51 % Rotamer: Outliers : 3.57 % Allowed : 23.92 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.19), residues: 1706 helix: -0.55 (0.17), residues: 869 sheet: -1.27 (0.57), residues: 103 loop : -2.31 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 326 TYR 0.025 0.002 TYR A 324 PHE 0.016 0.002 PHE B 387 TRP 0.018 0.002 TRP C 72 HIS 0.008 0.002 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00393 (14586) covalent geometry : angle 0.59611 (19618) hydrogen bonds : bond 0.04782 ( 596) hydrogen bonds : angle 5.40617 ( 1683) *********************** 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 257 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.690 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 1 MET cc_start: 0.0416 (pp-130) cc_final: 0.0105 (pp-130) REVERT: D 2 LYS cc_start: -0.0478 (OUTLIER) cc_final: -0.1381 (tptm) REVERT: D 51 TYR cc_start: -0.1242 (OUTLIER) cc_final: -0.2853 (m-80) REVERT: D 54 LYS cc_start: -0.1105 (OUTLIER) cc_final: -0.3380 (ttpt) REVERT: D 71 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5831 (pm20) REVERT: D 180 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.5230 (m-10) REVERT: D 239 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4727 (ptm-80) REVERT: C 2 LYS cc_start: 0.0597 (OUTLIER) cc_final: 0.0319 (ttpp) REVERT: C 68 PHE cc_start: 0.5242 (t80) cc_final: 0.5029 (t80) REVERT: C 193 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5861 (mt) REVERT: A 746 GLU cc_start: 0.5959 (tp30) cc_final: 0.5458 (tp30) REVERT: A 866 MET cc_start: 0.3392 (ptm) cc_final: 0.2925 (ptm) REVERT: B 648 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6020 (mm-30) REVERT: B 866 MET cc_start: -0.2183 (mmt) cc_final: -0.3116 (mmm) REVERT: B 916 PHE cc_start: 0.6461 (m-10) cc_final: 0.6235 (m-10) REVERT: B 961 ASN cc_start: 0.2320 (OUTLIER) cc_final: 0.1995 (m110) outliers start: 56 outliers final: 43 residues processed: 241 average time/residue: 0.2227 time to fit residues: 80.4397 Evaluate side-chains 251 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 71 GLU 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 2 LYS 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 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 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 829 GLN Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 696 THR 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 759 GLU Chi-restraints excluded: chain B residue 796 SER Chi-restraints excluded: chain B residue 809 LYS 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 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 129 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.256759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.227489 restraints weight = 59607.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.235476 restraints weight = 29159.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.240432 restraints weight = 17135.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.243791 restraints weight = 11551.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.245824 restraints weight = 8521.073| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4480 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14586 Z= 0.174 Angle : 0.588 14.966 19618 Z= 0.331 Chirality : 0.039 0.226 2078 Planarity : 0.003 0.044 2516 Dihedral : 5.844 56.440 1891 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.96 % Favored : 89.10 % Rotamer: Outliers : 3.95 % Allowed : 23.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.19), residues: 1706 helix: -0.41 (0.17), residues: 867 sheet: -1.32 (0.57), residues: 103 loop : -2.32 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 819 TYR 0.024 0.002 TYR A 324 PHE 0.017 0.002 PHE D 220 TRP 0.014 0.002 TRP C 72 HIS 0.009 0.002 HIS B 810 Details of bonding type rmsd covalent geometry : bond 0.00381 (14586) covalent geometry : angle 0.58821 (19618) hydrogen bonds : bond 0.04540 ( 596) hydrogen bonds : angle 5.28206 ( 1683) *********************** 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 266 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.629 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: 0.0221 (pp-130) cc_final: -0.0102 (pp-130) REVERT: D 2 LYS cc_start: -0.0417 (OUTLIER) cc_final: -0.1302 (tptm) REVERT: D 51 TYR cc_start: -0.1196 (OUTLIER) cc_final: -0.2808 (m-80) REVERT: D 54 LYS cc_start: -0.1050 (OUTLIER) cc_final: -0.3422 (ttpt) REVERT: D 71 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5856 (pm20) REVERT: D 180 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.5119 (m-10) REVERT: D 218 ILE cc_start: 0.6637 (mt) cc_final: 0.6254 (tt) REVERT: D 239 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.4717 (ptm-80) REVERT: C 68 PHE cc_start: 0.5294 (t80) cc_final: 0.5067 (t80) REVERT: C 193 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5837 (mp) REVERT: A 746 GLU cc_start: 0.5926 (tp30) cc_final: 0.5437 (tp30) REVERT: A 831 LYS cc_start: 0.6081 (mtmm) cc_final: 0.5402 (ptpp) REVERT: B 648 GLU cc_start: 0.6358 (mm-30) cc_final: 0.5929 (mm-30) REVERT: B 916 PHE cc_start: 0.6435 (m-10) cc_final: 0.6217 (m-10) REVERT: B 961 ASN cc_start: 0.2363 (OUTLIER) cc_final: 0.1749 (m-40) outliers start: 62 outliers final: 45 residues processed: 249 average time/residue: 0.2253 time to fit residues: 83.1224 Evaluate side-chains 255 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 71 GLU 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 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 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 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 B residue 346 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 696 THR 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 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 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 127 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 483 GLN ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A 711 GLN A 829 GLN A 979 HIS B 461 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.252902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.223383 restraints weight = 60295.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.231295 restraints weight = 29650.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.236211 restraints weight = 17564.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.239428 restraints weight = 11991.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.241680 restraints weight = 8971.303| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4615 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14586 Z= 0.258 Angle : 0.699 14.961 19618 Z= 0.390 Chirality : 0.043 0.229 2078 Planarity : 0.004 0.044 2516 Dihedral : 6.243 55.747 1891 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.49 % Favored : 87.63 % Rotamer: Outliers : 4.15 % Allowed : 24.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.19), residues: 1706 helix: -0.71 (0.17), residues: 863 sheet: -1.36 (0.55), residues: 108 loop : -2.51 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 819 TYR 0.039 0.002 TYR A 324 PHE 0.023 0.002 PHE B 387 TRP 0.016 0.003 TRP C 72 HIS 0.011 0.002 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00571 (14586) covalent geometry : angle 0.69934 (19618) hydrogen bonds : bond 0.05079 ( 596) hydrogen bonds : angle 5.61633 ( 1683) *********************** 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: 65 poor density : 199 time to evaluate : 0.573 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 2 LYS cc_start: -0.0526 (OUTLIER) cc_final: -0.1530 (tptm) REVERT: D 51 TYR cc_start: -0.1100 (OUTLIER) cc_final: -0.2691 (m-80) REVERT: D 54 LYS cc_start: -0.0928 (OUTLIER) cc_final: -0.3346 (ttpt) REVERT: D 71 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5891 (pm20) REVERT: D 180 TYR cc_start: 0.5460 (OUTLIER) cc_final: 0.5128 (m-10) REVERT: D 218 ILE cc_start: 0.6642 (mt) cc_final: 0.6297 (tt) REVERT: D 239 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5083 (ptm-80) REVERT: C 68 PHE cc_start: 0.5375 (t80) cc_final: 0.5155 (t80) REVERT: A 391 ASN cc_start: 0.1329 (OUTLIER) cc_final: 0.0429 (t0) REVERT: A 498 LEU cc_start: 0.6497 (pp) cc_final: 0.6221 (pp) REVERT: A 746 GLU cc_start: 0.5968 (tp30) cc_final: 0.5459 (tp30) REVERT: B 485 ILE cc_start: 0.4664 (tp) cc_final: 0.4017 (tt) REVERT: B 648 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6041 (mm-30) REVERT: B 916 PHE cc_start: 0.6482 (m-10) cc_final: 0.6279 (m-10) REVERT: B 961 ASN cc_start: 0.2371 (OUTLIER) cc_final: 0.1924 (m-40) outliers start: 65 outliers final: 48 residues processed: 250 average time/residue: 0.2151 time to fit residues: 80.6438 Evaluate side-chains 252 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 71 GLU 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 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 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 615 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 704 MET 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 821 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain B residue 582 ILE 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 696 THR 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 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 987 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 50 optimal weight: 0.0070 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A 979 HIS B 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.254414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.224814 restraints weight = 60907.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.232802 restraints weight = 29641.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.237800 restraints weight = 17509.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.241150 restraints weight = 11936.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.243293 restraints weight = 8849.888| |-----------------------------------------------------------------------------| r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4568 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14586 Z= 0.171 Angle : 0.610 14.954 19618 Z= 0.341 Chirality : 0.040 0.222 2078 Planarity : 0.003 0.044 2516 Dihedral : 6.028 56.858 1891 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.85 % Favored : 89.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.19), residues: 1706 helix: -0.56 (0.17), residues: 870 sheet: -1.33 (0.54), residues: 114 loop : -2.47 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 819 TYR 0.025 0.002 TYR A 324 PHE 0.028 0.002 PHE B 678 TRP 0.011 0.002 TRP C 72 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00376 (14586) covalent geometry : angle 0.60968 (19618) hydrogen bonds : bond 0.04498 ( 596) hydrogen bonds : angle 5.30971 ( 1683) *********************** 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 253 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.701 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: -0.0643 (OUTLIER) cc_final: -0.1506 (tptm) REVERT: D 51 TYR cc_start: -0.1251 (OUTLIER) cc_final: -0.2724 (m-80) REVERT: D 54 LYS cc_start: -0.0974 (OUTLIER) cc_final: -0.3249 (ttpt) REVERT: D 71 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5972 (pm20) REVERT: D 180 TYR cc_start: 0.4460 (OUTLIER) cc_final: 0.4148 (m-10) REVERT: D 218 ILE cc_start: 0.6594 (mt) cc_final: 0.6295 (tt) REVERT: D 239 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4992 (ptm-80) REVERT: C 68 PHE cc_start: 0.5383 (t80) cc_final: 0.5156 (t80) REVERT: A 746 GLU cc_start: 0.5862 (tp30) cc_final: 0.5328 (tp30) REVERT: A 831 LYS cc_start: 0.6062 (mtmm) cc_final: 0.5803 (mtmm) REVERT: B 648 GLU cc_start: 0.6510 (mm-30) cc_final: 0.5997 (mm-30) REVERT: B 809 LYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4802 (tttm) REVERT: B 961 ASN cc_start: 0.2449 (OUTLIER) cc_final: 0.1529 (m-40) outliers start: 55 outliers final: 42 residues processed: 236 average time/residue: 0.2288 time to fit residues: 80.0940 Evaluate side-chains 245 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 71 GLU 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 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 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 704 MET 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 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 696 THR 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 809 LYS Chi-restraints excluded: chain B residue 854 LEU 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 987 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 131 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 0.0770 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN ** 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 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 = 0.4941 r_free = 0.4941 target = 0.251617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.222060 restraints weight = 60204.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.230032 restraints weight = 29298.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.235042 restraints weight = 17195.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.238163 restraints weight = 11591.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.240379 restraints weight = 8691.507| |-----------------------------------------------------------------------------| r_work (final): 0.4834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4651 moved from start: 0.4293 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= 0.237 Angle : 0.675 14.963 19618 Z= 0.380 Chirality : 0.042 0.225 2078 Planarity : 0.004 0.044 2516 Dihedral : 6.241 57.345 1891 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.90 % Favored : 87.22 % Rotamer: Outliers : 3.51 % Allowed : 25.13 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.19), residues: 1706 helix: -0.70 (0.17), residues: 855 sheet: -1.68 (0.53), residues: 118 loop : -2.54 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 802 TYR 0.037 0.002 TYR A 324 PHE 0.023 0.002 PHE D 220 TRP 0.011 0.002 TRP B 757 HIS 0.012 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00519 (14586) covalent geometry : angle 0.67491 (19618) hydrogen bonds : bond 0.04905 ( 596) hydrogen bonds : angle 5.54324 ( 1683) *********************** 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 253 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.703 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: D 22 VAL cc_start: -0.0050 (OUTLIER) cc_final: -0.1121 (p) REVERT: D 51 TYR cc_start: -0.1027 (OUTLIER) cc_final: -0.2519 (m-80) REVERT: D 54 LYS cc_start: -0.0567 (OUTLIER) cc_final: -0.2825 (ttpt) REVERT: D 180 TYR cc_start: 0.4533 (OUTLIER) cc_final: 0.4199 (m-10) REVERT: D 218 ILE cc_start: 0.6616 (mt) cc_final: 0.6340 (tt) REVERT: D 239 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5105 (ptm-80) REVERT: C 192 TYR cc_start: 0.5482 (m-10) cc_final: 0.5193 (m-10) REVERT: A 622 LYS cc_start: 0.7386 (tptt) cc_final: 0.6787 (tptt) REVERT: A 746 GLU cc_start: 0.5930 (tp30) cc_final: 0.5434 (tp30) REVERT: A 829 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5551 (mm110) REVERT: A 831 LYS cc_start: 0.6214 (mtmm) cc_final: 0.5616 (ptpt) REVERT: B 485 ILE cc_start: 0.4457 (tp) cc_final: 0.4075 (tt) REVERT: B 961 ASN cc_start: 0.2523 (OUTLIER) cc_final: 0.1685 (m-40) outliers start: 55 outliers final: 44 residues processed: 238 average time/residue: 0.2260 time to fit residues: 80.3061 Evaluate side-chains 241 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 VAL 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 178 ILE 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 691 ILE Chi-restraints excluded: chain A residue 704 MET 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 860 GLU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 696 THR 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 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 987 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.249435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.219920 restraints weight = 60563.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.227839 restraints weight = 29983.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.232748 restraints weight = 17762.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.235769 restraints weight = 12076.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.237983 restraints weight = 9157.298| |-----------------------------------------------------------------------------| r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4718 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14586 Z= 0.284 Angle : 0.724 15.105 19618 Z= 0.407 Chirality : 0.044 0.225 2078 Planarity : 0.004 0.045 2516 Dihedral : 6.597 59.646 1891 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.54 % Favored : 86.58 % Rotamer: Outliers : 3.38 % Allowed : 25.70 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.19), residues: 1706 helix: -0.95 (0.17), residues: 855 sheet: -1.98 (0.50), residues: 129 loop : -2.60 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 447 TYR 0.042 0.003 TYR A 324 PHE 0.029 0.003 PHE B 544 TRP 0.014 0.003 TRP B 958 HIS 0.011 0.002 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00620 (14586) covalent geometry : angle 0.72434 (19618) hydrogen bonds : bond 0.05204 ( 596) hydrogen bonds : angle 5.78727 ( 1683) ********************** 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 247 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.752 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: D 38 GLU cc_start: 0.4950 (pm20) cc_final: 0.4624 (pm20) REVERT: D 51 TYR cc_start: -0.0966 (OUTLIER) cc_final: -0.2370 (m-80) REVERT: D 54 LYS cc_start: 0.0250 (OUTLIER) cc_final: -0.1401 (ttpt) REVERT: D 180 TYR cc_start: 0.4562 (OUTLIER) cc_final: 0.4224 (m-10) REVERT: D 218 ILE cc_start: 0.6605 (mt) cc_final: 0.6345 (tt) REVERT: D 239 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5177 (ptm-80) REVERT: C 192 TYR cc_start: 0.5490 (m-10) cc_final: 0.5175 (m-10) REVERT: C 209 GLU cc_start: 0.6128 (tt0) cc_final: 0.5431 (tt0) REVERT: A 622 LYS cc_start: 0.7433 (tptt) cc_final: 0.6781 (tptt) REVERT: A 746 GLU cc_start: 0.5990 (tp30) cc_final: 0.5571 (tp30) REVERT: A 831 LYS cc_start: 0.6258 (mtmm) cc_final: 0.5681 (ptpt) REVERT: B 485 ILE cc_start: 0.4581 (tp) cc_final: 0.4303 (tt) REVERT: B 660 LYS cc_start: 0.7589 (mmtp) cc_final: 0.7333 (mptt) REVERT: B 866 MET cc_start: -0.1376 (mmm) cc_final: -0.2094 (mmt) outliers start: 53 outliers final: 45 residues processed: 230 average time/residue: 0.2295 time to fit residues: 78.0141 Evaluate side-chains 241 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 666 ASN Chi-restraints excluded: chain A residue 704 MET 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 860 GLU Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 696 THR 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 790 ASN 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 810 HIS Chi-restraints excluded: chain B residue 854 LEU 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 987 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 614 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS B 461 ASN B 563 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.253745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.224777 restraints weight = 60150.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.232655 restraints weight = 29358.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.237689 restraints weight = 17299.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.240832 restraints weight = 11606.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.242852 restraints weight = 8646.730| |-----------------------------------------------------------------------------| r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14586 Z= 0.131 Angle : 0.598 15.421 19618 Z= 0.334 Chirality : 0.040 0.222 2078 Planarity : 0.003 0.044 2516 Dihedral : 6.058 59.070 1891 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.32 % Favored : 89.80 % Rotamer: Outliers : 2.61 % Allowed : 26.47 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.19), residues: 1706 helix: -0.57 (0.17), residues: 882 sheet: -1.64 (0.53), residues: 123 loop : -2.49 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 987 TYR 0.017 0.001 TYR B 940 PHE 0.024 0.002 PHE B 678 TRP 0.030 0.002 TRP C 72 HIS 0.005 0.001 HIS A 978 Details of bonding type rmsd covalent geometry : bond 0.00288 (14586) covalent geometry : angle 0.59815 (19618) hydrogen bonds : bond 0.04141 ( 596) hydrogen bonds : angle 5.16484 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.19 seconds wall clock time: 68 minutes 35.84 seconds (4115.84 seconds total)